Zinc in PDB 7opl: Cryoem Structure of Dna Polymerase Alpha - Primase Bound to Sars Cov NSP1

All present enzymatic activity of Cryoem Structure of Dna Polymerase Alpha - Primase Bound to Sars Cov NSP1:
2.7.7.7;

The structure of Cryoem Structure of Dna Polymerase Alpha - Primase Bound to Sars Cov NSP1 also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Cryoem Structure of Dna Polymerase Alpha - Primase Bound to Sars Cov NSP1 (pdb code 7opl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryoem Structure of Dna Polymerase Alpha - Primase Bound to Sars Cov NSP1, PDB code: 7opl:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryoem Structure of Dna Polymerase Alpha - Primase Bound to Sars Cov NSP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryoem Structure of Dna Polymerase Alpha - Primase Bound to Sars Cov NSP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:172.9 occ:1.00 SG A:CYS1283 2.3 135.6 1.0 SG A:CYS1315 2.3 171.2 1.0 SG A:CYS1286 2.3 147.7 1.0 SG A:CYS1310 2.3 149.6 1.0 CB A:CYS1315 2.7 171.2 1.0 OG1 A:THR1285 3.0 141.5 1.0 CB A:CYS1310 3.1 149.6 1.0 CB A:CYS1283 3.2 135.6 1.0 OG1 A:THR1288 3.4 139.1 1.0 CB A:CYS1286 4.0 147.7 1.0 CA A:CYS1315 4.2 171.2 1.0 N A:CYS1286 4.2 147.7 1.0 CB A:ASN1312 4.2 158.8 1.0 CB A:THR1285 4.4 141.5 1.0 CA A:CYS1310 4.6 149.6 1.0 CA A:CYS1283 4.6 135.6 1.0 CA A:CYS1286 4.7 147.7 1.0 ND2 A:ASN1312 4.7 158.8 1.0 CB A:THR1288 4.8 139.1 1.0 CG2 A:THR1285 4.8 141.5 1.0 O A:ALA1317 5.0 166.6 1.0

Zinc binding site 2 out of 3 in the Cryoem Structure of Dna Polymerase Alpha - Primase Bound to Sars Cov NSP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryoem Structure of Dna Polymerase Alpha - Primase Bound to Sars Cov NSP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:123.7 occ:1.00 SG A:CYS1353 2.3 93.6 1.0 SG A:CYS1374 2.3 94.2 1.0 SG A:CYS1348 2.3 90.8 1.0 SG A:CYS1371 2.3 91.5 1.0 CB A:CYS1374 2.7 94.2 1.0 CB A:CYS1353 2.9 93.6 1.0 CB A:CYS1348 3.0 90.8 1.0 N A:CYS1374 3.4 94.2 1.0 CB A:CYS1371 3.4 91.5 1.0 CA A:CYS1374 3.7 94.2 1.0 C A:ALA1373 4.3 92.9 1.0 CB A:ALA1373 4.4 92.9 1.0 CB A:ALA1377 4.4 85.4 1.0 CA A:CYS1353 4.4 93.6 1.0 CB A:ASN1355 4.5 89.7 1.0 CA A:CYS1348 4.5 90.8 1.0 C A:CYS1374 4.8 94.2 1.0 N A:ASN1355 4.8 89.7 1.0 CA A:ALA1373 4.8 92.9 1.0 O A:CYS1374 4.8 94.2 1.0 N A:ARG1354 4.9 95.7 1.0 CA A:CYS1371 4.9 91.5 1.0 C A:CYS1353 4.9 93.6 1.0 OE1 A:GLU1350 4.9 91.5 1.0

Zinc binding site 3 out of 3 in the Cryoem Structure of Dna Polymerase Alpha - Primase Bound to Sars Cov NSP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryoem Structure of Dna Polymerase Alpha - Primase Bound to Sars Cov NSP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:320.8 occ:1.00 CB C:CYS131 2.3 274.9 1.0 SG C:CYS128 2.3 274.3 1.0 SG C:CYS131 2.3 274.9 1.0 SG C:CYS122 2.3 275.0 1.0 SG C:CYS121 2.3 275.1 1.0 CB C:CYS128 3.3 274.3 1.0 CB C:CYS121 3.4 275.1 1.0 N C:CYS128 3.4 274.3 1.0 CB C:CYS122 3.5 275.0 1.0 CA C:CYS131 3.5 274.9 1.0 N C:CYS131 3.7 274.9 1.0 CA C:CYS128 3.9 274.3 1.0 C C:ILE127 4.0 269.0 1.0 N C:CYS122 4.0 275.0 1.0 O C:CYS128 4.1 274.3 1.0 C C:CYS121 4.1 275.1 1.0 CA C:CYS122 4.3 275.0 1.0 C C:CYS128 4.4 274.3 1.0 CA C:CYS121 4.4 275.1 1.0 CA C:ILE127 4.4 269.0 1.0 C C:CYS131 4.5 274.9 1.0 O C:CYS121 4.6 275.1 1.0 C C:LYS130 4.7 275.8 1.0 O C:ILE127 4.7 269.0 1.0 CE C:LYS130 4.7 275.8 1.0 CD C:ARG119 4.8 267.1 1.0 NE C:ARG119 4.9 267.1 1.0

M.L.Kilkenny, C.E.Veale, A.Guppy, S.W.Hardwick, D.Y.Chirgadze, N.J.Rzechorzek, J.D.Maman, L.Pellegrini. Structural Basis For the Interaction of Sars-Cov-2 Virulence Factor NSP1 with Dna Polymerase A - Primase. Protein Sci. 2021.
ISSN: ESSN 1469-896X
PubMed: 34719824
DOI: 10.1002/PRO.4220