Zinc in PDB 8fmg: Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au)
Protein crystallography data
The structure of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au), PDB code: 8fmg
was solved by
O.Rechkoblit,
D.F.Kreitler,
A.K.Aggarwal,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
58.12 /
1.79
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
145.192,
80.522,
406.841,
90,
90.62,
90
|
|
R / Rfree (%)
|
17.9 /
22.5
|
Other elements in 8fmg:
The structure of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au) also contains other interesting chemical elements:
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Zinc atom in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au)
(pdb code 8fmg). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the
Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au), PDB code: 8fmg:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 12 in 8fmg
Go back to
Zinc Binding Sites List in 8fmg
Zinc binding site 1 out
of 12 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au)
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:26.2
occ:1.00
|
SG
|
A:CYS32
|
2.3
|
22.3
|
1.0
|
|
SG
|
A:CYS87
|
2.3
|
22.2
|
1.0
|
|
SG
|
A:CYS90
|
2.3
|
21.1
|
1.0
|
|
SG
|
A:CYS35
|
2.3
|
22.6
|
1.0
|
|
HB2
|
A:CYS90
|
2.9
|
34.0
|
1.0
|
|
HB3
|
A:CYS35
|
3.0
|
26.7
|
1.0
|
|
HB3
|
A:CYS87
|
3.2
|
31.0
|
1.0
|
|
H
|
A:CYS87
|
3.2
|
32.0
|
1.0
|
|
HB3
|
A:CYS32
|
3.2
|
25.8
|
1.0
|
|
CB
|
A:CYS32
|
3.2
|
21.5
|
1.0
|
|
CB
|
A:CYS90
|
3.2
|
28.3
|
1.0
|
|
CB
|
A:CYS35
|
3.3
|
22.2
|
1.0
|
|
HB2
|
A:CYS32
|
3.3
|
25.8
|
1.0
|
|
CB
|
A:CYS87
|
3.4
|
25.8
|
1.0
|
|
H
|
A:CYS35
|
3.4
|
28.0
|
1.0
|
|
H
|
A:CYS90
|
3.7
|
30.0
|
1.0
|
|
HG22
|
A:THR37
|
3.7
|
34.0
|
1.0
|
|
HB3
|
A:CYS90
|
3.8
|
34.0
|
1.0
|
|
N
|
A:CYS35
|
3.9
|
23.4
|
1.0
|
|
N
|
A:CYS87
|
3.9
|
26.6
|
1.0
|
|
HB2
|
A:CYS35
|
4.0
|
26.7
|
1.0
|
|
HB2
|
A:LEU34
|
4.1
|
26.0
|
1.0
|
|
HB2
|
A:CYS87
|
4.1
|
31.0
|
1.0
|
|
CA
|
A:CYS35
|
4.1
|
24.1
|
1.0
|
|
CA
|
A:CYS87
|
4.2
|
25.3
|
1.0
|
|
HG21
|
A:THR37
|
4.3
|
34.0
|
1.0
|
|
N
|
A:CYS90
|
4.4
|
24.9
|
1.0
|
|
CA
|
A:CYS90
|
4.4
|
24.2
|
1.0
|
|
H
|
A:LEU34
|
4.4
|
23.8
|
1.0
|
|
O
|
A:HOH626
|
4.4
|
24.5
|
1.0
|
|
CG2
|
A:THR37
|
4.5
|
28.3
|
1.0
|
|
H
|
A:THR37
|
4.5
|
26.4
|
1.0
|
|
CA
|
A:CYS32
|
4.7
|
23.6
|
1.0
|
|
HA
|
A:LEU86
|
4.7
|
28.9
|
1.0
|
|
H
|
A:GLY36
|
4.7
|
23.6
|
1.0
|
|
C
|
A:LEU34
|
4.7
|
22.2
|
1.0
|
|
HA
|
A:CYS90
|
4.8
|
29.1
|
1.0
|
|
O
|
A:CYS87
|
4.8
|
23.9
|
1.0
|
|
HB3
|
A:LEU86
|
