Zinc in PDB 8r7b: Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051

Enzymatic activity of Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051

All present enzymatic activity of Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051:
2.1.1.56;

Protein crystallography data

The structure of Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051, PDB code: 8r7b was solved by C.Meyer, A.Garzia, M.Miller, D.J.Huggins, R.W.Myers, N.Liverton, S.Kargman, J.Nitsche, O.Ganichkin, S.Steinbacher, P.T.Meinke, T.Tuschl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.51 / 2.18
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.448, 101.071, 90.472, 90, 108.43, 90
R / Rfree (%) 19 / 24.4

Other elements in 8r7b:

The structure of Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051 also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051 (pdb code 8r7b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051, PDB code: 8r7b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8r7b

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Zinc binding site 1 out of 7 in the Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:66.0
occ:1.00
 ND1 A:HIS229 2.0 68.0 1.0
SG A:CYS210 2.3 61.0 1.0
SG A:CYS207 2.3 63.4 1.0
SG A:CYS226 2.4 63.5 1.0
CE1 A:HIS229 2.9 74.2 1.0
CG A:HIS229 3.0 66.8 1.0
CB A:CYS207 3.1 61.6 1.0
CB A:CYS210 3.4 69.3 1.0
CB A:CYS226 3.4 62.9 1.0
CB A:HIS229 3.4 71.5 1.0
N A:CYS210 3.8 69.1 1.0
NE2 A:HIS229 4.0 72.5 1.0
N A:CYS226 4.1 67.2 1.0
CA A:CYS210 4.1 65.1 1.0
CD2 A:HIS229 4.1 69.0 1.0
NH1 A:ARG212 4.2 73.0 1.0
CA A:CYS226 4.3 63.6 1.0
C A:LEU209 4.4 79.8 1.0
CB A:LEU209 4.5 89.2 1.0
N A:HIS229 4.6 70.8 1.0
CA A:CYS207 4.6 64.7 1.0
CA A:HIS229 4.7 72.5 1.0
C A:CYS210 4.8 62.2 1.0
CA A:LEU209 4.8 84.1 1.0
CB A:ARG212 4.8 58.6 1.0
N A:LEU209 4.8 93.8 1.0
CD A:ARG212 4.8 59.6 1.0
O A:CYS210 4.9 65.3 1.0
CB A:HIS228 4.9 64.5 1.0
C A:CYS226 5.0 63.3 1.0

Zinc binding site 2 out of 7 in 8r7b

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Zinc binding site 2 out of 7 in the Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:62.7
occ:1.00
 NE2 A:HIS257 2.0 70.3 1.0
ND1 A:HIS264 2.1 68.0 1.0
SG A:CYS261 2.3 68.3 1.0
SG A:CYS279 2.4 62.5 1.0
CE1 A:HIS264 3.0 69.1 1.0
CD2 A:HIS257 3.0 70.7 1.0
CE1 A:HIS257 3.0 69.7 1.0
CB A:CYS279 3.1 57.0 1.0
CG A:HIS264 3.1 73.3 1.0
CB A:CYS261 3.2 72.1 1.0
CB A:HIS264 3.5 82.3 1.0
ND1 A:HIS257 4.1 73.9 1.0
CG A:HIS257 4.1 74.6 1.0
NE2 A:HIS264 4.1 64.5 1.0
CD2 A:HIS264 4.2 70.4 1.0
N A:HIS264 4.3 79.0 1.0
CA A:HIS264 4.5 84.0 1.0
CA A:CYS261 4.6 76.0 1.0
N A:ASP415 4.6 61.2 1.0
CA A:CYS279 4.6 55.1 1.0
CA A:MET276 4.9 60.7 1.0
SG A:CYS414 5.0 77.7 1.0

