Zinc in PDB 8fmh: Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Dgamp Ligand (2 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-Dgamp Ligand (2 Tetramers in the Au), PDB code: 8fmh
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)
|
38.45 /
1.87
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.97,
295.678,
84.052,
90,
113.79,
90
|
R / Rfree (%)
|
21 /
25.3
|
Other elements in 8fmh:
The structure of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Dgamp Ligand (2 Tetramers in the Au) also contains other interesting chemical elements:
Zinc 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-Dgamp Ligand (2 Tetramers in the Au)
(pdb code 8fmh). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 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-Dgamp Ligand (2 Tetramers in the Au), PDB code: 8fmh:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 8fmh
Go back to
Zinc Binding Sites List in 8fmh
Zinc binding site 1 out
of 8 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Dgamp Ligand (2 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-Dgamp Ligand (2 Tetramers in the Au) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:37.0
occ:1.00
|
SG
|
A:CYS90
|
2.3
|
36.6
|
1.0
|
SG
|
A:CYS87
|
2.3
|
37.0
|
1.0
|
SG
|
A:CYS35
|
2.3
|
32.8
|
1.0
|
SG
|
A:CYS32
|
2.3
|
36.8
|
1.0
|
HB2
|
A:CYS90
|
2.8
|
43.2
|
1.0
|
H
|
A:CYS87
|
3.0
|
61.4
|
1.0
|
HB3
|
A:CYS87
|
3.1
|
47.9
|
1.0
|
HB3
|
A:CYS35
|
3.1
|
42.6
|
1.0
|
CB
|
A:CYS90
|
3.2
|
36.0
|
1.0
|
HB3
|
A:CYS32
|
3.2
|
42.5
|
1.0
|
CB
|
A:CYS32
|
3.3
|
35.4
|
1.0
|
CB
|
A:CYS87
|
3.3
|
39.9
|
1.0
|
CB
|
A:CYS35
|
3.3
|
35.5
|
1.0
|
HB2
|
A:CYS32
|
3.4
|
42.5
|
1.0
|
H
|
A:CYS35
|
3.4
|
45.1
|
1.0
|
HB3
|
A:CYS90
|
3.7
|
43.2
|
1.0
|
H
|
A:CYS90
|
3.7
|
51.6
|
1.0
|
N
|
A:CYS87
|
3.8
|
51.1
|
1.0
|
N
|
A:CYS35
|
3.8
|
37.5
|
1.0
|
HB2
|
A:LEU34
|
3.9
|
53.0
|
1.0
|
HB2
|
A:CYS87
|
4.1
|
47.9
|
1.0
|
HB2
|
A:CYS35
|
4.1
|
42.6
|
1.0
|
CA
|
A:CYS35
|
4.1
|
40.3
|
1.0
|
CA
|
A:CYS87
|
4.1
|
45.8
|
1.0
|
H
|
A:LEU34
|
4.3
|
53.9
|
1.0
|
N
