Zinc in PDB 7qgi: Crystal Structure of Sars-Cov-2 NSP14 in the Absence of NSP10
Protein crystallography data
The structure of Crystal Structure of Sars-Cov-2 NSP14 in the Absence of NSP10, PDB code: 7qgi
was solved by
J.A.Newman,
N.Imprachim,
Y.Yosaatmadja,
O.Gileadi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
61.10 /
1.65
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.539,
68.093,
138.428,
90,
90,
90
|
R / Rfree (%)
|
19.6 /
22.1
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Sars-Cov-2 NSP14 in the Absence of NSP10
(pdb code 7qgi). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
Crystal Structure of Sars-Cov-2 NSP14 in the Absence of NSP10, PDB code: 7qgi:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 7qgi
Go back to
Zinc Binding Sites List in 7qgi
Zinc binding site 1 out
of 3 in the Crystal Structure of Sars-Cov-2 NSP14 in the Absence of NSP10
Mono view
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 NSP14 in the Absence of NSP10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn601
b:17.2
occ:1.00
|
ND1
|
D:HIS264
|
2.0
|
14.0
|
1.0
|
NE2
|
D:HIS257
|
2.1
|
17.8
|
1.0
|
SG
|
D:CYS279
|
2.3
|
15.9
|
1.0
|
SG
|
D:CYS261
|
2.3
|
19.2
|
1.0
|
CE1
|
D:HIS264
|
2.8
|
13.2
|
1.0
|
CD2
|
D:HIS257
|
3.0
|
14.7
|
1.0
|
CB
|
D:CYS261
|
3.1
|
21.0
|
1.0
|
CE1
|
D:HIS257
|
3.1
|
18.2
|
1.0
|
CG
|
D:HIS264
|
3.1
|
18.4
|
1.0
|
CB
|
D:CYS279
|
3.2
|
11.0
|
1.0
|
CB
|
D:HIS264
|
3.5
|
21.1
|
1.0
|
NE2
|
D:HIS264
|
4.0
|
23.2
|
1.0
|
CD2
|
D:HIS264
|
4.1
|
16.7
|
1.0
|
ND1
|
D:HIS257
|
4.1
|
13.6
|
1.0
|
CG
|
D:HIS257
|
4.2
|
21.2
|
1.0
|
N
|
D:HIS264
|
4.3
|
25.3
|
1.0
|
CA
|
D:CYS261
|
4.5
|
20.7
|
1.0
|
N
|
D:ASP415
|
4.5
|
16.0
|
1.0
|
CA
|
D:HIS264
|
4.6
|
22.9
|
1.0
|
CA
|
D:CYS279
|
4.6
|
9.4
|
1.0
|
SG
|
D:CYS414
|
4.9
|
19.7
|
0.6
|
CA
|
D:CYS414
|
5.0
|
13.4
|
0.6
|
CA
|
D:CYS414
|
5.0
|
13.4
|
0.4
|
C
|
D:CYS261
|
5.0
|
22.9
|
1.0
|
|
Zinc binding site 2 out
of 3 in 7qgi
Go back to
Zinc Binding Sites List in 7qgi
Zinc binding site 2 out
of 3 in the Crystal Structure of Sars-Cov-2 NSP14 in the Absence of NSP10
Mono view
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 NSP14 in the Absence of NSP10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn602
b:18.6
occ:1.00
|
ND1
|
D:HIS487
|
2.1
|
16.7
|
1.0
|
SG
|
D:CYS484
|
2.2
|
18.9
|
1.0
|
SG
|
D:CYS477