4.8
|
30.1
|
1.0
|
|
C
|
A:CYS87
|
4.8
|
27.3
|
1.0
|
|
C
|
A:CYS35
|
4.8
|
22.1
|
1.0
|
|
CB
|
A:LEU34
|
4.9
|
21.6
|
1.0
|
|
O
|
A:HOH710
|
4.9
|
40.5
|
1.0
|
|
HA
|
A:CYS35
|
4.9
|
29.0
|
1.0
|
|
HA
|
A:CYS32
|
5.0
|
28.4
|
1.0
|
|
Zinc binding site 2 out
of 12 in 8fmg
Go back to
Zinc Binding Sites List in 8fmg
Zinc binding site 2 out
of 12 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au)
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:42.1
occ:1.00
|
SG
|
B:CYS32
|
2.3
|
44.2
|
1.0
|
|
SG
|
B:CYS87
|
2.3
|
50.8
|
1.0
|
|
SG
|
B:CYS90
|
2.3
|
46.8
|
1.0
|
|
SG
|
B:CYS35
|
2.3
|
40.0
|
1.0
|
|
HB2
|
B:CYS90
|
2.7
|
69.0
|
1.0
|
|
HB3
|
B:CYS35
|
3.1
|
48.4
|
1.0
|
|
CB
|
B:CYS90
|
3.1
|
57.5
|
1.0
|
|
H
|
B:CYS87
|
3.2
|
57.7
|
1.0
|
|
H
|
B:CYS35
|
3.2
|
51.0
|
1.0
|
|
HB3
|
B:CYS32
|
3.2
|
51.0
|
1.0
|
|
CB
|
B:CYS32
|
3.3
|
42.5
|
1.0
|
|
CB
|
B:CYS35
|
3.3
|
40.3
|
1.0
|
|
HB2
|
B:CYS32
|
3.3
|
51.0
|
1.0
|
|
HB3
|
B:CYS87
|
3.4
|
58.7
|
1.0
|
|
H
|
B:CYS90
|
3.4
|
65.1
|
1.0
|
|
CB
|
B:CYS87
|
3.5
|
48.9
|
1.0
|
|
HB2
|
B:LEU34
|
3.7
|
56.3
|
1.0
|
|
HB3
|
B:CYS90
|
3.7
|
69.0
|
1.0
|
|
N
|
B:CYS35
|
3.8
|
42.5
|
1.0
|
|
N
|
B:CYS87
|
4.0
|
48.0
|
1.0
|
|
HB2
|
B:CYS35
|
4.1
|
48.4
|
1.0
|
|
N
|
B:CYS90
|
4.1
|
54.3
|
1.0
|
|
CA
|
B:CYS35
|
4.1
|
39.5
|
1.0
|
|
CA
|
B:CYS90
|
4.2
|
56.9
|
1.0
|
|
HB2
|
B:CYS87
|
4.3
|
58.7
|
1.0
|
|
H
|
B:LEU34
|
4.3
|
58.9
|
1.0
|
|
CA
|
B:CYS87
|
4.3
|
51.7
|
1.0
|
|
HG1
|
B:THR37
|
4.4
|
43.4
|
1.0
|
|
CB
|
B:LEU34
|
4.5
|
46.9
|
1.0
|
|
OG1
|
B:THR37
|
4.6
|
36.2
|
1.0
|
|
HA
|
B:CYS90
|
4.6
|
68.3
|
1.0
|
|
HB3
|
B:LEU34
|
4.7
|
56.3
|
1.0
|
|
H
|
B:THR37
|
4.7
|
46.2
|
1.0
|
|
HA
|
B:LEU86
|
4.7
|
53.8
|
1.0
|
|
CA
|
B:CYS32
|
4.7
|
36.2
|
1.0
|
|
HB3
|
B:LEU86
|
4.7
|
57.6
|
1.0
|
|
C
|
B:LEU34
|
4.7
|
41.8
|
1.0
|
|
HB
|
B:THR37
|
4.9
|
47.2
|
1.0
|
|
HA
|
B:CYS35
|
4.9
|
47.4
|
1.0
|
|
H
|
B:GLY36
|
4.9
|
47.4
|
1.0
|
|
C
|
B:CYS87
|
5.0
|
53.0
|
1.0
|
|
HA
|
B:CYS32
|
5.0
|
43.5
|
1.0
|
|
C
|
B:CYS35
|
5.0
|
39.8
|
1.0
|
|
Zinc binding site 3 out
of 12 in 8fmg
Go back to
Zinc Binding Sites List in 8fmg
Zinc binding site 3 out
of 12 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au)
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn401
b:26.3
occ:1.00
|
SG
|
C:CYS35
|
2.3
|
21.5
|
1.0
|
|
SG
|
C:CYS87
|
2.3
|
21.1
|
1.0
|
|
SG
|
C:CYS32
|
2.3
|
21.6
|
1.0
|
|
SG
|
C:CYS90
|
2.3
|
24.2
|
1.0
|
|
HB2
|
C:CYS90
|
2.7
|
32.0
|
1.0
|
|
HB3
|
C:CYS35
|
3.0
|
24.5
|
1.0
|
|
CB
|
C:CYS90
|
3.1
|
26.7
|