|
A:CYS90
|
4.3
|
43.0
|
1.0
|
CA
|
A:CYS90
|
4.3
|
36.6
|
1.0
|
H
|
A:THR37
|
4.5
|
44.1
|
1.0
|
HG1
|
A:THR37
|
4.6
|
72.0
|
1.0
|
C
|
A:LEU34
|
4.6
|
33.8
|
1.0
|
HB
|
A:THR37
|
4.6
|
57.4
|
1.0
|
O
|
A:HOH568
|
4.6
|
40.2
|
1.0
|
HA
|
A:LEU86
|
4.7
|
52.1
|
1.0
|
O
|
A:HOH639
|
4.7
|
51.3
|
1.0
|
CA
|
A:CYS32
|
4.7
|
36.5
|
1.0
|
OG1
|
A:THR37
|
4.7
|
60.0
|
1.0
|
CB
|
A:LEU34
|
4.7
|
44.1
|
1.0
|
HA
|
A:CYS90
|
4.7
|
44.0
|
1.0
|
O
|
A:HOH640
|
4.7
|
49.2
|
1.0
|
H
|
A:GLY36
|
4.8
|
44.7
|
1.0
|
HD22
|
A:LEU86
|
4.8
|
50.9
|
1.0
|
O
|
A:CYS87
|
4.8
|
45.6
|
1.0
|
C
|
A:CYS87
|
4.8
|
45.6
|
1.0
|
HB3
|
A:LEU86
|
4.9
|
44.1
|
1.0
|
C
|
A:CYS35
|
4.9
|
34.8
|
1.0
|
O
|
A:HOH632
|
4.9
|
42.3
|
1.0
|
HB3
|
A:LEU34
|
4.9
|
53.0
|
1.0
|
HA
|
A:CYS87
|
4.9
|
54.9
|
1.0
|
HA
|
A:CYS35
|
4.9
|
48.4
|
1.0
|
C
|
A:LEU86
|
5.0
|
47.9
|
1.0
|
|
Zinc binding site 2 out
of 8 in 8fmh
Go back to
Zinc Binding Sites List in 8fmh
Zinc binding site 2 out
of 8 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Dgamp Ligand (2 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-Dgamp Ligand (2 Tetramers in the Au) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:71.6
occ:1.00
|
SG
|
B:CYS35
|
2.3
|
61.7
|
1.0
|
SG
|
B:CYS87
|
2.3
|
74.8
|
1.0
|
SG
|
B:CYS90
|
2.3
|
64.0
|
1.0
|
SG
|
B:CYS32
|
2.3
|
66.4
|
1.0
|
HB2
|
B:CYS90
|
2.7
|
85.8
|
1.0
|
CB
|
B:CYS90
|
3.1
|
71.5
|
1.0
|
HB3
|
B:CYS35
|
3.1
|
74.9
|
1.0
|
H
|
B:CYS35
|
3.2
|
77.1
|
1.0
|
HB3
|
B:CYS32
|
3.2
|
83.0
|
1.0
|
HB3
|
B:CYS87
|
3.2
|
86.5
|
1.0
|
H
|
B:CYS87
|
3.3
|
86.1
|
1.0
|
CB
|
B:CYS32
|
3.3
|
69.2
|
1.0
|
CB
|
B:CYS35
|
3.3
|
62.4
|
1.0
|
CB
|
B:CYS87
|
3.4
|
72.1
|
1.0
|
H
|
B:CYS90
|
3.4
|
96.0
|
1.0
|
HB2
|
B:CYS32
|
3.4
|
83.0
|
1.0
|
HB3
|
B:CYS90
|
3.7
|
85.8
|
1.0
|
N
|
B:CYS35
|
3.7
|
64.2
|
1.0
|
HB2
|
B:LEU34
|
3.8
|
74.8
|
1.0
|
N
|
B:CYS87
|
4.0
|
71.8
|
1.0
|
HG1
|
B:THR37
|
4.0
|
86.4
|
1.0
|
CA
|
B:CYS35
|
4.1
|
58.5
|
1.0
|
HB2
|
B:CYS35
|
4.1
|
74.9
|
1.0
|
N
|
B:CYS90
|
4.1
|
80.0
|
1.0
|
HB2
|
B:CYS87
|
4.1
|
86.5
|
1.0
|
OG1
|
B:THR37
