Zinc in PDB 8qz8: Tilapia Lake Virus Polymerase in Vrna Pre-Termination State (Transcriptase Conformation)

The structure of Tilapia Lake Virus Polymerase in Vrna Pre-Termination State (Transcriptase Conformation) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Tilapia Lake Virus Polymerase in Vrna Pre-Termination State (Transcriptase Conformation) (pdb code 8qz8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Tilapia Lake Virus Polymerase in Vrna Pre-Termination State (Transcriptase Conformation), PDB code: 8qz8:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Tilapia Lake Virus Polymerase in Vrna Pre-Termination State (Transcriptase Conformation)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tilapia Lake Virus Polymerase in Vrna Pre-Termination State (Transcriptase Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:115.1 occ:1.00 NE2 A:HIS296 2.0 55.2 1.0 ND1 A:HIS284 2.0 69.3 1.0 SG A:CYS161 2.3 76.4 1.0 SG A:CYS282 2.3 87.3 1.0 HB2 A:CYS282 2.8 78.7 1.0 CE1 A:HIS284 2.9 73.9 1.0 CD2 A:HIS296 2.9 51.0 1.0 HE1 A:HIS284 2.9 72.8 1.0 HD2 A:HIS296 3.0 58.9 1.0 HB2 A:HIS284 3.1 72.7 1.0 CB A:CYS282 3.1 82.2 1.0 CE1 A:HIS296 3.1 60.0 1.0 CG A:HIS284 3.2 67.0 1.0 HB2 A:CYS161 3.3 67.4 1.0 HE1 A:HIS296 3.4 59.7 1.0 CB A:CYS161 3.4 63.9 1.0 HB3 A:CYS282 3.4 78.9 1.0 H A:HIS284 3.5 72.7 1.0 HB3 A:CYS161 3.6 67.7 1.0 CB A:HIS284 3.6 69.2 1.0 HA A:LYS163 3.8 60.7 1.0 HB1 A:ALA294 3.8 70.5 1.0 H A:LYS163 3.9 60.0 1.0 NE2 A:HIS284 4.0 74.5 1.0 CG A:HIS296 4.1 50.4 1.0 ND1 A:HIS296 4.2 59.6 1.0 CD2 A:HIS284 4.2 71.6 1.0 N A:HIS284 4.2 73.6 1.0 HG2 A:LYS163 4.3 60.4 1.0 HB3 A:HIS284 4.3 72.3 1.0 H A:GLU283 4.4 78.3 1.0 HG3 A:GLU283 4.4 80.0 1.0 CA A:CYS282 4.5 79.1 1.0 CA A:HIS284 4.5 74.1 1.0 N A:LYS163 4.6 55.3 1.0 CA A:LYS163 4.6 62.3 1.0 N A:GLU283 4.7 70.8 1.0 CB A:ALA294 4.7 68.4 1.0 C A:CYS282 4.8 72.5 1.0 CA A:CYS161 4.8 66.5 1.0 HE2 A:HIS284 4.8 72.6 1.0 HB2 A:ALA294 4.9 70.8 1.0 HG2 A:GLU283 4.9 79.7 1.0 HD1 A:HIS296 4.9 60.0 1.0