1.0
|
|
H
|
C:CYS87
|
3.1
|
38.0
|
1.0
|
|
CB
|
C:CYS35
|
3.2
|
20.4
|
1.0
|
|
HB3
|
C:CYS32
|
3.3
|
22.2
|
1.0
|
|
CB
|
C:CYS32
|
3.3
|
18.5
|
1.0
|
|
H
|
C:CYS35
|
3.4
|
31.1
|
1.0
|
|
HB3
|
C:CYS87
|
3.4
|
27.8
|
1.0
|
|
HB2
|
C:CYS32
|
3.4
|
22.2
|
1.0
|
|
CB
|
C:CYS87
|
3.5
|
23.1
|
1.0
|
|
H
|
C:CYS90
|
3.6
|
34.8
|
1.0
|
|
HB3
|
C:CYS90
|
3.7
|
32.0
|
1.0
|
|
HG22
|
C:THR37
|
3.7
|
28.6
|
1.0
|
|
N
|
C:CYS35
|
3.8
|
25.9
|
1.0
|
|
N
|
C:CYS87
|
3.9
|
31.6
|
1.0
|
|
HB2
|
C:CYS35
|
4.0
|
24.5
|
1.0
|
|
HB2
|
C:LEU34
|
4.0
|
28.7
|
1.0
|
|
CA
|
C:CYS35
|
4.1
|
24.1
|
1.0
|
|
HG21
|
C:THR37
|
4.2
|
28.6
|
1.0
|
|
HB2
|
C:CYS87
|
4.2
|
27.8
|
1.0
|
|
CA
|
C:CYS87
|
4.3
|
30.3
|
1.0
|
|
N
|
C:CYS90
|
4.3
|
28.9
|
1.0
|
|
CA
|
C:CYS90
|
4.3
|
25.0
|
1.0
|
|
H
|
C:LEU34
|
4.3
|
24.9
|
1.0
|
|
CG2
|
C:THR37
|
4.4
|
23.8
|
1.0
|
|
O
|
C:HOH573
|
4.5
|
29.9
|
1.0
|
|
H
|
C:THR37
|
4.6
|
28.8
|
1.0
|
|
O
|
C:HOH705
|
4.7
|
34.3
|
1.0
|
|
C
|
C:LEU34
|
4.7
|
24.3
|
1.0
|
|
HA
|
C:CYS90
|
4.7
|
30.0
|
1.0
|
|
CA
|
C:CYS32
|
4.7
|
20.3
|
1.0
|
|
HA
|
C:LEU86
|
4.7
|
30.8
|
1.0
|
|
H
|
C:GLY36
|
4.8
|
28.3
|
1.0
|
|
HD22
|
C:LEU86
|
4.8
|
29.8
|
1.0
|
|
O
|
C:CYS87
|
4.8
|
27.6
|
1.0
|
|
O
|
C:HOH688
|
4.8
|
33.9
|
1.0
|
|
CB
|
C:LEU34
|
4.9
|
23.9
|
1.0
|
|
HB3
|
C:LEU86
|
4.9
|
28.0
|
1.0
|
|
C
|
C:CYS35
|
4.9
|
23.2
|
1.0
|
|
HA
|
C:CYS35
|
4.9
|
28.9
|
1.0
|
|
C
|
C:CYS87
|
4.9
|
30.2
|
1.0
|
|
HG23
|
C:THR37
|
5.0
|
28.6
|
1.0
|
|
Zinc binding site 4 out
of 12 in 8fmg
Go back to
Zinc Binding Sites List in 8fmg
Zinc binding site 4 out
of 12 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au)
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn401
b:35.5
occ:1.00
|
SG
|
D:CYS90
|
2.3
|
36.7
|
1.0
|
|
SG
|
D:CYS32
|
2.3
|
23.9
|
1.0
|
|
SG
|
D:CYS87
|
2.3
|
34.0
|
1.0
|
|
SG
|
D:CYS35
|
2.3
|
26.5
|
1.0
|
|
HG
|
E:SER257
|
2.8
|
63.1
|
1.0
|
|
HB3
|
D:CYS35
|
2.8
|
30.1
|
1.0
|
|
HB3
|
D:CYS32
|
3.0
|
30.4
|
1.0
|
|
CB
|
D:CYS32
|
3.1
|
25.4
|
1.0
|
|
HB2
|
D:CYS90
|
3.1
|
38.3
|
1.0
|
|
CB
|
D:CYS35
|
3.1
|
25.0
|
1.0
|
|
HB2
|
D:CYS32
|
3.2
|
30.4
|
1.0
|
|
H
|
D:CYS87
|
3.3
|
38.1
|
1.0
|
|
CB
|
D:CYS90
|
3.3
|
31.9
|
1.0
|
|
H
|
D:CYS35
|
3.4
|
31.8
|
1.0
|
|
HB3
|
D:CYS87
|
3.5
|
38.9
|
1.0
|
|
OG
|
E:SER257
|
3.5
|
52.6
|
1.0
|
|
CB
|
D:CYS87
|
3.6
|
32.4
|
1.0
|
|
H
|
D:CYS90
|
3.6
|
43.1
|
1.0
|
|
N
|
D:CYS35
|
3.8
|
26.5
|
1.0
|
|
HB2
|
D:CYS35
|
3.9
|
30.1
|
1.0
|
|
HB3
|
D:CYS90
|
4.0
|
38.3
|
1.0
|
|
HB2
|
D:LEU34
|
4.0
|
31.6
|
1.0
|
|
CA
|
D:CYS35
|