|
4.1
|
72.0
|
1.0
|
CA
|
B:CYS90
|
4.2
|
75.1
|
1.0
|
H
|
B:LEU34
|
4.2
|
73.8
|
1.0
|
CA
|
B:CYS87
|
4.3
|
72.5
|
1.0
|
H
|
B:THR37
|
4.4
|
77.5
|
1.0
|
H
|
B:GLY36
|
4.5
|
71.5
|
1.0
|
HA
|
B:CYS90
|
4.6
|
90.1
|
1.0
|
CB
|
B:LEU34
|
4.6
|
62.4
|
1.0
|
HD22
|
B:LEU86
|
4.6
|
78.5
|
1.0
|
C
|
B:LEU34
|
4.6
|
68.5
|
1.0
|
HB3
|
B:LEU34
|
4.7
|
74.8
|
1.0
|
CA
|
B:CYS32
|
4.7
|
68.8
|
1.0
|
HA
|
B:LEU86
|
4.8
|
80.5
|
1.0
|
C
|
B:CYS35
|
4.8
|
62.1
|
1.0
|
N
|
B:GLY36
|
4.9
|
59.6
|
1.0
|
HA
|
B:CYS35
|
4.9
|
70.2
|
1.0
|
C
|
B:CYS87
|
4.9
|
77.1
|
1.0
|
N
|
B:LEU34
|
4.9
|
61.5
|
1.0
|
O
|
B:CYS87
|
4.9
|
69.8
|
1.0
|
CA
|
B:LEU34
|
5.0
|
61.4
|
1.0
|
|
Zinc binding site 3 out
of 8 in 8fmh
Go back to
Zinc Binding Sites List in 8fmh
Zinc binding site 3 out
of 8 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Dgamp Ligand (2 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-Dgamp Ligand (2 Tetramers in the Au) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn403
b:42.6
occ:1.00
|
SG
|
C:CYS35
|
2.3
|
33.1
|
1.0
|
SG
|
C:CYS90
|
2.3
|
39.8
|
1.0
|
SG
|
C:CYS32
|
2.3
|
40.7
|
1.0
|
SG
|
C:CYS87
|
2.3
|
45.4
|
1.0
|
HB2
|
C:CYS90
|
2.9
|
50.6
|
1.0
|
HB3
|
C:CYS35
|
3.0
|
52.7
|
1.0
|
HB3
|
C:CYS32
|
3.2
|
45.3
|
1.0
|
H
|
C:CYS87
|
3.2
|
42.9
|
1.0
|
CB
|
C:CYS32
|
3.2
|
37.8
|
1.0
|
HB3
|
C:CYS87
|
3.2
|
40.8
|
1.0
|
CB
|
C:CYS90
|
3.2
|
42.1
|
1.0
|
CB
|
C:CYS35
|
3.2
|
43.9
|
1.0
|
HB2
|
C:CYS32
|
3.3
|
45.3
|
1.0
|
CB
|
C:CYS87
|
3.4
|
34.0
|
1.0
|
H
|
C:CYS35
|
3.6
|
47.7
|
1.0
|
H
|
C:CYS90
|
3.7
|
51.0
|
1.0
|
HB3
|
C:CYS90
|
3.8
|
50.6
|
1.0
|
HG22
|
C:THR37
|
3.9
|
51.6
|
1.0
|
N
|
C:CYS35
|
3.9
|
39.7
|
1.0
|
N
|
C:CYS87
|
3.9
|
35.7
|
1.0
|
HB2
|
C:CYS35
|
4.0
|
52.7
|
1.0
|
HB2
|
C:LEU34
|
4.0
|
50.0
|
1.0
|
HB2
|
C:CYS87
|
4.2
|
40.8
|
1.0
|
CA
|
C:CYS35
|
4.2
|
42.9
|
1.0
|
CA
|
C:CYS87
|
4.2
|
37.8
|
1.0
|
HG21
|
C:THR37
|
4.3
|
51.6
|
1.0
|
N
|
C:CYS90
|
4.4
|
42.5
|
1.0
|
CA
|
C:CYS90
|
4.4
|
44.0
|
1.0
|
H
|
C:LEU34
|
4.5
|
55.7
|
1.0
|
O
|
C:HOH623
|
4.5
|
42.3
|
1.0
|
CG2
|
C:THR37
|
