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

Enzymatic activity of 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;

Other elements in 7dfh:

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

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

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 7dfh

Go back to Magnesium Binding Sites List in 7dfh
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 7dfh

Go back to Magnesium Binding Sites List in 7dfh
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 7dfh

Go back to Magnesium Binding Sites List in 7dfh
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

Reference:

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.
Page generated: Thu Nov 25 10:00:03 2021

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