Zinc in PDB 6y5p: Ring-Dtc Domain of DELTEX1 Bound to Nad
Enzymatic activity of Ring-Dtc Domain of DELTEX1 Bound to Nad
All present enzymatic activity of Ring-Dtc Domain of DELTEX1 Bound to Nad:
2.3.2.27;
Protein crystallography data
The structure of Ring-Dtc Domain of DELTEX1 Bound to Nad, PDB code: 6y5p
was solved by
M.Gabrielsen,
L.Buetow,
D.T.Huang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
65.48 /
1.74
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.850,
85.254,
130.949,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.5 /
21.4
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Ring-Dtc Domain of DELTEX1 Bound to Nad
(pdb code 6y5p). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Ring-Dtc Domain of DELTEX1 Bound to Nad, PDB code: 6y5p:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6y5p
Go back to
Zinc Binding Sites List in 6y5p
Zinc binding site 1 out
of 4 in the Ring-Dtc Domain of DELTEX1 Bound to Nad
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Ring-Dtc Domain of DELTEX1 Bound to Nad within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn708
b:23.9
occ:1.00
|
ND1
|
A:HIS449
|
2.0
|
23.5
|
1.0
|
SG
|
A:CYS452
|
2.3
|
24.1
|
1.0
|
SG
|
A:CYS411
|
2.3
|
28.8
|
1.0
|
SG
|
A:CYS414
|
2.3
|
23.5
|
1.0
|
HB3
|
A:CYS411
|
2.8
|
32.7
|
1.0
|
HB2
|
A:HIS449
|
2.9
|
27.8
|
1.0
|
CE1
|
A:HIS449
|
2.9
|
25.8
|
1.0
|
HB3
|
A:CYS414
|
3.0
|
28.5
|
1.0
|
H
|
A:CYS414
|
3.0
|
29.4
|
1.0
|
CB
|
A:CYS411
|
3.0
|
27.2
|
1.0
|
HE1
|
A:HIS449
|
3.1
|
31.0
|
1.0
|
CG
|
A:HIS449
|
3.1
|
25.4
|
1.0
|
CB
|
A:CYS414
|
3.2
|
23.7
|
1.0
|
HB2
|
A:CYS411
|
3.2
|
32.7
|
1.0
|
H
|
A:HIS449
|
3.3
|
30.1
|
1.0
|
HB2
|
A:CYS452
|
3.3
|
29.3
|
1.0
|
CB
|
A:CYS452
|
3.4
|
24.4
|
1.0
|
CB
|
A:HIS449
|
3.5
|
23.1
|
1.0
|
HA
|
A:SER422
|
3.5
|
30.4
|
1.0
|
HB3
|
A:CYS452
|
3.6
|
29.3
|
1.0
|
HG
|
A:SER422
|
3.7
|
34.0
|
1.0
|
N
|
A:CYS414
|
3.7
|
24.4
|
1.0
|
HB
|
A:ILE413
|
3.8
|
25.6
|
1.0
|
H
|
A:GLY423
|
3.8
|
35.1
|
1.0
|
HB2
|
A:CYS414
|
4.0
|
28.5
|
1.0
|
N
|
A:HIS449
|
4.0
|
25.0
|
1.0
|
CA
|
A:CYS414
|
4.1
|
24.5
|
1.0
|
NE2
|
A:HIS449