4.6
|
43.0
|
1.0
|
H
|
C:THR37
|
4.6
|
46.5
|
1.0
|
O
|
C:HOH661
|
4.6
|
45.1
|
1.0
|
CA
|
C:CYS32
|
4.7
|
44.8
|
1.0
|
O
|
C:HOH667
|
4.7
|
54.3
|
1.0
|
O
|
C:HOH668
|
4.7
|
43.2
|
1.0
|
H
|
C:GLY36
|
4.7
|
46.9
|
1.0
|
C
|
C:LEU34
|
4.7
|
38.8
|
1.0
|
HA
|
C:LEU86
|
4.7
|
49.6
|
1.0
|
HA
|
C:CYS90
|
4.8
|
52.8
|
1.0
|
O
|
C:CYS87
|
4.8
|
48.0
|
1.0
|
HB3
|
C:LEU86
|
4.8
|
56.2
|
1.0
|
CB
|
C:LEU34
|
4.8
|
41.6
|
1.0
|
C
|
C:CYS87
|
4.9
|
45.3
|
1.0
|
HB
|
C:THR37
|
4.9
|
47.0
|
1.0
|
C
|
C:CYS35
|
4.9
|
37.5
|
1.0
|
HD22
|
C:LEU86
|
4.9
|
45.5
|
1.0
|
HA
|
C:CYS35
|
4.9
|
51.5
|
1.0
|
HA
|
C:CYS32
|
5.0
|
53.7
|
1.0
|
|
Zinc binding site 4 out
of 8 in 8fmh
Go back to
Zinc Binding Sites List in 8fmh
Zinc binding site 4 out
of 8 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Dgamp Ligand (2 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-Dgamp Ligand (2 Tetramers in the Au) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn402
b:56.8
occ:1.00
|
O
|
D:HOH607
|
2.1
|
55.7
|
1.0
|
SG
|
D:CYS90
|
2.3
|
47.9
|
1.0
|
SG
|
D:CYS35
|
2.3
|
60.5
|
1.0
|
SG
|
D:CYS87
|
2.3
|
56.3
|
1.0
|
SG
|
D:CYS32
|
2.3
|
48.5
|
1.0
|
HB2
|
D:CYS90
|
3.0
|
61.4
|
1.0
|
HB3
|
D:CYS32
|
3.0
|
58.0
|
1.0
|
HB3
|
D:CYS35
|
3.1
|
64.0
|
1.0
|
CB
|
D:CYS32
|
3.2
|
48.3
|
1.0
|
H
|
D:CYS35
|
3.2
|
58.1
|
1.0
|
CB
|
D:CYS90
|
3.3
|
51.2
|
1.0
|
CB
|
D:CYS35
|
3.3
|
53.3
|
1.0
|
HB2
|
D:CYS32
|
3.3
|
58.0
|
1.0
|
H
|
D:CYS87
|
3.3
|
69.7
|
1.0
|
H
|
D:CYS90
|
3.5
|
76.9
|
1.0
|
CB
|
D:CYS87
|
3.7
|
54.8
|
1.0
|
HB3
|
D:CYS87
|
3.7
|
65.8
|
1.0
|
N
|
D:CYS35
|
3.8
|
48.4
|
1.0
|
HB2
|
D:LEU34
|
3.8
|
62.7
|
1.0
|
HB3
|
D:CYS90
|
3.9
|
61.4
|
1.0
|
N
|
D:CYS87
|
4.0
|
58.1
|
1.0
|
HB2
|
D:CYS35
|
4.1
|
64.0
|
1.0
|
CA
|
D:CYS35
|
4.1
|
46.7
|
1.0
|
N
|
D:CYS90
|
4.2
|
64.1
|
1.0
|
HB
|
D:THR37
|
4.3
|
67.9
|
1.0
|
H
|
D:LEU34
|
4.3
|
60.8
|
1.0
|
CA
|
D:CYS90
|
4.4
|
53.1
|
1.0
|
CA
|
D:CYS87
|
4.4
|
58.9
|
1.0
|
H
|
D:THR37
|
4.4
|
62.5
|
1.0
|
HB2
|
D:CYS87
|
4.4
|
65.8
|
1.0
|
CA
|
D:CYS32
|
4.6
|
44.0
|
1.0
|
CB
|
D:LEU34
|
4.6
|
