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

The structure of Cryo-Em Structure of the Human Parainfluenza Virus HPIV3 L-P Polymerase in Monomeric 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 Monomeric Form (pdb code 8kdc). 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 Monomeric Form, PDB code: 8kdc:
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 Monomeric 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 Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3002 b:103.3 occ:1.00 ND1 A:HIS1364 2.0 74.3 1.0 NE2 A:HIS1366 2.0 77.5 1.0 SG A:CYS1180 2.3 86.7 1.0 SG A:CYS1177 2.4 88.9 1.0 CG A:HIS1364 2.8 74.3 1.0 CB A:HIS1364 2.9 74.3 1.0 CE1 A:HIS1366 2.9 77.5 1.0 CB A:CYS1177 3.1 88.9 1.0 CD2 A:HIS1366 3.1 77.5 1.0 CE1 A:HIS1364 3.2 74.3 1.0 CB A:CYS1180 4.0 86.7 1.0 CD2 A:HIS1364 4.0 74.3 1.0 ND1 A:HIS1366 4.1 77.5 1.0 NE2 A:HIS1364 4.2 74.3 1.0 CG A:HIS1366 4.2 77.5 1.0 CA A:HIS1364 4.4 74.3 1.0 N A:CYS1180 4.5 86.7 1.0 CA A:CYS1177 4.6 88.9 1.0 CG A:TYR1189 4.6 79.8 1.0 CD2 A:TYR1189 4.7 79.8 1.0 CD1 A:ILE1171 4.8 81.0 1.0 CA A:CYS1180 4.8 86.7 1.0 CD1 A:TYR1189 4.9 79.8 1.0 CB A:TYR1189 5.0 79.8 1.0 CE2 A:TYR1189 5.0 79.8 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of the Human Parainfluenza Virus HPIV3 L-P Polymerase in Monomeric 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 Monomeric Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3003 b:130.0 occ:1.00 OE2 A:GLU1164 2.0 80.7 1.0 SG A:CYS1372 2.3 101.4 1.0 SG A:CYS1132 2.3 82.9 1.0 SG A:CYS1371 2.4 110.5 1.0 CB A:CYS1132 3.1 82.9 1.0 CD A:GLU1164 3.2 80.7 1.0 CB A:CYS1371 3.6 110.5 1.0 N A:CYS1372 3.6 101.4 1.0 CB A:CYS1372 3.7 101.4 1.0 CA A:CYS1372 3.9 101.4 1.0 CG A:GLU1164 3.9 80.7 1.0 CA A:CYS1132 4.0 82.9 1.0 OE1 A:GLU1164 4.1 80.7 1.0 C A:CYS1371 4.1 110.5 1.0 CA A:CYS1371 4.5 110.5 1.0 N A:SER1133 4.7 74.5 1.0 C A:CYS1132 4.8 82.9 1.0 O A:CYS1371 4.8 110.5 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