Zinc in PDB 7orw: Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00265

Protein crystallography data

The structure of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00265, PDB code: 7orw was solved by V.O.Talibov, F.Kozielski, C.Sele, J.Lou, D.Dong, Q.Wang, X.Shi, M.Nyblom, A.Rogstam, T.Krojer, W.Knecht, S.Z.Fisher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.94 / 1.95
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 107.771, 107.771, 107.771, 90, 90, 90
R / Rfree (%) 17.5 / 20.9

Other elements in 7orw:

The structure of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00265 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00265 (pdb code 7orw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00265, PDB code: 7orw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7orw

Go back to Zinc Binding Sites List in 7orw
Zinc binding site 1 out of 2 in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00265


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00265 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:45.6
occ:1.00
NE2 A:HIS83 2.1 47.2 1.0
SG A:CYS77 2.2 45.4 1.0
SG A:CYS90 2.3 48.8 1.0
SG A:CYS74 2.3 44.4 1.0
CD2 A:HIS83 3.0 45.3 1.0
CE1 A:HIS83 3.1 49.3 1.0
CB A:CYS74 3.2 49.0 1.0
CB A:CYS90 3.2 56.5 1.0
CB A:CYS77 3.5 41.5 1.0
N A:CYS77 3.6 41.5 1.0
CA A:CYS77 4.0 40.0 1.0
CG A:HIS83 4.2 49.4 1.0
ND1 A:HIS83 4.2 46.2 1.0
O A:HOH353 4.2 50.7 1.0
CA A:CYS90 4.4 55.3 1.0
CB A:TYR76 4.5 44.8 1.0
C A:TYR76 4.6 42.6 1.0
CA A:CYS74 4.6 44.5 1.0
CA A:TYR76 4.9 41.5 1.0
N A:LYS93 4.9 50.4 1.0
CB A:LYS93 4.9 57.3 1.0
N A:TYR76 5.0 41.0 1.0
C A:CYS74 5.0 41.9 1.0

Zinc binding site 2 out of 2 in 7orw

Go back to Zinc Binding Sites List in 7orw
Zinc binding site 2 out of 2 in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00265


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00265 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:71.4
occ:1.00
SG A:CYS128 2.2 65.7 1.0
SG A:CYS117 2.2 63.7 1.0
SG A:CYS120 2.3 67.0 1.0
SG A:CYS130 2.6 81.4 1.0
CB A:CYS117 3.0 65.8 1.0
CB A:CYS130 3.4 82.3 1.0
CB A:CYS128 3.4 69.1 1.0
CB A:CYS120 3.5 66.3 1.0
N A:CYS120 3.7 74.3 1.0
CA A:CYS128 4.0 71.7 1.0
CA A:CYS120 4.2 66.4 1.0
N A:CYS130 4.2 84.9 1.0
CA A:CYS130 4.4 88.4 1.0
CB A:VAL119 4.4 82.2 1.0
CA A:CYS117 4.5 64.8 1.0
N A:SER129 4.5 86.7 1.0
C A:CYS128 4.6 77.3 1.0
C A:VAL119 4.8 79.0 1.0
CA A:VAL119 5.0 79.0 1.0
C A:CYS117 5.0 70.1 1.0
C A:CYS120 5.0 62.5 1.0
N A:GLY121 5.0 60.4 1.0
O A:MET122 5.0 53.4 1.0

Reference:

F.Kozielski, C.Sele, V.O.Talibov, J.Lou, D.Dong, Q.Wang, X.Shi, M.Nyblom, A.Rogstam, T.Krojer, Z.Fisher, W.Knecht. Identification of Fragments Binding to Sars-Cov-2 NSP10 Reveals Ligand-Binding Sites in Conserved Interfaces Between NSP10 and NSP14/NSP16 Rsc Chem Biol 2021.
ISSN: ESSN 2633-0679
DOI: 10.1039/D1CB00135C
Page generated: Fri Nov 5 16:55:58 2021

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