52.3
|
1.0
|
C
|
D:LEU34
|
4.6
|
48.5
|
1.0
|
HA
|
D:LEU86
|
4.7
|
57.4
|
1.0
|
HD21
|
D:LEU39
|
4.8
|
69.1
|
1.0
|
HB3
|
D:LEU34
|
4.8
|
62.7
|
1.0
|
HA
|
D:CYS90
|
4.8
|
63.7
|
1.0
|
H
|
D:GLY36
|
4.8
|
56.6
|
1.0
|
C
|
D:CYS35
|
4.8
|
45.4
|
1.0
|
O
|
D:CYS87
|
4.8
|
59.8
|
1.0
|
HG1
|
D:THR37
|
4.9
|
91.8
|
1.0
|
HA
|
D:CYS35
|
4.9
|
56.1
|
1.0
|
HB3
|
D:LEU86
|
4.9
|
52.9
|
1.0
|
C
|
D:CYS87
|
5.0
|
55.5
|
1.0
|
N
|
D:LEU34
|
5.0
|
50.6
|
1.0
|
HA
|
D:CYS32
|
5.0
|
52.8
|
1.0
|
CA
|
D:LEU34
|
5.0
|
46.9
|
1.0
|
|
Zinc binding site 5 out
of 8 in 8fmh
Go back to
Zinc Binding Sites List in 8fmh
Zinc binding site 5 out
of 8 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Dgamp Ligand (2 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-Dgamp Ligand (2 Tetramers in the Au) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn402
b:52.8
occ:1.00
|
SG
|
E:CYS90
|
2.3
|
59.1
|
1.0
|
SG
|
E:CYS35
|
2.3
|
48.1
|
1.0
|
SG
|
E:CYS87
|
2.3
|
51.7
|
1.0
|
SG
|
E:CYS32
|
2.3
|
50.8
|
1.0
|
HB2
|
E:CYS90
|
2.8
|
68.0
|
1.0
|
HB3
|
E:CYS35
|
2.9
|
53.9
|
1.0
|
HB3
|
E:CYS87
|
3.1
|
48.9
|
1.0
|
H
|
E:CYS87
|
3.1
|
57.8
|
1.0
|
CB
|
E:CYS90
|
3.2
|
56.6
|
1.0
|
CB
|
E:CYS35
|
3.2
|
45.0
|
1.0
|
HB3
|
E:CYS32
|
3.2
|
59.3
|
1.0
|
CB
|
E:CYS32
|
3.3
|
49.4
|
1.0
|
CB
|
E:CYS87
|
3.3
|
40.7
|
1.0
|
HB2
|
E:CYS32
|
3.4
|
59.3
|
1.0
|
H
|
E:CYS35
|
3.6
|
65.1
|
1.0
|
HB3
|
E:CYS90
|
3.7
|
68.0
|
1.0
|
H
|
E:CYS90
|
3.7
|
68.4
|
1.0
|
N
|
E:CYS87
|
3.9
|
48.1
|
1.0
|
N
|
E:CYS35
|
3.9
|
54.2
|
1.0
|
HB2
|
E:CYS35
|
3.9
|
53.9
|
1.0
|
HB2
|
E:CYS87
|
4.1
|
48.9
|
1.0
|
HB2
|
E:LEU34
|
4.1
|
62.3
|
1.0
|
CA
|
E:CYS35
|
4.1
|
49.5
|
1.0
|
CA
|
E:CYS87
|
4.1
|
49.3
|
1.0
|
N
|
E:CYS90
|
4.3
|
57.0
|
1.0
|
CA
|
E:CYS90
|
4.3
|
59.4
|
1.0
|
H
|
E:LEU34
|
4.4
|
62.5
|
1.0
|
HG1
|
E:THR37
|
4.4
|
74.5
|
1.0
|
O
|
E:CYS87
|
4.6
|
59.4
|
1.0
|
C
|
E:LEU34
|
4.6
|
50.1
|
1.0
|
OG1
|
E:THR37
|
4.6
|
62.1
|
1.0
|
H
|
E:THR37
|
4.7
|
49.7
|
1.0
|
CA
|
E:CYS32
|
4.7
|
41.9
|
1.0
|
HA
|
E:CYS90
|
4.7
|
71.2
|
1.0
|
HD22
|
E:LEU86
|
4.7
|
67.2
