Zinc in PDB 7diy: Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain
Protein crystallography data
The structure of Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain, PDB code: 7diy
was solved by
S.Lin,
H.Chen,
Z.M.Chen,
F.L.Yang,
F.Ye,
Y.Zheng,
J.Yang,
X.Lin,
H.L.Sun,
L.L.Wang,
A.Wen,
Y.Cao,
G.W.Lu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.77 /
2.69
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.929,
68.28,
109.739,
90,
90,
90
|
R / Rfree (%)
|
23 /
26.4
|
Other elements in 7diy:
The structure of Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain
(pdb code 7diy). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain, PDB code: 7diy:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7diy
Go back to
Zinc Binding Sites List in 7diy
Zinc binding site 1 out
of 4 in the Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain
![](/pictures/ZN/pdb/di/7diy-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/di/7diy-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:36.9
occ:1.00
|
SG
|
A:CYS90
|
2.1
|
37.9
|
1.0
|
SG
|
A:CYS74
|
2.2
|
37.0
|
1.0
|
SG
|
A:CYS77
|
2.3
|
36.5
|
1.0
|
NE2
|
A:HIS83
|
2.4
|
36.7
|
1.0
|
CB
|
A:CYS74
|
3.0
|
37.0
|
1.0
|
CD2
|
A:HIS83
|
3.1
|
37.1
|
1.0
|
CB
|
A:CYS90
|
3.2
|
38.2
|
1.0
|
CB
|
A:CYS77
|
3.2
|
36.0
|
1.0
|
N
|
A:CYS77
|
3.3
|
35.7
|
1.0
|
CE1
|
A:HIS83
|
3.5
|
36.5
|
1.0
|
CA
|
A:CYS77
|
3.8
|
35.6
|
1.0
|
CA
|
A:CYS90
|
4.2
|
38.7
|
1.0
|
C
|
A:TYR76
|
4.3
|
35.4
|
1.0
|
CG
|
A:HIS83
|
4.3
|
37.0
|
1.0
|
CB
|
A:TYR76
|
4.4
|
35.9
|
1.0
|
CA
|
A:CYS74
|
4.4
|
36.9
|
1.0
|
ND1
|
A:HIS83
|
4.5
|
36.7
|
1.0
|
CA
|
A:TYR76
|
4.7
|
35.5
|
1.0
|
O
|
A:CYS74
|
4.7
|
36.0
|
1.0
|
N
|
A:TYR76
|
4.8
|
35.7
|
1.0
|
C
|
A:CYS74
|
4.8
|
36.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7diy
Go back to
Zinc Binding Sites List in 7diy
Zinc binding site 2 out
of 4 in the Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain
![](/pictures/ZN/pdb/di/7diy-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/di/7diy-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn202
b:52.4
occ:1.00
|
SG
|
A:CYS128
|
1.8
|
56.0
|
1.0
|
SG
|
A:CYS117
|
2.3
|
51.8
|
1.0
|
SG
|
A:CYS130
|
2.3
|
54.8
|
1.0
|
SG
|
A:CYS120
|
2.5
|
51.9
|
1.0
|
CB
|
A:CYS117
|
2.7
|
50.3
|
1.0
|
CB
|
A:CYS128
|
3.1
|
51.4
|
1.0
|
CB
|
A:CYS120
|
3.5
|
52.8
|
1.0
|
N
|
A:CYS120
|
3.9
|
52.3
|
1.0
|
CA
|
A:CYS128
|
4.0
|
51.9
|
1.0
|
CB
|
A:CYS130
|
4.1
|
56.8
|
1.0
|
CA
|
A:CYS117
|
4.2
|
49.3
|
1.0
|
N
|
A:CYS130
|
4.2
|
56.3
|
1.0
|
CA
|
A:CYS120
|
4.2
|
52.1
|
1.0
|
N
|
A:SER129
|
4.5
|
54.3
|
1.0
|
C
|
A:CYS128
|
4.5
|
53.4
|
1.0
|
O
|
A:CYS130
|
4.6
|
58.3
|
1.0
|
CA
|
A:CYS130
|
4.7
|
57.4
|
1.0
|
N
|
A:GLY121
|
4.7
|
49.8
|
1.0
|
C
|
A:CYS120
|
4.7
|
50.7
|
1.0
|
CB
|
A:VAL119
|
4.8
|
54.5
|
1.0
|
C
|
A:CYS117
|
4.8
|
49.3
|
1.0
|
O
|
A:MET122
|
4.9
|
47.9
|
1.0
|
N
|
A:CYS117
|
5.0
|
48.0
|
1.0
|
O
|
A:CYS117
|
5.0
|
