Zinc in PDB 8psz: Tilapia Lake Virus Polymerase in Vrna Elongation State with Additional Mode B Promoter (Transcriptase Conformation)

The structure of Tilapia Lake Virus Polymerase in Vrna Elongation State with Additional Mode B Promoter (Transcriptase 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 Elongation State with Additional Mode B Promoter (Transcriptase Conformation) (pdb code 8psz). 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 Elongation State with Additional Mode B Promoter (Transcriptase Conformation), PDB code: 8psz:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Tilapia Lake Virus Polymerase in Vrna Elongation State with Additional Mode B Promoter (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 Elongation State with Additional Mode B Promoter (Transcriptase Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:53.3 occ:1.00 ND1 A:HIS284 2.0 18.4 1.0 NE2 A:HIS296 2.0 13.9 1.0 SG A:CYS161 2.3 20.8 1.0 SG A:CYS282 2.3 21.1 1.0 CE1 A:HIS284 2.9 18.2 1.0 HB2 A:HIS284 2.9 21.0 1.0 CD2 A:HIS296 3.0 6.8 1.0 CE1 A:HIS296 3.0 10.9 1.0 HE1 A:HIS284 3.1 20.3 1.0 CG A:HIS284 3.1 19.1 1.0 HB2 A:CYS282 3.1 25.2 1.0 HD2 A:HIS296 3.2 13.6 1.0 HE1 A:HIS296 3.2 14.4 1.0 CB A:CYS282 3.3 24.7 1.0 CB A:CYS161 3.4 15.3 1.0 HB2 A:CYS161 3.4 14.4 1.0 H A:HIS284 3.5 22.6 1.0 CB A:HIS284 3.5 19.2 1.0 HB3 A:CYS161 3.5 14.2 1.0 HB3 A:CYS282 3.7 24.8 1.0 HA A:LYS163 3.8 14.4 1.0 HB1 A:ALA294 3.8 18.9 1.0 H A:LYS163 3.9 13.0 1.0 NE2 A:HIS284 4.0 20.1 1.0 CD2 A:HIS284 4.1 21.2 1.0 ND1 A:HIS296 4.1 13.7 1.0 CG A:HIS296 4.2 11.6 1.0 HB3 A:HIS284 4.2 21.3 1.0 N A:HIS284 4.2 24.6 1.0 HG2 A:LYS163 4.3 13.9 1.0 HG3 A:GLU283 4.3 27.4 1.0 CA A:HIS284 4.5 22.6 1.0 H A:GLU283 4.5 27.7 1.0 CA A:LYS163 4.6 15.7 1.0 N A:LYS163 4.6 9.7 1.0 HG3 A:LYS163 4.6 13.8 1.0 CA A:CYS282 4.7 22.6 1.0 CB A:ALA294 4.7 16.4 1.0 N A:GLU283 4.8 27.8 1.0 HE2 A:HIS284 4.8 21.0 1.0 CA A:CYS161 4.8 14.6 1.0 HB2 A:ALA294 4.9 18.9 1.0 C A:CYS282 4.9 24.9 1.0 CG A:LYS163 4.9 14.7 1.0 HD1 A:HIS296 4.9 14.8 1.0 HG2 A:GLU283 5.0 27.8 1.0 HD2 A:HIS284 5.0 21.0 1.0