4.1
|
27.9
|
1.0
|
|
N
|
D:CYS87
|
4.1
|
31.7
|
1.0
|
|
H
|
D:LEU34
|
4.3
|
33.3
|
1.0
|
|
N
|
D:CYS90
|
4.3
|
35.9
|
1.0
|
|
HB2
|
D:CYS87
|
4.3
|
38.9
|
1.0
|
|
CA
|
D:CYS87
|
4.4
|
32.1
|
1.0
|
|
CA
|
D:CYS90
|
4.4
|
28.7
|
1.0
|
|
H
|
D:THR37
|
4.5
|
37.0
|
1.0
|
|
HB3
|
E:SER257
|
4.5
|
53.8
|
1.0
|
|
HB
|
D:THR37
|
4.5
|
42.7
|
1.0
|
|
CA
|
D:CYS32
|
4.5
|
29.1
|
1.0
|
|
CB
|
E:SER257
|
4.5
|
44.8
|
1.0
|
|
H
|
D:GLY36
|
4.6
|
35.8
|
1.0
|
|
HG2
|
E:PRO300
|
4.6
|
40.2
|
1.0
|
|
O
|
E:HOH663
|
4.6
|
38.8
|
1.0
|
|
HG3
|
E:PRO300
|
4.7
|
40.2
|
1.0
|
|
HB2
|
E:SER257
|
4.7
|
53.8
|
1.0
|
|
C
|
D:LEU34
|
4.7
|
24.2
|
1.0
|
|
HA
|
D:CYS35
|
4.8
|
33.5
|
1.0
|
|
C
|
D:CYS35
|
4.8
|
29.6
|
1.0
|
|
HA
|
D:LEU86
|
4.8
|
35.2
|
1.0
|
|
CB
|
D:LEU34
|
4.9
|
26.4
|
1.0
|
|
HG1
|
D:THR37
|
4.9
|
55.9
|
1.0
|
|
HA
|
D:CYS90
|
4.9
|
34.5
|
1.0
|
|
HA
|
D:CYS32
|
4.9
|
35.0
|
1.0
|
|
N
|
D:GLY36
|
4.9
|
29.8
|
1.0
|
|
OG1
|
D:THR37
|
5.0
|
46.6
|
1.0
|
|
N
|
D:LEU34
|
5.0
|
27.7
|
1.0
|
|
C
|
D:CYS32
|
5.0
|
24.1
|
1.0
|
|
Zinc binding site 5 out
of 12 in 8fmg
Go back to
Zinc Binding Sites List in 8fmg
Zinc binding site 5 out
of 12 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au)
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn401
b:24.4
occ:1.00
|
SG
|
E:CYS32
|
2.3
|
20.9
|
1.0
|
|
SG
|
E:CYS87
|
2.3
|
21.9
|
1.0
|
|
SG
|
E:CYS35
|
2.3
|
21.3
|
1.0
|
|
SG
|
E:CYS90
|
2.3
|
20.6
|
1.0
|
|
HB2
|
E:CYS90
|
2.8
|
25.7
|
1.0
|
|
HB3
|
E:CYS35
|
2.8
|
25.3
|
1.0
|
|
CB
|
E:CYS90
|
3.1
|
21.4
|
1.0
|
|
CB
|
E:CYS35
|
3.1
|
21.1
|
1.0
|
|
H
|
E:CYS87
|
3.2
|
24.8
|
1.0
|
|
HB3
|
E:CYS32
|
3.3
|
25.3
|
1.0
|
|
CB
|
E:CYS32
|
3.3
|
21.1
|
1.0
|
|
HB2
|
E:CYS32
|
3.4
|
25.3
|
1.0
|
|
HB3
|
E:CYS87
|
3.4
|
26.8
|
1.0
|
|
H
|
E:CYS35
|
3.4
|
27.6
|
1.0
|
|
CB
|
E:CYS87
|
3.5
|
22.3
|
1.0
|
|
H
|
E:CYS90
|
3.7
|
29.0
|
1.0
|
|
HB3
|
E:CYS90
|
3.7
|
25.7
|
1.0
|
|
N
|
E:CYS35
|
3.8
|
23.0
|
1.0
|
|
HB2
|
E:CYS35
|
3.9
|
25.3
|
1.0
|
|
N
|
E:CYS87
|
3.9
|
20.6
|
1.0
|
|
CA
|
E:CYS35
|
4.1
|
26.3
|
1.0
|
|
HB2
|
E:LEU34
|
4.1
|
23.3
|
1.0
|
|
HB2
|
E:CYS87
|
4.2
|
26.8
|
1.0
|
|
CA
|
E:CYS87
|
4.3
|
24.0
|
1.0
|
|
N
|
E:CYS90
|
4.3
|
24.1
|
1.0
|
|
CA
|
E:CYS90
|
4.3
|
20.8
|
1.0
|
|
O
|
E:HOH680
|
4.4
|
25.4
|
1.0
|
|
H
|
E:LEU34
|
4.4
|
23.4
|
1.0
|
|
HG1
|
E:THR37
|
4.5
|
51.4
|
1.0
|
|
O
|
E:HOH734
|
4.5
|
33.3
|
1.0
|
|
H
|
E:THR37
|
4.6
|
33.6
|
1.0
|
|
OG1
|
E:THR37
|
4.6
|
42.8
|
1.0
|
|
C
|
E:LEU34
|
4.7
|
18.7
|
1.0
|
|
O
|
E:HOH730
|
4.7
|
37.4
|
1.0
|
|
H
|
E:GLY36