Zinc binding site 3 out of 7 in 8r7b

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Zinc binding site 3 out of 7 in the Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:75.3
occ:1.00
 ND1 A:HIS487 2.1 70.2 1.0
SG A:CYS484 2.3 73.4 1.0
SG A:CYS477 2.3 75.5 1.0
SG A:CYS452 2.4 86.3 1.0
CE1 A:HIS487 3.0 69.3 1.0
CG A:HIS487 3.1 69.3 1.0
CB A:CYS452 3.2 86.5 1.0
CB A:CYS484 3.3 72.4 1.0
CB A:CYS477 3.3 75.2 1.0
CB A:HIS487 3.5 66.5 1.0
CA A:CYS452 3.6 90.1 1.0
N A:CYS484 4.0 77.0 1.0
NE2 A:HIS487 4.1 69.4 1.0
CA A:CYS484 4.2 73.3 1.0
CD2 A:HIS487 4.2 65.8 1.0
N A:CYS477 4.2 71.1 1.0
CA A:CYS477 4.4 69.9 1.0
N A:GLU453 4.6 107.8 1.0
N A:CYS452 4.6 88.6 1.0
CB A:THR475 4.6 67.2 1.0
C A:CYS452 4.6 94.5 1.0
N A:HIS487 4.6 70.4 1.0
OG1 A:THR475 4.7 68.4 1.0
CA A:HIS487 4.7 71.3 1.0
O A:CYS484 4.8 77.6 1.0
C A:CYS484 4.8 72.9 1.0

Zinc binding site 4 out of 7 in 8r7b

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Zinc binding site 4 out of 7 in the Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:51.3
occ:1.00
 ND1 B:HIS229 1.9 47.6 1.0
SG B:CYS226 2.3 56.4 1.0
SG B:CYS210 2.3 51.6 1.0
SG B:CYS207 2.3 52.0 1.0
CE1 B:HIS229 2.8 50.1 1.0
CG B:HIS229 3.0 48.5 1.0
CB B:CYS207 3.1 52.6 1.0
CB B:CYS226 3.3 48.6 1.0
CB B:HIS229 3.4 49.0 1.0
CB B:CYS210 3.5 52.6 1.0
N B:CYS226 3.9 50.2 1.0
N B:CYS210 3.9 59.0 1.0
NE2 B:HIS229 4.0 49.4 1.0
CD2 B:HIS229 4.0 46.0 1.0
CA B:CYS226 4.2 50.3 1.0
CA B:CYS210 4.2 53.3 1.0
NH1 B:ARG212 4.3 59.8 1.0
CB B:LEU209 4.5 73.4 1.0
N B:HIS229 4.6 51.8 1.0
C B:LEU209 4.6 68.6 1.0
CA B:HIS229 4.6 52.0 1.0
CA B:CYS207 4.6 57.2 1.0
CB B:ARG212 4.6 48.7 1.0
C B:CYS210 4.8 54.9 1.0
C B:CYS226 4.9 50.4 1.0
CA B:LEU209 4.9 68.3 1.0
CD B:ARG212 4.9 52.3 1.0
N B:LEU209 5.0 65.7 1.0
CG B:ARG212 5.0 49.6 1.0
C B:ALA225 5.0 47.0 1.0

Zinc binding site 5 out of 7 in 8r7b

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Zinc binding site 5 out of 7 in the Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:51.2
occ:1.00
 NE2 B:HIS257 2.0 55.1 1.0
ND1 B:HIS264 2.0 57.7 1.0
SG B:CYS261 2.3 49.5 1.0
SG B:CYS279 2.3 46.5 1.0
CE1 B:HIS264 3.0 57.0 1.0
CE1 B:HIS257 3.0 60.7 1.0
CD2 B:HIS257 3.0 53.9 1.0
CB B:CYS279 3.1 49.9 1.0
CB B:CYS261 3.1 52.1 1.0
CG B:HIS264 3.1 57.2 1.0
CB B:HIS264 3.5 62.9 1.0
ND1 B:HIS257 4.1 54.8 1.0
NE2 B:HIS264 4.1 52.8 1.0
CG B:HIS257 4.1 56.2 1.0
CD2 B:HIS264 4.2 54.9 1.0
N B:HIS264 4.3 65.1 1.0
O B:HOH761 4.5 57.0 1.0
CA B:HIS264 4.5 67.3 1.0
CA B:CYS261 4.5 52.8 1.0
CA B:CYS279 4.6 48.6 1.0
N B:ASP415 4.6 52.4 1.0
C B:CYS261 4.9 51.3 1.0
CA B:MET276 5.0 56.5 1.0

