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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: Sat Apr 8 01:56:05 2023

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