Zinc in PDB 8wgy: Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain

The structure of Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain (pdb code 8wgy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain, PDB code: 8wgy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn802 b:98.1 occ:1.00 NE2 E:HIS290 2.1 59.9 1.0 SG E:CYS282 2.3 64.6 1.0 SG E:CYS314 2.3 63.0 1.0 SG E:CYS285 2.3 58.3 1.0 CE1 E:HIS290 2.6 55.5 1.0 CB E:CYS314 3.2 56.5 1.0 CD2 E:HIS290 3.2 57.2 1.0 CB E:CYS282 3.5 53.4 1.0 ND1 E:HIS290 3.8 54.3 1.0 CA E:CYS314 3.8 57.5 1.0 CB E:CYS285 3.8 53.4 1.0 N E:CYS285 3.9 52.4 1.0 NE2 E:HIS294 3.9 58.8 1.0 CB E:LEU284 4.0 52.1 1.0 CG E:HIS290 4.1 57.2 1.0 O E:SER313 4.4 45.3 1.0 CA E:CYS285 4.4 54.4 1.0 CE1 E:HIS294 4.5 61.2 1.0 O E:CYS282 4.6 50.2 1.0 C E:LEU284 4.6 53.8 1.0 CA E:LEU284 4.7 51.6 1.0 N E:CYS314 4.7 57.8 1.0 CA E:CYS282 4.8 52.3 1.0 N E:LEU284 4.8 54.0 1.0 C E:CYS314 4.8 55.5 1.0 N E:LYS315 4.9 50.7 1.0 C E:CYS282 4.9 54.2 1.0 CD1 E:LEU284 4.9 53.5 1.0 CG E:LEU284 4.9 57.3 1.0 C E:SER313 5.0 51.7 1.0

Zinc binding site 2 out of 2 in the Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn801 b:102.0 occ:1.00 NE2 D:HIS290 2.1 57.0 1.0 SG D:CYS285 2.3 60.0 1.0 SG D:CYS282 2.3 56.8 1.0 SG D:CYS314 2.3 64.7 1.0 CE1 D:HIS290 2.6 55.1 1.0 CB D:CYS285 2.7 52.4 1.0 CB D:CYS282 3.0 53.2 1.0 CD2 D:HIS290 3.1 52.1 1.0 N D:CYS285 3.3 50.4 1.0 CA D:CYS285 3.6 52.2 1.0 CB D:CYS314 3.6 55.4 1.0 ND1 D:HIS290 3.6 54.3 1.0 CE1 D:HIS294 3.8 57.3 1.0 NE2 D:HIS294 3.8 59.3 1.0 CG D:HIS290 3.9 53.6 1.0 C D:LEU284 4.1 55.0 1.0 CB D:LEU284 4.2 51.7 1.0 CA D:CYS282 4.5 54.3 1.0 C D:CYS285 4.5 54.9 1.0 CA D:LEU284 4.5 52.9 1.0 N D:LEU284 4.6 54.1 1.0 CA D:CYS314 4.7 56.2 1.0 OH D:TYR278 4.7 61.3 1.0 C D:CYS282 4.9 54.1 1.0 N D:LYS286 5.0 52.8 1.0

Y.Xu, Y.Wu, Y.Zhang, K.Gao, X.Wu, Y.Yang, D.Li, B.Yang, Z.Zhang, C.Dong. Essential and Multifunctional Mpox Virus E5 Helicase-Primase in Double and Single Hexamer. Sci Adv V. 10 L1150 2024.
ISSN: ESSN 2375-2548
PubMed: 39167653
DOI: 10.1126/SCIADV.ADL1150