|
4.7
|
31.6
|
1.0
|
|
HA
|
E:CYS90
|
4.7
|
25.0
|
1.0
|
|
HA
|
E:LEU86
|
4.7
|
30.0
|
1.0
|
|
CA
|
E:CYS32
|
4.7
|
21.5
|
1.0
|
|
HD22
|
E:LEU86
|
4.8
|
28.4
|
1.0
|
|
HB3
|
E:LEU86
|
4.8
|
29.0
|
1.0
|
|
HA
|
E:CYS35
|
4.8
|
31.5
|
1.0
|
|
C
|
E:CYS35
|
4.8
|
28.6
|
1.0
|
|
HB
|
E:THR37
|
4.8
|
32.2
|
1.0
|
|
O
|
E:CYS87
|
4.8
|
22.8
|
1.0
|
|
C
|
E:CYS87
|
4.9
|
24.4
|
1.0
|
|
CB
|
E:LEU34
|
4.9
|
19.4
|
1.0
|
|
Zinc binding site 6 out
of 12 in 8fmg
Go back to
Zinc Binding Sites List in 8fmg
Zinc binding site 6 out
of 12 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au)
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn401
b:33.8
occ:1.00
|
SG
|
F:CYS87
|
2.3
|
29.3
|
1.0
|
|
SG
|
F:CYS32
|
2.3
|
27.4
|
1.0
|
|
SG
|
F:CYS90
|
2.3
|
39.1
|
1.0
|
|
SG
|
F:CYS35
|
2.3
|
30.5
|
1.0
|
|
HB3
|
F:CYS35
|
2.6
|
31.9
|
1.0
|
|
HB2
|
F:CYS90
|
3.0
|
45.1
|
1.0
|
|
CB
|
F:CYS35
|
3.0
|
26.6
|
1.0
|
|
HB3
|
F:CYS32
|
3.1
|
32.4
|
1.0
|
|
H
|
F:CYS35
|
3.1
|
36.5
|
1.0
|
|
CB
|
F:CYS32
|
3.2
|
27.0
|
1.0
|
|
H
|
F:CYS87
|
3.2
|
38.5
|
1.0
|
|
CB
|
F:CYS90
|
3.3
|
37.6
|
1.0
|
|
HB2
|
F:CYS32
|
3.3
|
32.4
|
1.0
|
|
HB3
|
F:CYS87
|
3.4
|
39.8
|
1.0
|
|
CB
|
F:CYS87
|
3.5
|
33.2
|
1.0
|
|
H
|
F:CYS90
|
3.6
|
49.0
|
1.0
|
|
N
|
F:CYS35
|
3.7
|
30.4
|
1.0
|
|
HB2
|
F:CYS35
|
3.8
|
31.9
|
1.0
|
|
HB3
|
F:CYS90
|
3.9
|
45.1
|
1.0
|
|
CA
|
F:CYS35
|
3.9
|
30.6
|
1.0
|
|
N
|
F:CYS87
|
4.0
|
32.1
|
1.0
|
|
HG22
|
F:THR37
|
4.0
|
39.4
|
0.7
|
|
HB2
|
F:LEU34
|
4.0
|
44.6
|
1.0
|
|
HG1
|
F:THR37
|
4.1
|
40.6
|
0.3
|
|
OG1
|
F:THR37
|
4.1
|
33.8
|
0.3
|
|
HB2
|
F:CYS87
|
4.2
|
39.8
|
1.0
|
|
N
|
F:CYS90
|
4.3
|
40.9
|
1.0
|
|
CA
|
F:CYS87
|
4.3
|
35.0
|
1.0
|
|
HG21
|
F:THR37
|
4.3
|
39.4
|
0.7
|
|
H
|
F:THR37
|
4.4
|
37.0
|
0.7
|
|
H
|
F:GLY36
|
4.4
|
37.9
|
1.0
|
|
H
|
F:THR37
|
4.4
|
37.0
|
0.3
|
|
H
|
F:LEU34
|
4.4
|
37.7
|
1.0
|
|
CA
|
F:CYS90
|
4.4
|
38.4
|
1.0
|
|
HB
|
F:THR37
|
4.6
|
39.8
|
0.7
|
|
CG2
|
F:THR37
|
4.6
|
32.8
|
0.7
|
|
CA
|
F:CYS32
|
4.6
|
27.5
|
1.0
|
|
HA
|
F:CYS35
|
4.7
|
36.8
|
1.0
|
|
C
|
F:LEU34
|
4.7
|
29.9
|
1.0
|
|
C
|
F:CYS35
|
4.7
|
29.3
|
1.0
|
|
N
|
F:GLY36
|
4.8
|
31.6
|
1.0
|
|
HA
|
F:LEU86
|
4.8
|
33.6
|
1.0
|
|
HA
|
F:CYS90
|
4.9
|
46.1
|
1.0
|
|
CB
|
F:LEU34
|
4.9
|
37.2
|
1.0
|
|
HB3
|
F:LEU86
|
4.9
|
37.2
|
1.0
|
|
O
|
F:CYS87
|
4.9
|
32.6
|
1.0
|
|
C
|
F:CYS87
|
4.9
|
32.6
|
1.0
|
|
HA
|
F:CYS32
|
5.0
|
33.0
|
1.0
|
|
Zinc binding site 7 out
of 12 in 8fmg
Go back to
Zinc Binding Sites List in 8fmg
Zinc binding site 7 out