|
2.3
|
16.0
|
1.0
|
SG
|
D:CYS452
|
2.4
|
25.3
|
1.0
|
CE1
|
D:HIS487
|
3.1
|
17.1
|
1.0
|
CG
|
D:HIS487
|
3.1
|
19.3
|
1.0
|
CB
|
D:CYS452
|
3.2
|
21.2
|
1.0
|
CB
|
D:CYS477
|
3.2
|
12.4
|
1.0
|
CB
|
D:CYS484
|
3.3
|
19.5
|
1.0
|
CB
|
D:HIS487
|
3.4
|
18.4
|
1.0
|
CA
|
D:CYS452
|
3.8
|
31.2
|
1.0
|
N
|
D:CYS484
|
3.9
|
17.0
|
1.0
|
CA
|
D:CYS484
|
4.2
|
16.7
|
1.0
|
NE2
|
D:HIS487
|
4.2
|
17.4
|
1.0
|
CD2
|
D:HIS487
|
4.2
|
18.4
|
1.0
|
N
|
D:CYS477
|
4.3
|
20.7
|
1.0
|
CA
|
D:CYS477
|
4.4
|
19.7
|
1.0
|
N
|
D:HIS487
|
4.5
|
19.8
|
1.0
|
N
|
D:CYS452
|
4.6
|
25.7
|
1.0
|
CA
|
D:HIS487
|
4.6
|
21.3
|
1.0
|
CB
|
D:THR475
|
4.6
|
12.0
|
1.0
|
OG1
|
D:THR475
|
4.6
|
17.3
|
1.0
|
C
|
D:CYS484
|
4.8
|
26.2
|
1.0
|
O
|
D:CYS484
|
4.9
|
19.7
|
1.0
|
|
Zinc binding site 3 out
of 3 in 7qgi
Go back to
Zinc Binding Sites List in 7qgi
Zinc binding site 3 out
of 3 in the Crystal Structure of Sars-Cov-2 NSP14 in the Absence of NSP10
Mono view
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 NSP14 in the Absence of NSP10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn603
b:26.9
occ:1.00
|
ND1
|
D:HIS229
|
2.1
|
23.8
|
1.0
|
SG
|
D:CYS210
|
2.3
|
28.7
|
1.0
|
SG
|
D:CYS207
|
2.4
|
26.9
|
1.0
|
SG
|
D:CYS226
|
2.4
|
24.4
|
1.0
|
CE1
|
D:HIS229
|
2.8
|
27.6
|
1.0
|
CB
|
D:CYS207
|
3.0
|
19.8
|
1.0
|
CG
|
D:HIS229
|
3.3
|
23.4
|
1.0
|
CB
|
D:CYS210
|
3.5
|
26.8
|
1.0
|
CB
|
D:CYS226
|
3.6
|
16.7
|
1.0
|
CB
|
D:HIS229
|
3.8
|
23.0
|
1.0
|
N
|
D:CYS210
|
3.8
|
26.8
|
1.0
|
N
|
D:CYS226
|
4.0
|
18.1
|
1.0
|
NE2
|
D:HIS229
|
4.0
|
27.5
|
1.0
|
NH1
|
D:ARG212
|
4.2
|
23.0
|
1.0
|
CA
|
D:CYS210
|
4.2
|
20.4
|
1.0
|
CD2
|
D:HIS229
|
4.3
|
22.4
|
1.0
|
CA
|
D:CYS226
|
4.4
|
17.3
|
1.0
|
C
|
D:LEU209
|
4.4
|
24.3
|
1.0
|
N
|
D:HIS229
|
4.5
|
22.9
|
1.0
|
CA
|
D:CYS207
|
4.5
|
24.1
|
1.0
|
CB
|
D:LEU209
|
4.6
|
20.5
|
1.0
|
N
|
D:LEU209
|
4.7
|
26.3
|
1.0
|
C
|
D:CYS210
|
4.7
|
22.3
|
1.0
|
CB
|
D:HIS228
|
4.8
|
19.5
|
1.0
|
CA
|
D:LEU209
|
4.8
|
25.7
|
1.0
|
CA
|
D:HIS229
|
4.8
|
22.7
|
1.0
|
CB
|
D:ARG212
|
4.8
|
28.7
|
1.0
|
CD
|
D:ARG212
|
4.8
|
15.3
|
1.0
|
C
|
D:CYS226
|
5.0
|
20.0
|
1.0
|
O
|
D:LEU209
|
5.0
|
27.6
|
1.0
|
|
Reference:
J.A.Newman,
N.Imprachim,
Y.Yosaatmadja,
O.Gileadi.
Crystal Structure of Sars-Cov-2 NSP14 in the Absence of NSP10 To Be Published.
Page generated: Wed Oct 30 09:52:55 2024
|