|
1.0
|
C
|
E:CYS87
|
4.8
|
54.2
|
1.0
|
HA
|
E:LEU86
|
4.8
|
67.6
|
1.0
|
H
|
E:GLY36
|
4.8
|
56.3
|
1.0
|
HB3
|
E:LEU86
|
4.8
|
66.2
|
1.0
|
HA
|
E:CYS35
|
4.9
|
59.4
|
1.0
|
O
|
G:HOH562
|
4.9
|
54.0
|
1.0
|
C
|
E:CYS35
|
4.9
|
45.9
|
1.0
|
CB
|
E:LEU34
|
4.9
|
51.9
|
1.0
|
HB
|
E:THR37
|
4.9
|
51.6
|
1.0
|
HA
|
E:CYS87
|
5.0
|
59.1
|
1.0
|
|
Zinc binding site 6 out
of 8 in 8fmh
Go back to
Zinc Binding Sites List in 8fmh
Zinc binding site 6 out
of 8 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Dgamp Ligand (2 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-Dgamp Ligand (2 Tetramers in the Au) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn402
b:73.1
occ:1.00
|
SG
|
F:CYS90
|
2.3
|
60.5
|
1.0
|
SG
|
F:CYS35
|
2.3
|
70.5
|
1.0
|
SG
|
F:CYS87
|
2.3
|
71.9
|
1.0
|
SG
|
F:CYS32
|
2.4
|
67.7
|
1.0
|
HB2
|
F:CYS90
|
2.5
|
83.8
|
1.0
|
HB3
|
F:CYS35
|
2.9
|
84.8
|
1.0
|
CB
|
F:CYS90
|
2.9
|
69.8
|
1.0
|
CB
|
F:CYS35
|
3.2
|
70.7
|
1.0
|
HB3
|
F:CYS32
|
3.2
|
68.2
|
1.0
|
H
|
F:CYS87
|
3.3
|
93.0
|
1.0
|
CB
|
F:CYS32
|
3.3
|
56.8
|
1.0
|
H
|
F:CYS35
|
3.4
|
78.9
|
1.0
|
HB3
|
F:CYS87
|
3.4
|
86.1
|
1.0
|
HB2
|
F:CYS32
|
3.5
|
68.2
|
1.0
|
HB3
|
F:CYS90
|
3.5
|
83.8
|
1.0
|
H
|
F:CYS90
|
3.5
|
92.7
|
1.0
|
CB
|
F:CYS87
|
3.5
|
71.8
|
1.0
|
HB2
|
F:LEU34
|
3.6
|
80.5
|
1.0
|
N
|
F:CYS35
|
3.6
|
65.8
|
1.0
|
HG1
|
F:THR37
|
3.9
|
94.2
|
1.0
|
HB2
|
F:CYS35
|
4.0
|
84.8
|
1.0
|
H
|
F:LEU34
|
4.0
|
83.6
|
1.0
|
CA
|
F:CYS35
|
4.0
|
63.7
|
1.0
|
N
|
F:CYS87
|
4.0
|
77.5
|
1.0
|
CA
|
F:CYS90
|
4.1
|
72.8
|
1.0
|
N
|
F:CYS90
|
4.1
|
77.2
|
1.0
|
OG1
|
F:THR37
|
4.2
|
78.5
|
1.0
|
C
|
F:LEU34
|
4.3
|
72.9
|
1.0
|
HB2
|
F:CYS87
|
4.3
|
86.1
|
1.0
|
CA
|
F:CYS87
|
4.4
|
75.7
|
1.0
|
CB
|
F:LEU34
|
4.5
|
67.1
|
1.0
|
HA
|
F:CYS90
|
4.5
|
87.3
|
1.0
|
H
|
F:GLY36
|
4.7
|
74.9
|
1.0
|
N
|
F:LEU34
|
4.7
|
69.7
|
1.0
|
HA
|
F:LEU86
|
4.7
|
77.7
|
1.0
|
CA
|
F:LEU34
|
4.7
|
68.9
|
1.0
|
CA
|
F:CYS32
|
4.7
|
59.9
|
1.0
|
HA
|
F:CYS35
|
4.7
|
76.4
|
1.0
|
H
|
F:THR37
|
4.7
|
82.4
|
1.0
|
HB3
|
F:LEU34
|
4.9
|
80.5
|
1.0
