Magnesium in PDB 7dfg: Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Favipiravir

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

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

Fluorine	(F)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Favipiravir (pdb code 7dfg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Favipiravir, PDB code: 7dfg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Favipiravir


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 Favipiravir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1004 b:48.2 occ:1.00 O A:POP1003 2.7 65.0 1.0 O4 A:POP1003 3.1 65.0 1.0 O A:TYR619 3.3 29.8 1.0 O1 A:POP1003 3.4 65.0 1.0 P2 A:POP1003 3.4 65.0 1.0 P1 A:POP1003 3.5 65.0 1.0 O2 A:POP1003 3.7 65.0 1.0 O5 A:POP1003 3.8 65.0 1.0 OD2 A:ASP618 4.0 35.5 1.0 OAH P:1RP1201 4.1 0.5 1.0 O A:HOH1103 4.2 34.3 1.0 OD2 A:ASP760 4.2 32.7 1.0 C A:TYR619 4.5 29.8 1.0 OD1 A:ASP618 4.6 35.5 1.0 CG A:ASP618 4.6 35.5 1.0 MG A:MG1005 4.7 48.2 1.0 O6 A:POP1003 4.8 65.0 1.0 O3 A:POP1003 4.9 65.0 1.0 N A:LYS621 5.0 35.2 1.0

Magnesium binding site 2 out of 4 in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Favipiravir


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 Favipiravir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:48.2 occ:1.00 OAH P:1RP1201 2.8 0.5 1.0 OD2 A:ASP761 2.9 29.5 1.0 OD2 A:ASP760 3.0 32.7 1.0 OD1 A:ASP760 3.1 32.7 1.0 CG A:ASP760 3.3 32.7 1.0 O3' P:U20 3.5 40.7 1.0 CG A:ASP761 3.6 29.5 1.0 PAX P:1RP1201 3.7 0.5 1.0 O A:HOH1103 3.8 34.3 1.0 OD1 A:ASP761 4.2 29.5 1.0 N A:ASP761 4.3 29.5 1.0 CB A:ASP761 4.4 29.5 1.0 CA A:ASP761 4.5 29.5 1.0 CB A:ASP760 4.6 32.7 1.0 OAG P:1RP1201 4.6 0.5 1.0 MG A:MG1004 4.7 48.2 1.0 C3' P:U20 4.8 40.7 1.0 OP1 P:U20 4.8 40.7 1.0 C A:ASP760 4.8 32.7 1.0 O5' P:1RP1201 4.8 0.5 1.0 C5' P:1RP1201 4.8 0.5 1.0 C5' P:U20 4.9 40.7 1.0

Magnesium binding site 3 out of 4 in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Favipiravir


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 Favipiravir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1007 b:40.1 occ:1.00 OD1 A:ASN209 2.1 34.1 1.0 O6 A:POP1006 2.1 50.1 1.0 O2 A:POP1006 2.2 50.1 1.0 OD2 A:ASP218 2.6 46.0 1.0 CG A:ASN209 3.2 34.1 1.0 P2 A:POP1006 3.4 50.1 1.0 P1 A:POP1006 3.4 50.1 1.0 CG A:ASP218 3.4 46.0 1.0 O A:POP1006 3.7 50.1 1.0 ND2 A:ASN209 3.7 34.1 1.0 CB A:ASP218 3.9 46.0 1.0 OD2 A:ASP208 4.0 35.0 1.0 O4 A:POP1006 4.1 50.1 1.0 CG A:ASP208 4.2 35.0 1.0 O1 A:POP1006 4.3 50.1 1.0 OD1 A:ASP208 4.3 35.0 1.0 O A:ASP208 4.3 35.0 1.0 OD1 A:ASP218 4.4 46.0 1.0 O3 A:POP1006 4.4 50.1 1.0 CB A:ASN209 4.4 34.1 1.0 O5 A:POP1006 4.5 50.1 1.0 C A:ASP208 4.6 35.0 1.0 MG A:MG1008 4.7 41.2 1.0 CA A:ASN209 4.7 34.1 1.0 N A:ASN209 4.7 34.1 1.0 CB A:ASP208 4.9 35.0 1.0

Magnesium binding site 4 out of 4 in the Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Favipiravir


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Favipiravir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1008 b:41.2 occ:1.00 OD1 A:ASP218 2.1 46.0 1.0 O4 A:POP1006 2.5 50.1 1.0 OD2 A:ASP218 2.6 46.0 1.0 CG A:ASP218 2.7 46.0 1.0 P2 A:POP1006 3.7 50.1 1.0 O6 A:POP1006 3.7 50.1 1.0 CA A:GLY220 4.1 51.0 1.0 N A:GLY220 4.1 51.0 1.0 CB A:ASP218 4.1 46.0 1.0 NZ A:LYS73 4.2 58.8 1.0 C A:GLY220 4.5 51.0 1.0 O A:ASP218 4.5 46.0 1.0 OD2 A:ASP221 4.6 51.0 1.0 N A:ASP221 4.6 51.0 1.0 O5 A:POP1006 4.7 50.1 1.0 MG A:MG1007 4.7 40.1 1.0 C A:ASP218 4.7 46.0 1.0 CA A:ASP218 4.7 46.0 1.0 O A:POP1006 4.8 50.1 1.0 O1 A:POP1006 4.9 50.1 1.0 CG A:ASP221 4.9 51.0 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.