Zinc in PDB 8kdb: Cryo-Em Structure of the Human Parainfluenza Virus HPIV3 L-P Polymerase in Dimeric Form

The structure of Cryo-Em Structure of the Human Parainfluenza Virus HPIV3 L-P Polymerase in Dimeric Form also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of the Human Parainfluenza Virus HPIV3 L-P Polymerase in Dimeric Form (pdb code 8kdb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of the Human Parainfluenza Virus HPIV3 L-P Polymerase in Dimeric Form, PDB code: 8kdb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of the Human Parainfluenza Virus HPIV3 L-P Polymerase in Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the Human Parainfluenza Virus HPIV3 L-P Polymerase in Dimeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3002 b:67.1 occ:1.00 ND1 A:HIS1364 2.0 44.5 1.0 NE2 A:HIS1366 2.0 48.7 1.0 SG A:CYS1180 2.3 59.0 1.0 SG A:CYS1177 2.3 57.2 1.0 CG A:HIS1364 2.9 44.5 1.0 CE1 A:HIS1366 3.0 48.7 1.0 CB A:HIS1364 3.1 44.5 1.0 CD2 A:HIS1366 3.1 48.7 1.0 CE1 A:HIS1364 3.1 44.5 1.0 CB A:CYS1177 3.2 57.2 1.0 CB A:CYS1180 3.6 59.0 1.0 CD2 A:HIS1364 4.1 44.5 1.0 N A:CYS1180 4.1 59.0 1.0 ND1 A:HIS1366 4.1 48.7 1.0 NE2 A:HIS1364 4.2 44.5 1.0 CG A:HIS1366 4.2 48.7 1.0 CA A:CYS1180 4.4 59.0 1.0 CG A:TYR1189 4.5 47.8 1.0 CD2 A:TYR1189 4.5 47.8 1.0 CA A:HIS1364 4.6 44.5 1.0 CD1 A:TYR1189 4.7 47.8 1.0 CA A:CYS1177 4.7 57.2 1.0 CE2 A:TYR1189 4.8 47.8 1.0 CD1 A:ILE1171 4.9 50.9 1.0 CE1 A:TYR1189 4.9 47.8 1.0 CB A:TYR1189 4.9 47.8 1.0 CZ A:TYR1189 4.9 47.8 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of the Human Parainfluenza Virus HPIV3 L-P Polymerase in Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the Human Parainfluenza Virus HPIV3 L-P Polymerase in Dimeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3003 b:85.0 occ:1.00 OE2 A:GLU1164 2.0 49.7 1.0 SG A:CYS1372 2.3 65.4 1.0 SG A:CYS1132 2.3 54.5 1.0 SG A:CYS1371 2.3 76.4 1.0 CD A:GLU1164 3.1 49.7 1.0 CG A:GLU1164 3.5 49.7 1.0 CB A:CYS1132 3.5 54.5 1.0 CB A:CYS1371 3.6 76.4 1.0 CB A:CYS1372 3.6 65.4 1.0 N A:CYS1372 3.7 65.4 1.0 CA A:CYS1372 3.8 65.4 1.0 C A:CYS1371 4.1 76.4 1.0 CA A:CYS1132 4.1 54.5 1.0 OE1 A:GLU1164 4.2 49.7 1.0 N A:SER1133 4.4 48.7 1.0 CA A:CYS1371 4.5 76.4 1.0 O A:CYS1371 4.6 76.4 1.0 OG A:SER1133 4.7 48.7 1.0 C A:CYS1132 4.8 54.5 1.0 CB A:GLU1164 4.8 49.7 1.0

J.Xie, M.Ouizougun-Oubari, L.Wang, G.Zhai, D.Wu, Z.Lin, M.Wang, B.Ludeke, X.Yan, T.Nilsson, L.Gao, X.Huang, R.Fearns, S.Chen. Structural Basis For Dimerization of A Paramyxovirus Polymerase Complex. Nat Commun V. 15 3163 2024.
ISSN: ESSN 2041-1723
PubMed: 38605025
DOI: 10.1038/S41467-024-47470-7