|
C
|
F:CYS35
|
4.9
|
70.7
|
1.0
|
O
|
F:CYS87
|
5.0
|
69.8
|
1.0
|
O
|
F:LEU34
|
5.0
|
73.9
|
1.0
|
HD12
|
F:LEU34
|
5.0
|
98.4
|
1.0
|
|
Zinc binding site 7 out
of 8 in 8fmh
Go back to
Zinc Binding Sites List in 8fmh
Zinc binding site 7 out
of 8 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Dgamp Ligand (2 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-Dgamp Ligand (2 Tetramers in the Au) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn404
b:50.6
occ:1.00
|
SG
|
G:CYS90
|
2.3
|
50.5
|
1.0
|
SG
|
G:CYS87
|
2.3
|
49.6
|
1.0
|
SG
|
G:CYS35
|
2.3
|
47.7
|
1.0
|
SG
|
G:CYS32
|
2.3
|
48.8
|
1.0
|
HB2
|
G:CYS90
|
2.7
|
64.4
|
1.0
|
CB
|
G:CYS90
|
3.1
|
53.7
|
1.0
|
HB3
|
G:CYS35
|
3.1
|
50.0
|
1.0
|
H
|
G:CYS87
|
3.1
|
66.2
|
1.0
|
HB3
|
G:CYS87
|
3.2
|
67.5
|
1.0
|
CB
|
G:CYS35
|
3.3
|
41.6
|
1.0
|
H
|
G:CYS35
|
3.3
|
60.5
|
1.0
|
CB
|
G:CYS32
|
3.4
|
49.3
|
1.0
|
HB3
|
G:CYS32
|
3.4
|
59.1
|
1.0
|
CB
|
G:CYS87
|
3.4
|
56.3
|
1.0
|
HB2
|
G:CYS32
|
3.5
|
59.1
|
1.0
|
H
|
G:CYS90
|
3.6
|
72.8
|
1.0
|
HB3
|
G:CYS90
|
3.7
|
64.4
|
1.0
|
HG22
|
G:THR37
|
3.7
|
69.7
|
1.0
|
N
|
G:CYS35
|
3.8
|
50.4
|
1.0
|
N
|
G:CYS87
|
3.9
|
55.2
|
1.0
|
HB2
|
G:LEU34
|
4.0
|
58.5
|
1.0
|
HB2
|
G:CYS35
|
4.1
|
50.0
|
1.0
|
CA
|
G:CYS35
|
4.1
|
41.1
|
1.0
|
HB2
|
G:CYS87
|
4.2
|
67.5
|
1.0
|
HG21
|
G:THR37
|
4.2
|
69.7
|
1.0
|
CA
|
G:CYS87
|
4.2
|
59.8
|
1.0
|
N
|
G:CYS90
|
4.2
|
60.7
|
1.0
|
CA
|
G:CYS90
|
4.3
|
53.2
|
1.0
|
H
|
G:LEU34
|
4.3
|
59.4
|
1.0
|
CG2
|
G:THR37
|
4.4
|
58.0
|
1.0
|
H
|
G:THR37
|
4.5
|
54.6
|
1.0
|
O
|
G:HOH531
|
4.5
|
49.3
|
1.0
|
H
|
G:GLY36
|
4.6
|
52.8
|
1.0
|
C
|
G:LEU34
|
4.6
|
42.2
|
1.0
|
HA
|
G:CYS90
|
4.7
|
63.9
|
1.0
|
CA
|
G:CYS32
|
4.8
|
52.6
|
1.0
|
HB
|
G:THR37
|
4.8
|
60.9
|
1.0
|
C
|
G:CYS35
|
4.8
|
45.8
|
1.0
|
HD22
|
G:LEU86
|
4.8
|
54.2
|
1.0
|
O
|
G:HOH612
|
4.8
|
53.9
|
1.0
|
O
|
G:CYS87
|
4.8
|
51.4
|
1.0
|
HA
|
G:LEU86
|
4.8
|
58.4
|
1.0
|
CB
|
G:LEU34
|
4.8
|
48.7
|
1.0
|
HB3
|
G:LEU86
|
4.8
|
55.2
|
1.0
|
C
|
G:CYS87
|
4.9
|
53.0
|
1.0
|
HA
|
G:CYS35
|
4.9
|
49.3
|
1.0
|
N
