Magnesium in PDB 7dfh: Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin

All present enzymatic activity of Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin:
2.7.7.48;

The structure of Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin (pdb code 7dfh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin, PDB code: 7dfh:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:61.6 occ:1.00 O6 A:POP1006 2.3 81.7 1.0 OD1 A:ASN209 2.8 56.5 1.0 O2 A:POP1006 3.0 81.7 1.0 O A:POP1006 3.0 81.7 1.0 P2 A:POP1006 3.3 81.7 1.0 P1 A:POP1006 3.7 81.7 1.0 OD2 A:ASP218 3.7 71.3 1.0 NZ A:LYS50 3.9 75.6 1.0 CG A:ASN209 4.0 56.5 1.0 O A:ASP208 4.1 53.4 1.0 CE1 A:PHE35 4.1 56.2 1.0 O5 A:POP1006 4.3 81.7 1.0 O4 A:POP1006 4.3 81.7 1.0 OD2 A:ASP208 4.3 53.4 1.0 CG A:ASP208 4.4 53.4 1.0 CD1 A:PHE35 4.4 56.2 1.0 C A:ASP208 4.5 53.4 1.0 CG A:ASP218 4.5 71.3 1.0 CB A:ASP208 4.6 53.4 1.0 O3 A:POP1006 4.7 81.7 1.0 O1 A:POP1006 4.7 81.7 1.0 OD1 A:ASP208 4.7 53.4 1.0 CB A:ASP218 4.8 71.3 1.0 CE A:LYS50 4.8 75.6 1.0 N A:ASN209 4.8 56.5 1.0 ND2 A:ASN209 4.8 56.5 1.0 CA A:ASN209 4.8 56.5 1.0 OH A:TYR217 5.0 62.7 1.0

Magnesium binding site 2 out of 3 in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1004 b:87.7 occ:1.00 OD2 A:ASP760 2.4 52.0 1.0 O2P P:RVP1201 2.7 0.5 1.0 O A:TYR619 3.5 47.9 1.0 CG A:ASP760 3.6 52.0 1.0 O6 A:POP1007 3.7 112.1 1.0 O A:POP1007 3.7 112.1 1.0 P P:RVP1201 3.9 0.5 1.0 O4 A:POP1007 3.9 112.1 1.0 P2 A:POP1007 4.0 112.1 1.0 O A:HOH1102 4.1 73.9 1.0 N A:TYR619 4.2 47.9 1.0 O5' P:RVP1201 4.2 0.5 1.0 OD1 A:ASP760 4.2 52.0 1.0 MG A:MG1005 4.5 80.7 1.0 C A:TYR619 4.5 47.9 1.0 C5' P:RVP1201 4.6 0.5 1.0 O3 A:POP1007 4.6 112.1 1.0 CB A:ASP760 4.7 52.0 1.0 CA A:TYR619 4.7 47.9 1.0 P1 A:POP1007 4.7 112.1 1.0 CB A:TYR619 4.7 47.9 1.0 CB A:CYS622 4.8 57.5 1.0 O1 A:POP1007 4.9 112.1 1.0 CB A:ASP618 4.9 53.3 1.0 O3' P:G20 5.0 79.0 1.0 O1P P:RVP1201 5.0 0.5 1.0

Magnesium binding site 3 out of 3 in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Ribavirin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:80.7 occ:1.00 O2P P:RVP1201 3.6 0.5 1.0 CB A:ASP761 3.7 49.1 1.0 CG A:ASP761 3.7 49.1 1.0 OD2 A:ASP761 3.8 49.1 1.0 O A:HOH1102 4.0 73.9 1.0 OD1 A:ASP760 4.1 52.0 1.0 OP1 P:G20 4.2 79.0 1.0 OD1 A:ASP761 4.3 49.1 1.0 O3' P:G20 4.3 79.0 1.0 CA A:ASP761 4.3 49.1 1.0 O5' P:G20 4.4 79.0 1.0 C5' P:G20 4.4 79.0 1.0 MG A:MG1004 4.5 87.7 1.0 P P:RVP1201 4.6 0.5 1.0 OD2 A:ASP760 4.6 52.0 1.0 N A:ASP761 4.6 49.1 1.0 CG A:ASP760 4.7 52.0 1.0 C4' P:G20 4.9 79.0 1.0 P P:G20 5.0 79.0 1.0

W.Yin, X.Luan, Z.Li, Y.Xie, Z.Zhou, J.Liu, M.Gao, X.Wang, F.Zhou, Q.Wang, Q.Wang, D.Shen, Y.Zhang, G.Tian, H.Aisa, D.Wei, Y.Jiang, G.Xiao, H.Jiang, L.Zhang, X.Yu, J.Shen, S.Zhang, H.Xu. Structural Basis For Repurpose and Design of Nucleotide Drugs For Treating Covid-19 To Be Published.