|
4.1
|
28.9
|
1.0
|
CD2
|
A:HIS449
|
4.2
|
27.1
|
1.0
|
HB2
|
A:SER422
|
4.2
|
29.6
|
1.0
|
HB3
|
A:HIS449
|
4.2
|
27.8
|
1.0
|
CA
|
A:HIS449
|
4.3
|
22.2
|
1.0
|
CA
|
A:SER422
|
4.4
|
25.3
|
1.0
|
H
|
A:ILE413
|
4.4
|
29.6
|
1.0
|
OG
|
A:SER422
|
4.4
|
28.2
|
1.0
|
H
|
A:GLU416
|
4.5
|
32.4
|
1.0
|
CA
|
A:CYS411
|
4.5
|
24.5
|
1.0
|
H
|
A:CYS452
|
4.5
|
26.3
|
1.0
|
CB
|
A:SER422
|
4.6
|
24.6
|
1.0
|
N
|
A:GLY423
|
4.6
|
29.2
|
1.0
|
HB2
|
A:GLU416
|
4.6
|
37.5
|
1.0
|
H
|
A:MET415
|
4.6
|
28.6
|
1.0
|
CB
|
A:ILE413
|
4.7
|
21.3
|
1.0
|
CA
|
A:CYS452
|
4.7
|
20.4
|
1.0
|
HD23
|
A:LEU418
|
4.8
|
36.8
|
1.0
|
O
|
A:CYS411
|
4.8
|
29.4
|
1.0
|
HB3
|
A:TYR448
|
4.8
|
30.5
|
1.0
|
C
|
A:ILE413
|
4.8
|
29.1
|
1.0
|
HA
|
A:CYS414
|
4.8
|
29.4
|
1.0
|
HE2
|
A:HIS449
|
4.8
|
34.7
|
1.0
|
C
|
A:CYS411
|
4.9
|
28.9
|
1.0
|
C
|
A:CYS414
|
4.9
|
27.3
|
1.0
|
HA
|
A:TYR448
|
4.9
|
25.4
|
1.0
|
HA
|
A:CYS411
|
4.9
|
29.5
|
1.0
|
O
|
A:GLU416
|
5.0
|
30.0
|
1.0
|
O
|
A:HIS449
|
5.0
|
21.8
|
1.0
|
HA
|
A:CYS452
|
5.0
|
24.6
|
1.0
|
N
|
A:MET415
|
5.0
|
23.8
|
1.0
|
HD21
|
B:LEU590
|
5.0
|
34.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6y5p
Go back to
Zinc Binding Sites List in 6y5p
Zinc binding site 2 out
of 4 in the Ring-Dtc Domain of DELTEX1 Bound to Nad
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Ring-Dtc Domain of DELTEX1 Bound to Nad within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn709
b:26.2
occ:1.00
|
ND1
|
A:HIS446
|
2.0
|
27.7
|
1.0
|
SG
|
A:CYS444
|
2.3
|
25.7
|
1.0
|
SG
|
A:CYS468
|
2.3
|
24.8
|
1.0
|
SG
|
A:CYS471
|
2.4
|
30.8
|
1.0
|
CE1
|
A:HIS446
|
2.9
|
27.8
|
1.0
|
HB2
|
A:CYS444
|
2.9
|
32.7
|
1.0
|
HE1
|
A:HIS446
|
3.0
|
33.4
|
1.0
|
HB2
|
A:HIS446
|
3.0
|
28.4
|
1.0
|
CG
|
A:HIS446
|
3.1
|
24.0
|
1.0
|
CB
|
A:CYS444
|
3.1
|
27.2
|
1.0
|
H
|
A:CYS471
|
3.2
|
33.4
|
1.0
|
CB
|
A:CYS468
|
3.2
|
20.2
|
1.0
|
HB3
|
A:CYS468
|
3.2
|
24.3
|
1.0
|
HB2
|
A:CYS468
|
3.2
|
24.3
|
1.0
|
HB3
|
A:CYS471
|
3.3
|
35.5
|
1.0
|
HB3
|
A:CYS444
|
3.4
|
32.7
|
1.0
|
CB
|
A:CYS471
|
3.4
|
29.5
|
1.0
|
CB
|
A:HIS446
|
3.5
|
23.6
|
1.0
|
HB
|
A:THR470
