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Zinc in PDB 9fwt: Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259

Enzymatic activity of Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259

All present enzymatic activity of Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259:
2.1.1.56;

Protein crystallography data

The structure of Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259, PDB code: 9fwt was solved by T.Krojer, F.Kozielski, C.Sele, M.Nyblom, S.Z.Fisher, W.Knecht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.53 / 1.64
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.963, 99.926, 51.223, 90, 114.7, 90
R / Rfree (%) 18.4 / 21.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259 (pdb code 9fwt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259, PDB code: 9fwt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 9fwt

Go back to Zinc Binding Sites List in 9fwt
Zinc binding site 1 out of 4 in the Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:21.3
occ:1.00
 NE2 A:HIS83 2.1 21.5 1.0
SG A:CYS74 2.3 21.7 1.0
SG A:CYS77 2.3 21.1 1.0
SG A:CYS90 2.4 24.2 1.0
CD2 A:HIS83 3.1 21.1 1.0
CE1 A:HIS83 3.1 19.7 1.0
CB A:CYS74 3.2 18.8 1.0
CB A:CYS90 3.3 26.8 1.0
CB A:CYS77 3.4 19.8 1.0
N A:CYS77 3.5 19.7 1.0
CA A:CYS77 3.9 19.4 1.0
CG A:HIS83 4.2 21.1 1.0
ND1 A:HIS83 4.2 20.9 1.0
C A:TYR76 4.4 19.4 1.0
O A:HOH430 4.4 47.5 1.0
CA A:CYS90 4.4 28.2 1.0
O A:HOH375 4.4 27.1 1.0
CB A:TYR76 4.4 19.3 1.0
CA A:CYS74 4.6 18.5 1.0
O A:CYS74 4.8 18.5 1.0
CA A:TYR76 4.8 19.1 1.0
C A:CYS74 4.9 18.3 1.0
CB A:LYS93 4.9 20.6 1.0
N A:LYS93 4.9 20.2 1.0
N A:TYR76 4.9 18.7 1.0

Zinc binding site 2 out of 4 in 9fwt

Go back to Zinc Binding Sites List in 9fwt
Zinc binding site 2 out of 4 in the Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:38.4
occ:1.00
 SG A:CYS117 2.2 36.7 0.5
SG A:CYS117 2.3 46.1 0.5
SG A:CYS128 2.3 37.2 1.0
SG A:CYS120 2.4 34.4 1.0
SG A:CYS130 2.4 51.2 1.0
CB A:CYS117 2.8 41.1 0.5
CB A:CYS117 3.0 34.4 0.5
CB A:CYS130 3.3 51.7 1.0
CB A:CYS120 3.4 34.8 1.0
CB A:CYS128 3.6 40.6 1.0
N A:CYS130 3.7 51.1 1.0
N A:CYS120 3.8 36.6 1.0
N A:SER129 3.9 47.1 1.0
CA A:CYS128 4.0 41.9 1.0
CA A:CYS130 4.1 52.0 1.0
CA A:CYS120 4.2 34.9 1.0
CA A:CYS117 4.2 39.2 0.5
C A:CYS128 4.2 44.9 1.0
C A:SER129 4.5 50.6 1.0
CA A:CYS117 4.5 33.9 0.5
O A:CYS117 4.6 39.1 0.5
C A:CYS117 4.7 38.7 0.5
CB A:VAL119 4.7 41.8 1.0
CA A:SER129 4.8 49.2 1.0
NZ A:LYS124 4.8 53.0 1.0
C A:VAL119 4.8 38.8 1.0
C A:CYS117 4.9 36.0 0.5
C A:CYS120 5.0 33.7 1.0

Zinc binding site 3 out of 4 in 9fwt

Go back to Zinc Binding Sites List in 9fwt
Zinc binding site 3 out of 4 in the Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:37.8
occ:1.00
 NE2 B:HIS257 2.0 40.9 1.0
ND1 B:HIS264 2.1 60.0 1.0
SG B:CYS279 2.3 34.8 1.0
SG B:CYS261 2.4 49.5 1.0
CE1 B:HIS257 3.0 41.5 1.0
CD2 B:HIS257 3.0 40.1 1.0
CE1 B:HIS264 3.1 60.5 1.0
CG B:HIS264 3.1 58.7 1.0
CB B:CYS261 3.1 52.6 1.0
CB B:CYS279 3.2 31.1 1.0
CB B:HIS264 3.4 58.1 1.0
ND1 B:HIS257 4.2 41.3 1.0
CG B:HIS257 4.2 39.8 1.0
NE2 B:HIS264 4.2 60.3 1.0
CD2 B:HIS264 4.2 59.4 1.0
N B:HIS264 4.3 58.6 1.0
O B:HOH546 4.4 34.0 1.0
CA B:HIS264 4.5 58.4 1.0
CA B:CYS261 4.6 54.0 1.0
CA B:CYS279 4.6 29.7 1.0
CG2 B:VAL263 4.7 60.9 1.0
CE1 B:HIS283 4.9 39.6 1.0
C B:CYS261 4.9 55.7 1.0

Zinc binding site 4 out of 4 in 9fwt

Go back to Zinc Binding Sites List in 9fwt
Zinc binding site 4 out of 4 in the Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:35.0
occ:1.00
 ND1 B:HIS229 1.8 33.6 1.0
SG B:CYS207 2.3 35.7 1.0
SG B:CYS210 2.3 37.7 1.0
SG B:CYS226 2.4 30.3 1.0
CE1 B:HIS229 2.6 35.7 1.0
CB B:CYS207 3.0 37.2 1.0
CG B:HIS229 3.1 32.9 1.0
CB B:CYS226 3.4 26.6 1.0
CB B:CYS210 3.5 40.8 1.0
CB B:HIS229 3.7 29.2 1.0
NE2 B:HIS229 3.8 36.3 1.0
N B:CYS210 3.9 42.5 1.0
N B:CYS226 4.0 25.2 1.0
CD2 B:HIS229 4.1 35.4 1.0
CA B:CYS210 4.2 40.9 1.0
CA B:CYS226 4.3 25.5 1.0
C B:LEU209 4.3 44.3 1.0
NH1 B:ARG212 4.4 41.5 1.0
CA B:CYS207 4.5 38.4 1.0
N B:HIS229 4.6 28.2 1.0
N B:LEU209 4.6 46.0 1.0
CB B:LEU209 4.7 46.0 1.0
CB B:ARG212 4.7 34.4 1.0
C B:CYS210 4.7 40.2 1.0
CD B:ARG212 4.7 38.4 1.0
CA B:LEU209 4.8 45.5 1.0
CA B:HIS229 4.8 28.0 1.0
O B:LEU209 4.9 44.9 1.0
CB B:HIS228 5.0 28.7 1.0
C B:CYS226 5.0 25.6 1.0
O B:CYS210 5.0 40.2 1.0

Reference:

T.Krojer, F.Kozielski, C.Sele, M.Nyblom, S.Z.Fisher, W.Knecht. Ensemble Model of Ligand-Free Sars-Cov-2 NSP10-NSP14 (Exon) and in Complex with Partially Bound VT00259 To Be Published.
Page generated: Fri Aug 22 17:42:40 2025

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