Zinc binding site 2 out of 3 in the Tilapia Lake Virus Polymerase in Vrna Elongation State with Additional Mode B Promoter (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 Elongation State with Additional Mode B Promoter (Transcriptase Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:92.4 occ:1.00 NE2 C:HIS191 2.0 54.9 1.0 ND1 C:HIS184 2.1 55.0 1.0 SG C:CYS233 2.3 68.9 1.0 SG C:CYS235 2.3 63.5 1.0 HB3 C:HIS184 2.6 52.4 1.0 HB2 C:CYS235 2.9 60.6 1.0 CG C:HIS184 2.9 54.2 1.0 CD2 C:HIS191 2.9 55.4 1.0 CE1 C:HIS191 3.1 54.5 1.0 HD2 C:HIS191 3.1 54.9 1.0 CE1 C:HIS184 3.1 54.1 1.0 CB C:HIS184 3.1 52.0 1.0 CB C:CYS235 3.2 60.6 1.0 HB2 C:CYS233 3.2 66.3 1.0 HE1 C:HIS191 3.3 54.9 1.0 H C:CYS235 3.3 60.8 1.0 CB C:CYS233 3.3 67.4 1.0 HE1 C:HIS184 3.4 52.4 1.0 HB2 C:HIS184 3.5 51.8 1.0 HA C:CYS233 3.7 66.6 1.0 HB3 C:CYS235 3.9 59.8 1.0 HD2 C:PRO234 4.0 61.6 1.0 N C:CYS235 4.0 59.6 1.0 CA C:CYS233 4.0 67.0 1.0 HD13 C:ILE179 4.1 52.4 1.0 CD2 C:HIS184 4.1 51.6 1.0 CG C:HIS191 4.1 54.2 1.0 ND1 C:HIS191 4.1 53.3 1.0 CA C:CYS235 4.1 60.5 1.0 HB3 C:CYS233 4.1 66.8 1.0 NE2 C:HIS184 4.2 54.0 1.0 C C:CYS233 4.3 67.6 1.0 HA C:CYS235 4.4 60.8 1.0 CA C:HIS184 4.5 48.9 1.0 HA C:HIS184 4.5 51.6 1.0 N C:PRO234 4.7 64.4 1.0 HG22 C:VAL193 4.7 51.7 1.0 CD C:PRO234 4.7 62.9 1.0 HG23 C:VAL193 4.8 52.0 1.0 O C:CYS233 4.9 65.6 1.0 HD11 C:ILE179 4.9 52.0 1.0 HD1 C:HIS191 4.9 54.8 1.0 HD2 C:HIS184 4.9 51.7 1.0 CD1 C:ILE179 4.9 53.9 1.0 HE2 C:HIS184 5.0 52.3 1.0

Zinc binding site 3 out of 3 in the Tilapia Lake Virus Polymerase in Vrna Elongation State with Additional Mode B Promoter (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 Elongation State with Additional Mode B Promoter (Transcriptase Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:110.4 occ:1.00 SG C:CYS146 2.3 71.8 1.0 SG C:CYS159 2.3 67.0 1.0 SG C:CYS163 2.3 60.9 1.0 SG C:CYS164 2.4 64.7 1.0 HB2 C:CYS164 2.5 58.0 1.0 CB C:CYS164 2.9 58.5 1.0 HB3 C:CYS159 3.2 62.4 1.0 HA C:CYS146 3.2 68.4 1.0 HB3 C:CYS146 3.3 68.4 1.0 CB C:CYS146 3.4 68.3 1.0 H C:CYS164 3.4 57.1 1.0 CB C:CYS159 3.4 62.4 1.0 N C:CYS164 3.6 56.8 1.0 HB3 C:CYS164 3.7 57.8 1.0 CB C:CYS163 3.7 53.9 1.0 HB2 C:CYS163 3.7 54.2 1.0 HE3 C:LYS170 3.7 57.6 1.0 CA C:CYS164 3.8 55.4 1.0 CA C:CYS146 3.8 67.6 1.0 HB2 C:CYS159 3.9 62.5 1.0 HD3 C:LYS170 4.0 57.8 1.0 HD2 C:LYS170 4.1 57.6 1.0 HB2 C:PHE161 4.1 56.5 1.0 H C:CYS159 4.2 62.6 1.0 C C:CYS163 4.2 54.5 1.0 HB2 C:CYS146 4.2 68.7 1.0 HA C:CYS164 4.3 57.3 1.0 CD C:LYS170 4.4 59.1 1.0 CA C:CYS163 4.5 52.1 1.0 HB3 C:CYS163 4.5 54.2 1.0 CE C:LYS170 4.5 58.8 1.0 H C:CYS163 4.5 54.0 1.0 O C:CYS146 4.6 68.2 1.0 CA C:CYS159 4.7 62.4 1.0 C C:CYS146 4.7 69.3 1.0 N C:CYS159 4.7 63.0 1.0 N C:CYS163 4.8 52.4 1.0 N C:CYS146 4.9 68.2 1.0 HD2 C:PHE161 5.0 56.7 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