Zinc binding site 6 out of 7 in 8r7b

Go back to Zinc Binding Sites List in 8r7b
Zinc binding site 6 out of 7 in the Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:83.2
occ:1.00
 ND1 B:HIS487 2.1 84.4 1.0
SG B:CYS452 2.3 101.5 1.0
SG B:CYS484 2.3 77.0 1.0
SG B:CYS477 2.3 82.0 1.0
CE1 B:HIS487 3.0 85.2 1.0
CG B:HIS487 3.1 73.0 1.0
CB B:CYS452 3.2 91.3 1.0
CB B:CYS484 3.3 81.9 1.0
CB B:CYS477 3.3 87.7 1.0
CB B:HIS487 3.5 69.6 1.0
CA B:CYS452 3.7 94.3 1.0
N B:CYS477 4.1 79.2 1.0
N B:CYS484 4.1 73.6 1.0
NE2 B:HIS487 4.2 84.6 1.0
CD2 B:HIS487 4.2 78.6 1.0
CA B:CYS484 4.3 76.7 1.0
CA B:CYS477 4.3 84.6 1.0
N B:CYS452 4.6 90.8 1.0
N B:HIS487 4.6 73.3 1.0
CB B:THR475 4.6 75.5 1.0
OG1 B:THR475 4.7 73.6 1.0
CA B:HIS487 4.7 78.2 1.0
C B:CYS452 4.8 95.5 1.0
N B:GLU453 4.8 104.8 1.0
O B:CYS484 4.9 91.3 1.0
C B:CYS484 4.9 81.8 1.0

Zinc binding site 7 out of 7 in 8r7b

Go back to Zinc Binding Sites List in 8r7b
Zinc binding site 7 out of 7 in the Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Sars-Cov-2 NSP14 in Complex with Sah and Tdi-015051 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn612

b:88.0
occ:1.00
 N3 B:IMD605 2.2 69.2 1.0
N3 B:IMD606 2.3 110.5 1.0
N3 B:IMD604 2.3 76.6 1.0
SG B:CYS208 2.4 73.5 1.0
C2 B:IMD604 2.9 75.0 1.0
C2 B:IMD605 2.9 64.6 1.0
C2 B:IMD606 3.1 111.1 1.0
C4 B:IMD606 3.4 115.6 1.0
C4 B:IMD605 3.5 67.2 1.0
C4 B:IMD604 3.5 73.0 1.0
CB B:CYS208 3.5 73.3 1.0
CA B:CYS208 4.1 69.6 1.0
N1 B:IMD604 4.1 72.9 1.0
N1 B:IMD605 4.1 64.6 1.0
N1 B:IMD606 4.3 120.0 1.0
C5 B:IMD604 4.4 74.7 1.0
C5 B:IMD606 4.4 116.6 1.0
C5 B:IMD605 4.4 67.8 1.0
O B:HOH745 4.6 64.0 1.0
N B:CYS208 4.9 64.9 1.0

Reference:

C.Meyer, A.Garzia, M.Miller, D.J.Huggins, R.W.Myers, H.H.Hoffmann, A.W.Ashbrook, S.Jannath, N.Liverton, S.Kargman, M.Zimmerman, A.M.Nelson, J.Cangialosi, S.Penalva-Lopez, V.Sharma, L.Ramos-Espiritu, M.R.Menezes, C.Larson, J.Nitsche, H.Alwaseem, H.Molina, S.Steinbacher, J.F.Glickman, D.S.Perlin, C.Rice, P.T.Meinke, T.Tuschl. Small-Molecule Inhibition of Sars-Cov-2 Guanine-N7 Rna Cap Methyltransferase To Be Published.
Page generated: Thu Oct 31 10:24:57 2024

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