49.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7diy
Go back to
Zinc Binding Sites List in 7diy
Zinc binding site 3 out
of 4 in the Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain
![](/pictures/ZN/pdb/di/7diy-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/di/7diy-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:38.4
occ:1.00
|
ND1
|
B:HIS229
|
2.2
|
38.6
|
1.0
|
SG
|
B:CYS210
|
2.2
|
39.4
|
1.0
|
SG
|
B:CYS207
|
2.2
|
38.2
|
1.0
|
SG
|
B:CYS226
|
2.2
|
37.5
|
1.0
|
CE1
|
B:HIS229
|
2.8
|
39.1
|
1.0
|
CB
|
B:CYS210
|
2.9
|
39.7
|
1.0
|
CB
|
B:CYS226
|
3.2
|
37.0
|
1.0
|
CB
|
B:CYS207
|
3.3
|
38.1
|
1.0
|
CG
|
B:HIS229
|
3.3
|
38.7
|
1.0
|
N
|
B:CYS226
|
3.8
|
36.7
|
1.0
|
CB
|
B:HIS229
|
3.9
|
38.2
|
1.0
|
NE2
|
B:HIS229
|
4.0
|
39.6
|
1.0
|
CA
|
B:CYS226
|
4.1
|
36.4
|
1.0
|
CA
|
B:CYS210
|
4.2
|
40.6
|
1.0
|
CD2
|
B:HIS229
|
4.3
|
39.3
|
1.0
|
O
|
B:LEU209
|
4.3
|
41.0
|
1.0
|
O
|
B:CYS208
|
4.4
|
42.2
|
1.0
|
NH1
|
B:ARG212
|
4.5
|
39.0
|
1.0
|
C
|
B:LEU209
|
4.5
|
40.9
|
1.0
|
N
|
B:CYS210
|
4.5
|
40.8
|
1.0
|
CB
|
B:ARG212
|
4.6
|
38.4
|
1.0
|
N
|
B:HIS229
|
4.6
|
37.3
|
1.0
|
CA
|
B:CYS207
|
4.7
|
38.3
|
1.0
|
CD
|
B:ARG212
|
4.8
|
38.4
|
1.0
|
CB
|
B:LEU209
|
4.8
|
40.5
|
1.0
|
C
|
B:CYS226
|
4.9
|
36.1
|
1.0
|
CA
|
B:HIS229
|
4.9
|
37.7
|
1.0
|
C
|
B:ALA225
|
5.0
|
36.4
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7diy
Go back to
Zinc Binding Sites List in 7diy
Zinc binding site 4 out
of 4 in the Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain
![](/pictures/ZN/pdb/di/7diy-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/di/7diy-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exoribonuclease Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:40.8
occ:1.00
|
ND1
|
B:HIS264
|
2.0
|
40.4
|
1.0
|
SG
|
B:CYS279
|
2.1
|
40.3
|
1.0
|
NE2
|
B:HIS257
|
2.2
|
41.1
|
1.0
|
SG
|
B:CYS261
|
2.2
|
42.3
|
1.0
|
CE1
|
B:HIS264
|
2.9
|
39.9
|
1.0
|
CB
|
B:CYS261
|
3.0
|
42.8
|
1.0
|
CE1
|
B:HIS257
|
3.1
|
41.8
|
1.0
|
CG
|
B:HIS264
|
3.1
|
40.5
|
1.0
|
CB
|
B:CYS279
|
3.1
|
39.2
|
1.0
|
CD2
|
B:HIS257
|
3.2
|
40.8
|
1.0
|
CB
|
B:HIS264
|
3.6
|
41.0
|
1.0
|
NE2
|
B:HIS264
|
4.1
|
39.7
|
1.0
|
CD2
|
B:HIS264
|
4.2
|
40.1
|
1.0
|
ND1
|
B:HIS257
|
4.2
|
41.9
|
1.0
|
CG
|
B:HIS257
|
4.3
|
41.3
|
1.0
|
CA
|
B:CYS261
|
4.4
|
43.9
|
1.0
|
CA
|
B:CYS279
|
4.6
|
38.8
|
1.0
|
N
|
B:HIS264
|
4.6
|
42.6
|
1.0
|
CA
|
B:HIS264
|
4.7
|
41.8
|
1.0
|
CG2
|
B:VAL263
|
4.8
|
42.8
|
1.0
|
C
|
B:CYS261
|
4.9
|
44.4
|
1.0
|
CE1
|
B:HIS283
|
4.9
|
42.0
|
1.0
|
|
Reference:
S.Lin,
H.Chen,
Z.Chen,
F.Yang,
F.Ye,
Y.Zheng,
J.Yang,
X.Lin,
H.Sun,
L.Wang,
A.Wen,
H.Dong,
Q.Xiao,
D.Deng,
Y.Cao,
G.Lu.
Crystal Structure of Sars-Cov-2 NSP10 Bound to NSP14-Exon Domain Reveals An Exoribonuclease with Both Structural and Functional Integrity. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33956156
DOI: 10.1093/NAR/GKAB320
Page generated: Mon Jul 12 17:01:56 2021
|