|
3.6
|
32.1
|
1.0
|
H
|
A:HIS446
|
3.7
|
28.4
|
1.0
|
N
|
A:CYS471
|
3.8
|
27.8
|
1.0
|
HH
|
A:TYR475
|
4.0
|
34.5
|
1.0
|
NE2
|
A:HIS446
|
4.0
|
32.1
|
1.0
|
HH
|
A:TYR448
|
4.1
|
33.9
|
1.0
|
CD2
|
A:HIS446
|
4.1
|
33.1
|
1.0
|
HB3
|
A:HIS446
|
4.2
|
28.4
|
1.0
|
CA
|
A:CYS471
|
4.2
|
28.5
|
1.0
|
HB2
|
A:CYS471
|
4.2
|
35.5
|
1.0
|
HB3
|
A:ALA473
|
4.3
|
34.8
|
1.0
|
HD23
|
A:LEU441
|
4.4
|
30.9
|
1.0
|
N
|
A:HIS446
|
4.4
|
23.6
|
1.0
|
H
|
A:THR470
|
4.5
|
30.5
|
1.0
|
H
|
A:ALA473
|
4.5
|
31.9
|
1.0
|
CA
|
A:CYS444
|
4.5
|
25.5
|
1.0
|
CB
|
A:THR470
|
4.5
|
26.7
|
1.0
|
CA
|
A:HIS446
|
4.6
|
26.2
|
1.0
|
CA
|
A:CYS468
|
4.6
|
23.1
|
1.0
|
H
|
A:LYS472
|
4.7
|
31.1
|
1.0
|
O
|
A:HOH1046
|
4.7
|
45.3
|
1.0
|
HG22
|
A:THR470
|
4.7
|
44.2
|
1.0
|
C
|
A:CYS444
|
4.8
|
24.0
|
1.0
|
HE2
|
A:TYR475
|
4.8
|
32.1
|
1.0
|
HE2
|
A:HIS446
|
4.8
|
38.6
|
1.0
|
OH
|
A:TYR475
|
4.8
|
28.7
|
1.0
|
C
|
A:THR470
|
4.8
|
32.7
|
1.0
|
OH
|
A:TYR448
|
4.8
|
28.2
|
1.0
|
C
|
A:CYS471
|
4.9
|
29.5
|
1.0
|
H
|
A:CYS444
|
4.9
|
30.4
|
1.0
|
HA
|
A:CYS468
|
4.9
|
27.8
|
1.0
|
HB3
|
A:LEU441
|
5.0
|
29.8
|
1.0
|
HB2
|
A:ALA473
|
5.0
|
34.8
|
1.0
|
HA
|
A:CYS471
|
5.0
|
34.3
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6y5p
Go back to
Zinc Binding Sites List in 6y5p
Zinc binding site 3 out
of 4 in the Ring-Dtc Domain of DELTEX1 Bound to Nad
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Ring-Dtc Domain of DELTEX1 Bound to Nad within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn704
b:50.3
occ:1.00
|
ND1
|
B:HIS446
|
2.0
|
60.3
|
1.0
|
SG
|
B:CYS471
|
2.1
|
54.0
|
1.0
|
SG
|
B:CYS444
|
2.3
|
0.4
|
1.0
|
SG
|
B:CYS468
|
2.4
|
87.2
|
1.0
|
HB2
|
B:CYS444
|
2.4
|
75.1
|
1.0
|
CB
|
B:CYS444
|
2.8
|
62.5
|
1.0
|
HB2
|
B:HIS446
|
2.9
|
53.0
|
1.0
|
CE1
|
B:HIS446
|
2.9
|
60.3
|
1.0
|
HB3
|
B:CYS444
|
3.1
|
75.1
|
1.0
|
CG
|
B:HIS446
|
3.1
|
59.0
|
1.0
|
HE1
|
B:HIS446
|
3.1
|
72.5
|
1.0
|
H
|
B:CYS471
|
3.2
|
63.0
|
1.0
|
HB3
|
B:CYS468
|
3.2
|
62.5
|
1.0
|
CB
|
B:CYS468
|
3.2
|
52.1
|
1.0
|
HB2
|
B:CYS468
|
3.3
|
62.5
|
1.0
|
HB3
|
B:CYS471
|
3.3
|
57.1
|
1.0
|