of 12 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au)
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn401
b:29.2
occ:1.00
|
SG
|
G:CYS90
|
2.3
|
19.9
|
1.0
|
|
SG
|
G:CYS32
|
2.3
|
21.7
|
1.0
|
|
SG
|
G:CYS35
|
2.3
|
19.5
|
1.0
|
|
SG
|
G:CYS87
|
2.3
|
20.8
|
1.0
|
|
HB2
|
G:CYS90
|
2.9
|
27.0
|
1.0
|
|
HB3
|
G:CYS35
|
3.0
|
18.1
|
1.0
|
|
H
|
G:CYS87
|
3.2
|
29.9
|
1.0
|
|
CB
|
G:CYS90
|
3.2
|
22.5
|
1.0
|
|
CB
|
G:CYS35
|
3.2
|
15.1
|
1.0
|
|
HB3
|
G:CYS32
|
3.2
|
24.0
|
1.0
|
|
CB
|
G:CYS32
|
3.3
|
20.0
|
1.0
|
|
H
|
G:CYS35
|
3.3
|
22.2
|
1.0
|
|
HB3
|
G:CYS87
|
3.4
|
29.5
|
1.0
|
|
HB2
|
G:CYS32
|
3.4
|
24.0
|
1.0
|
|
CB
|
G:CYS87
|
3.5
|
24.6
|
1.0
|
|
H
|
G:CYS90
|
3.7
|
32.9
|
1.0
|
|
HG22
|
G:THR37
|
3.8
|
27.1
|
1.0
|
|
HB3
|
G:CYS90
|
3.8
|
27.0
|
1.0
|
|
N
|
G:CYS35
|
3.8
|
18.5
|
1.0
|
|
N
|
G:CYS87
|
4.0
|
24.9
|
1.0
|
|
HB2
|
G:CYS35
|
4.0
|
18.1
|
1.0
|
|
HB2
|
G:LEU34
|
4.0
|
23.5
|
1.0
|
|
CA
|
G:CYS35
|
4.1
|
19.5
|
1.0
|
|
HB2
|
G:CYS87
|
4.2
|
29.5
|
1.0
|
|
HG21
|
G:THR37
|
4.2
|
27.1
|
1.0
|
|
CA
|
G:CYS87
|
4.3
|
20.9
|
1.0
|
|
N
|
G:CYS90
|
4.4
|
27.4
|
1.0
|
|
CA
|
G:CYS90
|
4.4
|
23.8
|
1.0
|
|
H
|
G:LEU34
|
4.4
|
26.6
|
1.0
|
|
CG2
|
G:THR37
|
4.5
|
22.6
|
1.0
|
|
H
|
G:THR37
|
4.5
|
25.3
|
1.0
|
|
O
|
G:HOH602
|
4.7
|
26.6
|
1.0
|
|
H
|
G:GLY36
|
4.7
|
25.7
|
1.0
|
|
C
|
G:LEU34
|
4.7
|
20.2
|
1.0
|
|
HA
|
G:LEU86
|
4.7
|
28.5
|
1.0
|
|
CA
|
G:CYS32
|
4.7
|
22.0
|
1.0
|
|
HB3
|
G:LEU86
|
4.7
|
29.1
|
1.0
|
|
HA
|
G:CYS90
|
4.8
|
28.6
|
1.0
|
|
C
|
G:CYS35
|
4.8
|
19.9
|
1.0
|
|
O
|
G:CYS87
|
4.8
|
22.8
|
1.0
|
|
HD22
|
G:LEU86
|
4.8
|
32.0
|
1.0
|
|
CB
|
G:LEU34
|
4.9
|
19.6
|
1.0
|
|
HA
|
G:CYS35
|
4.9
|
23.4
|
1.0
|
|
C
|
G:CYS87
|
4.9
|
20.2
|
1.0
|
|
HB
|
G:THR37
|
4.9
|
27.0
|
1.0
|
|
Zinc binding site 8 out
of 12 in 8fmg
Go back to
Zinc Binding Sites List in 8fmg
Zinc binding site 8 out
of 12 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au)
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn401
b:30.7
occ:1.00
|
SG
|
H:CYS32
|
2.3
|
24.2
|
1.0
|
|
SG
|
H:CYS87
|
2.3
|
28.6
|
1.0
|
|
SG
|
H:CYS90
|
2.3
|
29.7
|
1.0
|
|
SG
|
H:CYS35
|
2.3
|
29.8
|
1.0
|
|
HB2
|
H:CYS90
|
2.8
|
33.0
|
1.0
|
|
CB
|
H:CYS90
|
3.2
|
27.5
|
1.0
|
|
HB3
|
H:CYS32
|
3.2
|
34.9
|
1.0
|
|
H
|
H:CYS87
|
3.2
|
30.3
|
1.0
|
|
CB
|
H:CYS32
|
3.2
|
29.1
|
1.0
|
|
HB3
|
H:CYS35
|
3.3
|
34.9
|
1.0
|
|
H
|
H:CYS35
|
3.3
|
31.8
|
1.0
|
|
HB2
|
H:CYS32
|
3.3
|
34.9
|
1.0
|
|
CB
|
H:CYS35
|
3.4
|
29.1
|
1.0
|
|
HB3
|
H:CYS87
|
3.5
|
33.4
|
1.0
|
|
CB
|
H:CYS87