|
G:GLY36
|
5.0
|
44.0
|
1.0
|
|
Zinc binding site 8 out
of 8 in 8fmh
Go back to
Zinc Binding Sites List in 8fmh
Zinc binding site 8 out
of 8 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Dgamp Ligand (2 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-Dgamp Ligand (2 Tetramers in the Au) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn402
b:101.3
occ:1.00
|
SG
|
H:CYS35
|
2.3
|
87.0
|
1.0
|
SG
|
H:CYS87
|
2.3
|
94.7
|
1.0
|
SG
|
H:CYS32
|
2.3
|
88.4
|
1.0
|
SG
|
H:CYS90
|
2.3
|
86.8
|
1.0
|
HB2
|
H:CYS90
|
2.7
|
98.2
|
1.0
|
HB3
|
H:CYS35
|
3.0
|
104.6
|
1.0
|
H
|
H:CYS35
|
3.0
|
101.1
|
1.0
|
HB3
|
H:CYS32
|
3.1
|
103.9
|
1.0
|
HB2
|
H:CYS32
|
3.1
|
103.9
|
1.0
|
CB
|
H:CYS32
|
3.1
|
86.6
|
1.0
|
CB
|
H:CYS90
|
3.1
|
81.8
|
1.0
|
CB
|
H:CYS35
|
3.2
|
87.2
|
1.0
|
H
|
H:CYS87
|
3.3
|
117.9
|
1.0
|
HB3
|
H:CYS87
|
3.3
|
108.9
|
1.0
|
CB
|
H:CYS87
|
3.5
|
90.8
|
1.0
|
H
|
H:CYS90
|
3.5
|
112.1
|
1.0
|
HG22
|
H:THR37
|
3.5
|
100.3
|
1.0
|
N
|
H:CYS35
|
3.7
|
84.2
|
1.0
|
HB3
|
H:CYS90
|
3.7
|
98.2
|
1.0
|
HB2
|
H:LEU34
|
3.8
|
115.9
|
1.0
|
HG21
|
H:THR37
|
3.9
|
100.3
|
1.0
|
HB2
|
H:CYS35
|
4.0
|
104.6
|
1.0
|
CA
|
H:CYS35
|
4.0
|
83.9
|
1.0
|
N
|
H:CYS87
|
4.0
|
98.2
|
1.0
|
CG2
|
H:THR37
|
4.2
|
83.6
|
1.0
|
N
|
H:CYS90
|
4.2
|
93.4
|
1.0
|
HB2
|
H:CYS87
|
4.2
|
108.9
|
1.0
|
CA
|
H:CYS90
|
4.2
|
91.2
|
1.0
|
H
|
H:LEU34
|
4.3
|
112.6
|
1.0
|
CA
|
H:CYS87
|
4.3
|
92.1
|
1.0
|
H
|
H:THR37
|
4.4
|
95.6
|
1.0
|
H
|
H:GLY36
|
4.4
|
94.2
|
1.0
|
CA
|
H:CYS32
|
4.6
|
87.3
|
1.0
|
HD12
|
H:LEU34
|
4.7
|
120.1
|
1.0
|
HB
|
H:THR37
|
4.7
|
99.8
|
1.0
|
HA
|
H:CYS90
|
4.7
|
109.4
|
1.0
|
C
|
H:LEU34
|
4.7
|
88.6
|
1.0
|
C
|
H:CYS35
|
4.7
|
80.7
|
1.0
|
CB
|
H:LEU34
|
4.7
|
96.5
|
1.0
|
HA
|
H:CYS35
|
4.8
|
100.7
|
1.0
|
HA
|
H:LEU86
|
4.8
|
111.1
|
1.0
|
O
|
H:CYS87
|
4.8
|
96.7
|
1.0
|
N
|
H:GLY36
|
4.8
|
78.5
|
1.0
|
HA
|
H:CYS32
|
4.9
|
104.8
|
1.0
|
C
|
H:CYS87
|
4.9
|
99.3
|
1.0
|
HG23
|
H:THR37
|
4.9
|
100.3
|
1.0
|
HD22
|
H:LEU86
|
5.0
|
118.9
|
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
|