Magnesium 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:

Zinc

(Zn)

3 atoms

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

Magnesium binding site 1 out of 2 in the Tilapia Lake Virus Polymerase in Vrna Initiation State (Replicase 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 Initiation State (Replicase Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:83.3 occ:1.00 OD1 B:ASP213 2.0 57.2 1.0 O2A F:CTP1 2.1 71.2 1.0 OD1 B:ASP289 2.6 59.9 1.0 CG B:ASP213 3.0 56.6 1.0 OD2 B:ASP213 3.3 54.5 1.0 PA F:CTP1 3.4 84.1 1.0 CG B:ASP289 3.5 48.2 1.0 OD1 B:ASP290 3.5 59.7 1.0 HB2 B:ASP290 3.5 53.1 1.0 OD2 B:ASP289 3.6 53.8 1.0 H5'2 F:CTP1 3.7 64.2 1.0 HZ1 B:LYS319 3.8 46.0 1.0 O1A F:CTP1 3.9 71.3 1.0 HZ2 B:LYS319 3.9 46.1 1.0 CG B:ASP290 4.0 63.2 1.0 O5' F:CTP1 4.2 79.2 1.0 CB B:ASP290 4.2 56.7 1.0 NZ B:LYS319 4.3 53.0 1.0 CB B:ASP213 4.3 50.7 1.0 MG F:MG101 4.3 70.3 1.0 HB2 B:ASP213 4.3 49.5 1.0 C5' F:CTP1 4.3 64.3 1.0 HA B:ASP290 4.5 50.6 1.0 H5'1 F:CTP1 4.5 64.0 1.0 HZ3 B:LYS319 4.5 45.5 1.0 O3A F:CTP1 4.6 66.5 1.0 N B:ASP290 4.6 50.3 1.0 CA B:ASP290 4.7 42.2 1.0 HA B:ASP213 4.7 50.4 1.0 H B:ASP290 4.7 53.6 1.0 C B:ASP289 4.9 43.9 1.0 HB3 B:ASP213 4.9 50.2 1.0 CB B:ASP289 4.9 49.9 1.0 OD2 B:ASP290 4.9 60.7 1.0

Magnesium binding site 2 out of 2 in the Tilapia Lake Virus Polymerase in Vrna Initiation State (Replicase 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 Initiation State (Replicase Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg101 b:70.3 occ:1.00 OD2 B:ASP213 1.8 54.5 1.0 O2B F:CTP1 1.9 65.5 1.0 O B:CYS214 2.1 59.5 1.0 OD2 B:ASP289 2.2 53.8 1.0 O2G F:CTP1 2.4 70.5 1.0 CG B:ASP213 2.9 56.6 1.0 PB F:CTP1 3.0 74.8 1.0 C B:CYS214 3.1 49.4 1.0 O2A F:CTP1 3.1 71.2 1.0 O3A F:CTP1 3.2 66.5 1.0 H B:CYS214 3.2 50.4 1.0 HZ1 B:LYS319 3.4 46.0 1.0 HA B:THR215 3.4 52.3 1.0 O3B F:CTP1 3.4 72.1 1.0 CG B:ASP289 3.4 48.2 1.0 PG F:CTP1 3.4 74.8 1.0 N B:CYS214 3.6 44.2 1.0 OD1 B:ASP213 3.6 57.2 1.0 H5'1 F:CTP1 3.7 64.0 1.0 PA F:CTP1 3.8 84.1 1.0 HB3 B:ASP213 3.9 50.2 1.0 CA B:CYS214 3.9 44.0 1.0 N B:THR215 3.9 45.7 1.0 CB B:ASP213 4.0 50.7 1.0 HE3 B:LYS319 4.0 44.8 1.0 O3G F:CTP1 4.0 60.1 1.0 OD1 B:ASP289 4.1 59.9 1.0 CA B:THR215 4.1 45.3 1.0 NZ B:LYS319 4.2 53.0 1.0 HB2 B:TYR217 4.2 46.8 1.0 C B:ASP213 4.3 46.5 1.0 MG B:MG601 4.3 83.3 1.0 HB2 B:CYS214 4.3 51.2 1.0 HB2 B:ASP289 4.3 51.7 1.0 HZ2 B:LYS319 4.3 46.1 1.0 O1B F:CTP1 4.4 72.2 1.0 HB2 B:SER316 4.4 47.9 1.0 C5' F:CTP1 4.4 64.3 1.0 H B:LYS216 4.5 55.0 1.0 CB B:ASP289 4.5 49.9 1.0 CE B:LYS319 4.5 48.3 1.0 H5'2 F:CTP1 4.5 64.2 1.0 H B:TYR217 4.5 47.2 1.0 HE2 B:LYS319 4.6 45.4 1.0 CA B:ASP213 4.6 46.3 1.0 O5' F:CTP1 4.6 79.2 1.0 HA B:CYS214 4.7 50.0 1.0 HA B:ASP213 4.7 50.4 1.0 CB B:CYS214 4.7 49.9 1.0 H B:THR215 4.7 52.9 1.0 O1G F:CTP1 4.7 70.9 1.0 HB2 B:ASP213 4.8 49.5 1.0 C B:THR215 4.8 56.2 1.0 N B:LYS216 4.8 55.9 1.0 HB3 B:ASP289 4.8 51.4 1.0 HZ3 B:LYS319 4.8 45.5 1.0 O1A F:CTP1 5.0 71.3 1.0 HB3 B:SER316 5.0 47.4 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