|
3.6
|
27.9
|
1.0
|
|
H
|
H:CYS90
|
3.6
|
39.1
|
1.0
|
|
HB3
|
H:CYS90
|
3.8
|
33.0
|
1.0
|
|
HB2
|
H:LEU34
|
3.8
|
37.7
|
1.0
|
|
N
|
H:CYS35
|
3.9
|
26.5
|
1.0
|
|
N
|
H:CYS87
|
4.0
|
25.2
|
1.0
|
|
N
|
H:CYS90
|
4.2
|
32.6
|
1.0
|
|
HB2
|
H:CYS35
|
4.2
|
34.9
|
1.0
|
|
CA
|
H:CYS35
|
4.2
|
25.8
|
1.0
|
|
CA
|
H:CYS90
|
4.3
|
29.0
|
1.0
|
|
HB2
|
H:CYS87
|
4.3
|
33.4
|
1.0
|
|
CA
|
H:CYS87
|
4.3
|
29.4
|
1.0
|
|
H
|
H:LEU34
|
4.4
|
35.5
|
1.0
|
|
HB
|
H:THR37
|
4.5
|
33.8
|
1.0
|
|
H
|
H:THR37
|
4.6
|
30.5
|
1.0
|
|
CA
|
H:CYS32
|
4.7
|
24.4
|
1.0
|
|
CB
|
H:LEU34
|
4.7
|
31.4
|
1.0
|
|
HA
|
H:CYS90
|
4.7
|
34.9
|
1.0
|
|
C
|
H:LEU34
|
4.8
|
30.2
|
1.0
|
|
O
|
H:CYS87
|
4.8
|
32.9
|
1.0
|
|
HA
|
H:LEU86
|
4.8
|
35.1
|
1.0
|
|
HB3
|
H:LEU86
|
4.8
|
31.9
|
1.0
|
|
H
|
H:GLY36
|
4.9
|
34.5
|
1.0
|
|
C
|
H:CYS87
|
4.9
|
32.5
|
1.0
|
|
HG1
|
H:THR37
|
4.9
|
40.3
|
1.0
|
|
HA
|
H:CYS32
|
5.0
|
29.2
|
1.0
|
|
Zinc binding site 9 out
of 12 in 8fmg
Go back to
Zinc Binding Sites List in 8fmg
Zinc binding site 9 out
of 12 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au)
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Zn401
b:20.0
occ:1.00
|
SG
|
K:CYS90
|
2.3
|
20.6
|
1.0
|
|
SG
|
K:CYS35
|
2.3
|
20.2
|
1.0
|
|
SG
|
K:CYS32
|
2.3
|
21.6
|
1.0
|
|
SG
|
K:CYS87
|
2.3
|
21.1
|
1.0
|
|
HB2
|
K:CYS90
|
2.8
|
33.5
|
1.0
|
|
HB3
|
K:CYS35
|
3.0
|
27.1
|
1.0
|
|
H
|
K:CYS87
|
3.1
|
22.7
|
1.0
|
|
CB
|
K:CYS90
|
3.2
|
27.9
|
1.0
|
|
CB
|
K:CYS35
|
3.2
|
22.6
|
1.0
|
|
HB3
|
K:CYS32
|
3.2
|
26.6
|
1.0
|
|
HB3
|
K:CYS87
|
3.2
|
27.1
|
1.0
|
|
CB
|
K:CYS32
|
3.2
|
22.2
|
1.0
|
|
HB2
|
K:CYS32
|
3.3
|
26.6
|
1.0
|
|
H
|
K:CYS35
|
3.3
|
28.1
|
1.0
|
|
CB
|
K:CYS87
|
3.4
|
22.5
|
1.0
|
|
H
|
K:CYS90
|
3.7
|
25.6
|
1.0
|
|
HB3
|
K:CYS90
|
3.7
|
33.5
|
1.0
|
|
HG22
|
K:THR37
|
3.7
|
28.9
|
1.0
|
|
N
|
K:CYS35
|
3.8
|
23.4
|
1.0
|
|
N
|
K:CYS87
|
3.9
|
18.9
|
1.0
|
|
HB2
|
K:CYS35
|
4.0
|
27.1
|
1.0
|
|
CA
|
K:CYS35
|
4.1
|
17.6
|
1.0
|
|
HB2
|
K:LEU34
|
4.1
|
19.4
|
1.0
|
|
HB2
|
K:CYS87
|
4.2
|
27.1
|
1.0
|
|
CA
|
K:CYS87
|
4.2
|
22.0
|
1.0
|
|
HG21
|
K:THR37
|
4.3
|
28.9
|
1.0
|
|
N
|
K:CYS90
|
4.3
|
21.4
|
1.0
|
|
CA
|
K:CYS90
|
4.3
|
16.4
|
1.0
|
|
H
|
K:LEU34
|
4.4
|
22.9
|
1.0
|
|
O
|
K:HOH666
|
4.4
|
22.1
|
1.0
|
|
CG2
|
K:THR37
|
4.5
|
24.1
|
1.0
|
|
H
|
K:THR37
|
4.6
|
24.2
|
1.0
|
|
C
|
K:LEU34
|
4.6
|
20.0
|
1.0
|
|
H
|
K:GLY36
|
4.6
|
24.4
|
1.0
|
|
HA
|
K:LEU86
|
4.7
|
28.0
|
1.0
|
|
CA
|
K:CYS32
|
4.7
|
21.8
|
1.0
|
|
HA
|
K:CYS90
|
4.7
|
19.8
|
1.0
|
|
HB3
|
