Zinc in PDB 8pt6: Tilapia Lake Virus Polymerase in Vrna Initiation State (Replicase Conformation)

The structure of Tilapia Lake Virus Polymerase in Vrna Initiation State (Replicase Conformation) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Tilapia Lake Virus Polymerase in Vrna Initiation State (Replicase Conformation) (pdb code 8pt6). 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 Initiation State (Replicase Conformation), PDB code: 8pt6:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Tilapia Lake Virus Polymerase in Vrna Initiation State (Replicase 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 Initiation State (Replicase Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:98.2 occ:1.00 NE2 A:HIS296 2.0 39.4 1.0 ND1 A:HIS284 2.0 53.8 1.0 SG A:CYS282 2.3 64.9 1.0 SG A:CYS161 2.3 61.9 1.0 CE1 A:HIS284 2.8 52.7 1.0 HE1 A:HIS284 2.8 54.1 1.0 CE1 A:HIS296 3.0 40.4 1.0 HB2 A:CYS282 3.0 58.7 1.0 CD2 A:HIS296 3.0 38.2 1.0 HE1 A:HIS296 3.2 44.0 1.0 HB2 A:HIS284 3.2 54.0 1.0 CG A:HIS284 3.2 51.3 1.0 CB A:CYS282 3.2 60.0 1.0 HD2 A:HIS296 3.2 43.4 1.0 HB2 A:CYS161 3.5 53.8 1.0 CB A:CYS161 3.5 52.0 1.0 HB3 A:CYS282 3.5 58.6 1.0 HA A:LYS163 3.6 45.4 1.0 HB3 A:CYS161 3.6 54.8 1.0 CB A:HIS284 3.7 51.9 1.0 H A:HIS284 3.7 54.3 1.0 H A:LYS163 3.8 46.5 1.0 NE2 A:HIS284 4.0 49.8 1.0 HB1 A:ALA294 4.0 55.7 1.0 ND1 A:HIS296 4.1 37.7 1.0 CG A:HIS296 4.2 40.7 1.0 CD2 A:HIS284 4.2 50.2 1.0 HG2 A:LYS163 4.3 45.7 1.0 N A:HIS284 4.4 51.9 1.0 H A:GLU283 4.4 60.0 1.0 HB3 A:HIS284 4.4 54.3 1.0 CA A:LYS163 4.4 35.1 1.0 N A:LYS163 4.4 41.9 1.0 HG2 A:GLU283 4.6 60.8 1.0 CA A:CYS282 4.6 60.8 1.0 CA A:HIS284 4.7 51.6 1.0 N A:GLU283 4.7 58.0 1.0 HE2 A:HIS284 4.7 54.0 1.0 CA A:CYS161 4.9 54.3 1.0 HD1 A:HIS296 4.9 43.1 1.0 C A:CYS282 4.9 61.0 1.0 CB A:ALA294 4.9 55.3 1.0

