Magnesium 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:

Zinc

(Zn)

3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Tilapia Lake Virus Polymerase in Vrna Elongation State with Additional Mode B Promoter (Transcriptase Conformation), PDB code: 8psz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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 B:Mg602 b:25.0 occ:1.00 OD2 B:ASP213 2.1 18.5 0.5 O8 B:A0I601 2.1 25.9 1.0 O B:CYS214 2.1 26.5 1.0 O6 B:A0I601 2.8 21.2 1.0 O4 B:A0I601 2.8 21.3 1.0 CG B:ASP213 3.1 17.1 0.5 OD2 B:ASP289 3.2 28.4 1.0 HB3 B:ASP213 3.2 14.1 0.5 C B:CYS214 3.3 12.0 1.0 P3 B:A0I601 3.4 42.8 1.0 H B:CYS214 3.5 14.4 1.0 HA B:THR215 3.6 15.2 1.0 OD1 B:ASP213 3.7 18.7 0.5 O7 B:A0I601 3.8 8.3 1.0 HB2 B:ASP289 3.8 15.7 1.0 H10 B:A0I601 3.8 19.4 1.0 P2 B:A0I601 3.8 40.2 1.0 H9 B:A0I601 3.8 20.3 1.0 N B:CYS214 3.9 13.1 1.0 CG B:ASP289 4.0 21.3 1.0 P1 B:A0I601 4.0 33.9 1.0 HB3 B:ASP213 4.1 13.7 0.5 CB B:ASP213 4.2 14.8 0.5 C9 B:A0I601 4.2 19.8 1.0 CB B:ASP213 4.2 13.5 0.5 CA B:CYS214 4.2 13.5 1.0 N B:THR215 4.2 10.9 1.0 N4 B:A0I601 4.3 24.6 1.0 O9 B:A0I601 4.3 26.4 1.0 CA B:THR215 4.3 18.7 1.0 CB B:ASP289 4.4 17.7 1.0 O10 B:A0I601 4.5 26.8 1.0 HO3' P:A21 4.6 18.9 1.0 O B:ASP289 4.6 29.0 1.0 HB2 B:CYS214 4.6 13.8 1.0 O3 B:A0I601 4.6 24.8 1.0 HB2 B:SER316 4.6 12.8 1.0 HB2 B:ASP213 4.7 13.6 0.5 C B:ASP213 4.7 13.0 0.5 C B:ASP213 4.7 13.2 0.5 HB3 B:ASP289 4.8 15.8 1.0 HB2 B:TYR217 4.8 13.9 1.0 CG B:ASP213 4.8 16.9 0.5 HA B:ASP213 4.9 13.5 0.5 HD2 B:LYS319 4.9 13.6 1.0 CA B:ASP213 4.9 12.6 0.5 HA B:ASP213 4.9 13.3 0.5 CA B:ASP213 4.9 13.2 0.5 OD1 B:ASP289 4.9 27.9 1.0 HB2 B:ASP213 5.0 13.8 0.5 HA B:CYS214 5.0 14.4 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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 B:Mg603 b:23.5 occ:1.00 OD1 B:ASP213 2.1 15.1 0.5 O B:HOH734 2.1 20.9 1.0 O B:HOH711 2.1 5.8 1.0 O B:HOH706 2.1 21.0 1.0 OD1 B:ASP290 2.1 22.4 1.0 O B:GLY212 2.2 10.8 1.0 CG B:ASP213 3.1 16.9 0.5 C B:GLY212 3.1 12.7 1.0 CG B:ASP290 3.2 18.9 1.0 HB2 B:ASP213 3.5 13.8 0.5 HA B:ASP290 3.5 13.2 1.0 H B:GLY212 3.6 12.0 1.0 HA B:ASP213 3.7 13.5 0.5 HA B:ASP213 3.7 13.3 0.5 OD2 B:ASP213 3.7 14.4 0.5 OD1 B:ASP213 3.8 18.7 0.5 OD2 B:ASP290 3.8 18.3 1.0 N B:GLY212 3.8 14.3 1.0 H B:PHE291 3.9 12.3 1.0 N B:ASP213 3.9 13.5 0.5 N B:ASP213 3.9 13.7 0.5 O B:HOH724 4.0 16.6 1.0 CA B:GLY212 4.1 7.8 1.0 HA B:ILE329 4.1 12.9 1.0 CA B:ASP213 4.1 13.2 0.5 CA B:ASP213 4.1 12.6 0.5 CB B:ASP213 4.1 13.5 0.5 CB B:ASP213 4.2 14.8 0.5 HG13 B:ILE329 4.2 13.1 1.0 O B:PHE291 4.3 19.8 1.0 CA B:ASP290 4.3 8.3 1.0 CB B:ASP290 4.4 13.3 1.0 CG B:ASP213 4.4 17.1 0.5 C B:ASN211 4.5 9.2 1.0 N B:PHE291 4.5 8.0 1.0 OE1 B:GLU328 4.5 23.3 1.0 OE2 B:GLU328 4.5 19.6 1.0 H B:ASN330 4.6 13.4 1.0 H B:ASP213 4.6 13.5 0.5 H B:ASP213 4.7 13.4 0.5 O B:GLU328 4.7 11.5 1.0 HA2 B:GLY212 4.7 11.6 1.0 HB2 B:ASP213 4.7 13.6 0.5 HA3 B:GLY212 4.7 10.1 1.0 HB3 B:ASN211 4.8 10.8 1.0 C B:ASP290 4.8 12.7 1.0 HB3 B:ASP213 4.8 14.1 0.5 HA B:ASN211 4.9 9.0 1.0 CD B:GLU328 4.9 22.3 1.0 HB3 B:ASP290 4.9 14.3 1.0 O B:ASN211 4.9 10.1 1.0 HB2 B:ASP290 4.9 13.6 1.0 O B:ASP289 5.0 29.0 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