K:LEU86
|
4.7
|
30.8
|
1.0
|
|
HD22
|
K:LEU86
|
4.8
|
20.8
|
1.0
|
|
C
|
K:CYS35
|
4.8
|
19.7
|
1.0
|
|
HA
|
K:CYS35
|
4.8
|
21.1
|
1.0
|
|
C
|
K:CYS87
|
4.9
|
21.3
|
1.0
|
|
O
|
K:CYS87
|
4.9
|
21.7
|
1.0
|
|
CB
|
K:LEU34
|
5.0
|
16.2
|
1.0
|
|
N
|
K:GLY36
|
5.0
|
20.3
|
1.0
|
|
Zinc binding site 10 out
of 12 in 8fmg
Go back to
Zinc Binding Sites List in 8fmg
Zinc binding site 10 out
of 12 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au)
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (3 Tetramers in the Au) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn401
b:32.1
occ:1.00
|
SG
|
L:CYS35
|
2.3
|
29.3
|
1.0
|
|
SG
|
L:CYS32
|
2.3
|
30.2
|
1.0
|
|
SG
|
L:CYS90
|
2.3
|
36.3
|
1.0
|
|
SG
|
L:CYS87
|
2.3
|
25.4
|
1.0
|
|
HB2
|
L:CYS90
|
2.8
|
40.8
|
1.0
|
|
HB3
|
L:CYS35
|
3.0
|
34.6
|
1.0
|
|
CB
|
L:CYS90
|
3.2
|
34.0
|
1.0
|
|
HB3
|
L:CYS32
|
3.2
|
36.4
|
1.0
|
|
CB
|
L:CYS32
|
3.2
|
30.3
|
1.0
|
|
H
|
L:CYS35
|
3.2
|
36.5
|
1.0
|
|
H
|
L:CYS87
|
3.3
|
36.6
|
1.0
|
|
CB
|
L:CYS35
|
3.3
|
28.8
|
1.0
|
|
HB2
|
L:CYS32
|
3.3
|
36.4
|
1.0
|
|
H
|
L:CYS90
|
3.5
|
46.5
|
1.0
|
|
HB3
|
L:CYS87
|
3.5
|
37.5
|
1.0
|
|
CB
|
L:CYS87
|
3.6
|
31.2
|
1.0
|
|
N
|
L:CYS35
|
3.8
|
30.4
|
1.0
|
|
HB3
|
L:CYS90
|
3.8
|
40.8
|
1.0
|
|
HB2
|
L:CYS35
|
4.0
|
34.6
|
1.0
|
|
N
|
L:CYS87
|
4.0
|
30.5
|
1.0
|
|
HB2
|
L:LEU34
|
4.0
|
34.5
|
1.0
|
|
CA
|
L:CYS35
|
4.1
|
33.2
|
1.0
|
|
N
|
L:CYS90
|
4.2
|
38.7
|
1.0
|
|
CA
|
L:CYS90
|
4.3
|
36.4
|
1.0
|
|
HB2
|
L:CYS87
|
4.3
|
37.5
|
1.0
|
|
CA
|
L:CYS87
|
4.4
|
34.9
|
1.0
|
|
H
|
L:LEU34
|
4.4
|
28.1
|
1.0
|
|
H
|
L:GLY36
|
4.4
|
39.3
|
1.0
|
|
H
|
L:THR37
|
4.5
|
40.5
|
1.0
|
|
HG23
|
L:THR37
|
4.6
|
42.5
|
1.0
|
|
O
|
L:HOH695
|
4.6
|
45.1
|
1.0
|
|
CA
|
L:CYS32
|
4.7
|
26.5
|
1.0
|
|
HG1
|
L:THR37
|
4.7
|
50.8
|
1.0
|
|
HA
|
L:CYS90
|
4.7
|
43.7
|
1.0
|
|
OG1
|
L:THR37
|
4.7
|
42.4
|
1.0
|
|
HA
|
L:LEU86
|
4.8
|
31.9
|
1.0
|
|
C
|
L:CYS35
|
4.8
|
33.7
|
1.0
|
|
C
|
L:LEU34
|
4.8
|
30.5
|
1.0
|
|
HD22
|
L:LEU86
|
4.8
|
41.9
|
1.0
|
|
N
|
L:GLY36
|
4.9
|
32.7
|
1.0
|
|
O
|
L:CYS87
|
4.9
|
31.0
|
1.0
|
|
HA
|
L:CYS35
|
4.9
|
39.9
|
1.0
|
|
HB3
|
L:LEU86
|
4.9
|
32.5
|
1.0
|
|
CB
|
L:LEU34
|
4.9
|
28.8
|
1.0
|
|
C
|
L:CYS87
|
5.0
|
32.3
|
1.0
|
|
Reference:
O.Rechkoblit,
D.Sciaky,
D.F.Kreitler,
A.Buku,
J.Kottur,
A.K.Aggarwal.
Activation of Cbass-CAP5 Endonuclease Immune Effector By Cyclic Nucleotides: A View at High Resolution Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01220-X
Page generated: Wed Oct 30 20:27:42 2024
|