Zinc binding site 2 out of 3 in the Tilapia Lake Virus Polymerase in Vrna Initiation State (Replicase 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 Initiation State (Replicase Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:171.8 occ:1.00 HZ1 C:LYS170 2.2 105.8 1.0 SG C:CYS159 2.3 111.1 1.0 SG C:CYS146 2.3 127.4 1.0 SG C:CYS163 2.3 119.1 1.0 SG C:CYS164 2.3 108.5 1.0 NZ C:LYS170 3.0 104.3 1.0 HB3 C:CYS159 3.1 101.4 1.0 HZ2 C:LYS170 3.2 105.3 1.0 CB C:CYS159 3.3 103.7 1.0 HB2 C:CYS163 3.4 109.6 1.0 HB2 C:CYS164 3.4 105.1 1.0 HE3 C:LYS170 3.5 106.2 1.0 H C:CYS164 3.5 105.5 1.0 CB C:CYS163 3.5 111.3 1.0 CB C:CYS164 3.6 106.2 1.0 HZ3 C:LYS170 3.6 104.9 1.0 HB2 C:PHE161 3.6 98.5 1.0 HA C:CYS146 3.7 127.7 1.0 CE C:LYS170 3.7 106.6 1.0 CB C:CYS146 3.8 128.2 1.0 N C:CYS164 3.8 105.2 1.0 HB2 C:CYS159 3.8 101.5 1.0 HE2 C:LYS170 3.9 105.8 1.0 HB3 C:CYS146 4.0 127.6 1.0 H C:CYS159 4.2 100.4 1.0 CA C:CYS146 4.3 129.0 1.0 HB3 C:CYS163 4.3 109.6 1.0 HB3 C:CYS164 4.3 105.7 1.0 H C:CYS163 4.3 108.6 1.0 CA C:CYS164 4.3 105.2 1.0 C C:CYS163 4.3 107.0 1.0 CA C:CYS163 4.4 107.0 1.0 H C:PHE161 4.4 98.3 1.0 HB2 C:CYS146 4.5 128.2 1.0 CA C:CYS159 4.5 102.2 1.0 CB C:PHE161 4.6 100.1 1.0 HD2 C:PHE161 4.6 98.4 1.0 N C:CYS159 4.7 99.1 1.0 N C:CYS163 4.7 107.2 1.0 HB3 C:PHE161 4.8 98.7 1.0 HA C:CYS164 4.9 105.7 1.0 O C:PHE161 4.9 101.6 1.0 O C:CYS146 5.0 127.7 1.0

Zinc binding site 3 out of 3 in the Tilapia Lake Virus Polymerase in Vrna Initiation State (Replicase 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 Initiation State (Replicase Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:170.5 occ:1.00 HB2 C:CYS233 1.4 135.6 1.0 CB C:CYS233 1.8 137.1 1.0 HB3 C:CYS233 1.9 135.7 1.0 HG C:CYS233 2.0 135.6 1.0 NE2 C:HIS191 2.1 134.3 1.0 ND1 C:HIS184 2.1 124.9 1.0 SG C:CYS235 2.3 130.8 1.0 SG C:CYS233 2.3 139.0 1.0 CE1 C:HIS191 2.7 131.8 1.0 HE1 C:HIS191 2.9 131.6 1.0 CE1 C:HIS184 2.9 125.8 1.0 CD2 C:HIS191 3.0 134.0 1.0 HE1 C:HIS184 3.0 126.2 1.0 HB3 C:HIS184 3.1 126.0 1.0 CG C:HIS184 3.2 124.5 1.0 HB2 C:CYS235 3.2 125.6 1.0 CA C:CYS233 3.3 135.7 1.0 HD2 C:HIS191 3.3 131.7 1.0 H C:CYS235 3.3 125.8 1.0 CB C:CYS235 3.4 126.5 1.0 HA C:CYS233 3.6 135.6 1.0 CB C:HIS184 3.6 125.2 1.0 ND1 C:HIS191 3.7 129.3 1.0 CG C:HIS191 3.9 132.5 1.0 C C:CYS233 4.0 136.8 1.0 HD2 C:PRO234 4.0 126.8 1.0 HB2 C:HIS184 4.0 126.3 1.0 N C:CYS235 4.1 125.8 1.0 NE2 C:HIS184 4.1 124.2 1.0 HB3 C:CYS235 4.1 124.7 1.0 HD12 C:ILE179 4.2 129.7 1.0 N C:CYS233 4.2 134.6 1.0 CD2 C:HIS184 4.3 123.7 1.0 CA C:CYS235 4.3 124.9 1.0 N C:PRO234 4.4 129.4 1.0 HD1 C:HIS191 4.5 131.3 1.0 H C:CYS233 4.5 135.6 1.0 HG22 C:VAL193 4.6 137.5 1.0 O C:CYS233 4.6 135.7 1.0 HA C:CYS235 4.7 124.9 1.0 CD C:PRO234 4.7 126.7 1.0 HE2 C:HIS184 4.9 126.2 1.0 HA C:HIS184 4.9 126.5 1.0 CA C:HIS184 4.9 125.8 1.0 CD1 C:ILE179 5.0 130.1 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