CB
|
B:CYS471
|
3.4
|
47.5
|
1.0
|
CB
|
B:HIS446
|
3.5
|
44.1
|
1.0
|
HB
|
B:THR470
|
3.7
|
53.2
|
1.0
|
H
|
B:HIS446
|
3.8
|
58.8
|
1.0
|
N
|
B:CYS471
|
3.9
|
52.4
|
1.0
|
HB3
|
B:HIS446
|
4.0
|
53.0
|
1.0
|
HB3
|
B:ALA473
|
4.1
|
60.8
|
1.0
|
NE2
|
B:HIS446
|
4.1
|
62.0
|
1.0
|
HH
|
B:TYR448
|
4.1
|
59.4
|
1.0
|
HB2
|
B:CYS471
|
4.1
|
57.1
|
1.0
|
CD2
|
B:HIS446
|
4.2
|
57.4
|
1.0
|
CA
|
B:CYS471
|
4.2
|
45.2
|
1.0
|
HH
|
B:TYR475
|
4.2
|
87.1
|
1.0
|
HD12
|
B:LEU441
|
4.2
|
53.6
|
1.0
|
CA
|
B:CYS444
|
4.2
|
53.0
|
1.0
|
H
|
B:ALA473
|
4.4
|
57.1
|
1.0
|
N
|
B:HIS446
|
4.5
|
48.9
|
1.0
|
H
|
B:THR470
|
4.5
|
70.3
|
1.0
|
C
|
B:CYS444
|
4.6
|
56.3
|
1.0
|
CB
|
B:THR470
|
4.6
|
44.3
|
1.0
|
HD13
|
B:LEU441
|
4.6
|
53.6
|
1.0
|
HG22
|
B:THR470
|
4.6
|
63.1
|
1.0
|
CA
|
B:HIS446
|
4.7
|
43.7
|
1.0
|
CA
|
B:CYS468
|
4.7
|
41.5
|
1.0
|
HB2
|
B:ALA473
|
4.7
|
60.8
|
1.0
|
O
|
B:CYS444
|
4.7
|
66.7
|
1.0
|
HA
|
B:CYS444
|
4.7
|
63.6
|
1.0
|
H
|
B:LYS472
|
4.7
|
78.7
|
1.0
|
HB2
|
B:LEU441
|
4.8
|
60.2
|
1.0
|
C
|
B:CYS471
|
4.8
|
51.8
|
1.0
|
HE1
|
B:TYR475
|
4.8
|
60.8
|
1.0
|
CB
|
B:ALA473
|
4.8
|
50.6
|
1.0
|
HE2
|
B:HIS446
|
4.8
|
74.5
|
1.0
|
OH
|
B:TYR448
|
4.9
|
49.4
|
1.0
|
CD1
|
B:LEU441
|
4.9
|
44.6
|
1.0
|
H
|
B:CYS444
|
4.9
|
70.2
|
1.0
|
C
|
B:THR470
|
4.9
|
55.9
|
1.0
|
HA
|
B:CYS468
|
5.0
|
49.8
|
1.0
|
OH
|
B:TYR475
|
5.0
|
72.5
|
1.0
|
N
|
B:LYS472
|
5.0
|
65.5
|
1.0
|
HA
|
B:CYS471
|
5.0
|
54.3
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6y5p
Go back to
Zinc Binding Sites List in 6y5p
Zinc binding site 4 out
of 4 in the Ring-Dtc Domain of DELTEX1 Bound to Nad
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Ring-Dtc Domain of DELTEX1 Bound to Nad within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn705
b:71.6
occ:1.00
|
SG
|
B:CYS411
|
2.0
|
47.0
|
1.0
|
ND1
|
B:HIS449
|
2.2
|
45.9
|
1.0
|
SG
|
B:CYS452
|
2.3
|
49.0
|
1.0
|
SG
|
B:CYS414
|
2.4
|
60.0
|
1.0
|
HB2
|
B:HIS449
|
2.7
|
58.6
|
1.0
|
HB3
|
B:CYS414
|
2.9
|
48.8
|
1.0
|
HB3
|
B:CYS411
|
3.0
|
57.7
|
1.0
|
H
|
B:CYS414
|
3.1
|
43.9
|
1.0
|
CB
|
B:CYS411
|
3.1
|
48.0
|