Zinc binding site 2 out of 3 in the Tilapia Lake Virus Polymerase in Vrna Pre-Termination State (Transcriptase Conformation)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tilapia Lake Virus Polymerase in Vrna Pre-Termination State (Transcriptase Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:174.2 occ:1.00 HD1 C:HIS184 1.3 115.3 1.0 NE2 C:HIS191 2.0 115.1 1.0 ND1 C:HIS184 2.0 118.2 1.0 SG C:CYS235 2.3 120.9 1.0 SG C:CYS233 2.3 129.4 1.0 HB3 C:HIS184 2.5 115.5 1.0 CG C:HIS184 2.9 116.1 1.0 CD2 C:HIS191 2.9 110.6 1.0 HB2 C:CYS235 3.0 119.4 1.0 HD2 C:HIS191 3.1 111.2 1.0 CE1 C:HIS191 3.1 112.6 1.0 CB C:HIS184 3.1 116.7 1.0 CE1 C:HIS184 3.1 116.8 1.0 CB C:CYS235 3.2 120.7 1.0 HA C:CYS233 3.2 124.2 1.0 HE1 C:HIS191 3.3 111.6 1.0 H C:CYS235 3.4 119.2 1.0 HE1 C:HIS184 3.4 115.0 1.0 HB2 C:HIS184 3.4 114.5 1.0 CB C:CYS233 3.6 123.8 1.0 CA C:CYS233 3.8 124.4 1.0 HD2 C:PRO234 3.9 116.6 1.0 HB3 C:CYS235 3.9 118.7 1.0 HB2 C:CYS233 4.0 124.2 1.0 N C:CYS235 4.0 119.7 1.0 CD2 C:HIS184 4.1 113.7 1.0 CG C:HIS191 4.1 108.8 1.0 ND1 C:HIS191 4.1 108.4 1.0 NE2 C:HIS184 4.1 117.0 1.0 CA C:CYS235 4.2 121.6 1.0 C C:CYS233 4.3 124.5 1.0 HB3 C:CYS233 4.4 124.2 1.0 HA C:CYS235 4.4 119.6 1.0 CA C:HIS184 4.4 114.9 1.0 HG22 C:VAL193 4.5 113.5 1.0 HA C:HIS184 4.5 114.5 1.0 N C:PRO234 4.5 116.5 1.0 HG13 C:ILE179 4.6 107.8 1.0 CD C:PRO234 4.7 115.7 1.0 HG23 C:VAL193 4.7 113.5 1.0 HD2 C:HIS184 4.9 114.1 1.0 HD1 C:HIS191 4.9 110.9 1.0 O C:CYS233 4.9 125.0 1.0 CG2 C:VAL193 5.0 112.2 1.0

Zinc binding site 3 out of 3 in the Tilapia Lake Virus Polymerase in Vrna Pre-Termination State (Transcriptase Conformation)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tilapia Lake Virus Polymerase in Vrna Pre-Termination State (Transcriptase Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:192.9 occ:1.00 HB2 C:CYS146 1.9 134.3 1.0 SG C:CYS159 2.3 131.3 1.0 SG C:CYS163 2.3 119.9 1.0 SG C:CYS164 2.3 123.4 1.0 SG C:CYS146 2.4 133.3 1.0 CB C:CYS146 2.5 135.9 1.0 HB3 C:CYS146 3.0 134.2 1.0 HD2 C:LYS170 3.5 106.2 1.0 HB2 C:CYS163 3.6 111.8 1.0 H C:CYS164 3.7 114.5 1.0 CB C:CYS163 3.7 109.9 1.0 CA C:CYS146 3.7 136.9 1.0 O C:CYS146 3.8 134.1 1.0 CB C:CYS159 3.9 126.2 1.0 HD3 C:LYS170 3.9 106.7 1.0 HA C:CYS146 4.0 134.5 1.0 HB3 C:CYS159 4.0 125.1 1.0 H C:CYS159 4.0 125.2 1.0 CB C:CYS164 4.0 116.6 1.0 C C:CYS146 4.0 135.2 1.0 N C:CYS164 4.1 112.4 1.0 CD C:LYS170 4.1 106.7 1.0 HB2 C:PHE161 4.2 113.2 1.0 HE2 C:LYS170 4.3 106.2 1.0 HB3 C:CYS164 4.3 115.4 1.0 HB3 C:CYS163 4.3 111.7 1.0 HB2 C:CYS159 4.5 125.4 1.0 H C:CYS163 4.6 112.1 1.0 C C:CYS163 4.6 110.2 1.0 HB2 C:CYS164 4.6 115.1 1.0 CA C:CYS163 4.6 109.7 1.0 CA C:CYS164 4.7 114.5 1.0 N C:CYS159 4.8 124.2 1.0 CE C:LYS170 4.8 107.4 1.0 N C:CYS146 4.9 135.8 1.0 CA C:CYS159 4.9 125.2 1.0 H C:CYS146 4.9 134.1 1.0 H C:PHE161 4.9 113.9 1.0 N C:CYS163 5.0 113.6 1.0

B.Arragain, M.Pelosse, A.Thompson, S.Cusack. Structural and Functional Analysis of the Minimal Orthomyxovirus-Like Polymerase of Tilapia Lake Virus From the Highly Diverged Amnoonviridae Family. Nat Commun V. 14 8145 2023.
ISSN: ESSN 2041-1723
PubMed: 38066000
DOI: 10.1038/S41467-023-44044-X