1.0
|
CG
|
B:HIS449
|
3.1
|
44.7
|
1.0
|
CE1
|
B:HIS449
|
3.2
|
43.5
|
1.0
|
HB2
|
B:CYS452
|
3.2
|
50.1
|
1.0
|
CB
|
B:CYS414
|
3.2
|
40.6
|
1.0
|
CB
|
B:CYS452
|
3.3
|
41.7
|
1.0
|
HA
|
B:SER422
|
3.3
|
60.5
|
1.0
|
HE1
|
B:HIS449
|
3.4
|
52.2
|
1.0
|
H
|
B:HIS449
|
3.4
|
53.5
|
1.0
|
HB2
|
B:CYS411
|
3.4
|
57.7
|
1.0
|
CB
|
B:HIS449
|
3.4
|
48.8
|
1.0
|
HB3
|
B:CYS452
|
3.5
|
50.1
|
1.0
|
H
|
B:GLY423
|
3.7
|
60.3
|
1.0
|
N
|
B:CYS414
|
3.8
|
36.5
|
1.0
|
HB2
|
B:SER422
|
3.8
|
64.3
|
1.0
|
HB
|
B:ILE413
|
3.9
|
43.6
|
1.0
|
HB2
|
B:CYS414
|
4.0
|
48.8
|
1.0
|
HB3
|
B:HIS449
|
4.1
|
58.6
|
1.0
|
CA
|
B:CYS414
|
4.1
|
36.0
|
1.0
|
N
|
B:HIS449
|
4.1
|
44.5
|
1.0
|
OG
|
B:SER422
|
4.1
|
60.7
|
1.0
|
CA
|
B:SER422
|
4.2
|
50.4
|
1.0
|
NE2
|
B:HIS449
|
4.2
|
50.9
|
1.0
|
CD2
|
B:HIS449
|
4.2
|
47.6
|
1.0
|
CB
|
B:SER422
|
4.2
|
53.5
|
1.0
|
CA
|
B:HIS449
|
4.4
|
47.0
|
1.0
|
N
|
B:GLY423
|
4.5
|
50.2
|
1.0
|
H
|
B:GLU416
|
4.5
|
71.9
|
1.0
|
H
|
B:CYS452
|
4.5
|
53.8
|
1.0
|
HG
|
B:SER422
|
4.5
|
72.9
|
1.0
|
CA
|
B:CYS411
|
4.5
|
41.4
|
1.0
|
H
|
B:ILE413
|
4.6
|
44.3
|
1.0
|
CA
|
B:CYS452
|
4.6
|
36.7
|
1.0
|
HB2
|
B:GLU416
|
4.7
|
56.6
|
1.0
|
H
|
B:MET415
|
4.7
|
47.5
|
1.0
|
HD21
|
A:LEU590
|
4.8
|
50.8
|
1.0
|
CB
|
B:ILE413
|
4.8
|
36.3
|
1.0
|
HB3
|
B:TYR448
|
4.8
|
46.3
|
1.0
|
HA
|
B:CYS414
|
4.9
|
43.3
|
1.0
|
O
|
B:CYS411
|
4.9
|
45.3
|
1.0
|
HA
|
B:CYS452
|
4.9
|
44.1
|
1.0
|
C
|
B:CYS414
|
4.9
|
49.3
|
1.0
|
C
|
B:CYS411
|
4.9
|
40.9
|
1.0
|
O
|
B:HIS449
|
4.9
|
43.6
|
1.0
|
C
|
B:SER422
|
4.9
|
48.6
|
1.0
|
C
|
B:ILE413
|
4.9
|
37.2
|
1.0
|
HD23
|
B:LEU418
|
4.9
|
63.9
|
1.0
|
HE2
|
B:HIS449
|
5.0
|
61.2
|
1.0
|
N
|
B:CYS452
|
5.0
|
44.8
|
1.0
|
HA
|
B:CYS411
|
5.0
|
49.8
|
1.0
|
O
|
B:GLU416
|
5.0
|
48.0
|
1.0
|
|
Reference:
C.Chatrin,
M.Gabrielsen,
L.Buetow,
M.A.Nakasone,
S.F.Ahmed,
D.Sumpton,
G.J.Sibbet,
B.O.Smith,
D.T.Huang.
Structural Insights Into Adp-Ribosylation of Ubiquitin By Deltex Family E3 Ubiquitin Ligases. Sci Adv V. 6 2020.
ISSN: ESSN 2375-2548
PubMed: 32948590
DOI: 10.1126/SCIADV.ABC0418
Page generated: Tue Oct 29 11:23:41 2024
|