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Magnesium in PDB 7dok: Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir

Enzymatic activity of Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir

All present enzymatic activity of Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir:
2.7.7.48;

Other elements in 7dok:

The structure of Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir 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 (Extended Conformation) Bound to Penciclovir (pdb code 7dok). 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 (Extended Conformation) Bound to Penciclovir, PDB code: 7dok:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7dok

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Magnesium binding site 1 out of 4 in the Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir


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 (Extended Conformation) Bound to Penciclovir within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg1202

b:41.1
occ:1.00
 O5 P:HCU1201 2.7 0.5 1.0
OD2 A:ASP760 3.7 26.0 1.0
P1 P:HCU1201 3.7 0.5 1.0
O3' P:U20 3.7 46.3 1.0
OP1 P:U20 4.1 46.3 1.0
MG A:MG1004 4.2 30.0 1.0
OD2 A:ASP761 4.3 24.2 1.0
C5' P:U20 4.3 46.3 1.0
CG A:ASP761 4.4 24.2 1.0
CB A:ASP761 4.4 24.2 1.0
O4 P:HCU1201 4.5 0.5 1.0
O5' P:U20 4.6 46.3 1.0
C3' P:U20 4.6 46.3 1.0
CG A:ASP760 4.7 26.0 1.0
O3 P:HCU1201 4.7 0.5 1.0
C4' P:U20 4.8 46.3 1.0
OD1 A:ASP761 4.9 24.2 1.0
P P:U20 5.0 46.3 1.0

Magnesium binding site 2 out of 4 in 7dok

Go back to Magnesium Binding Sites List in 7dok
Magnesium binding site 2 out of 4 in the Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir


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 (Extended Conformation) Bound to Penciclovir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:30.0
occ:1.00
 O A:HOH1101 2.9 52.3 1.0
O4 A:POP1003 3.1 61.4 1.0
O5 P:HCU1201 3.3 0.5 1.0
O A:TYR619 3.5 26.0 1.0
O5 A:POP1003 3.7 61.4 1.0
OD2 A:ASP760 3.8 26.0 1.0
C9 P:HCU1201 3.9 0.5 1.0
OD1 A:ASP760 3.9 26.0 1.0
P2 A:POP1003 4.0 61.4 1.0
CG A:ASP760 4.0 26.0 1.0
CB A:CYS622 4.1 28.2 1.0
MG P:MG1202 4.2 41.1 1.0
OD2 A:ASP618 4.2 31.6 1.0
O3 P:HCU1201 4.3 0.5 1.0
P1 P:HCU1201 4.4 0.5 1.0
C A:TYR619 4.6 26.0 1.0
CB A:TYR619 4.8 26.0 1.0
O1 A:POP1003 4.8 61.4 1.0
N A:TYR619 4.9 26.0 1.0
N A:CYS622 5.0 28.2 1.0

Magnesium binding site 3 out of 4 in 7dok

Go back to Magnesium Binding Sites List in 7dok
Magnesium binding site 3 out of 4 in the Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir


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 (Extended Conformation) Bound to Penciclovir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1005

b:30.0
occ:1.00
 O6 A:POP1007 1.7 50.1 1.0
OD2 A:ASP218 2.1 58.5 1.0
OD1 A:ASP218 2.1 58.5 1.0
CG A:ASP218 2.4 58.5 1.0
P2 A:POP1007 2.7 50.1 1.0
O5 A:POP1007 2.8 50.1 1.0
O4 A:POP1007 3.7 50.1 1.0
MG A:MG1006 3.8 30.0 1.0
CB A:ASP218 3.9 58.5 1.0
O1 A:POP1007 3.9 50.1 1.0
O A:POP1007 3.9 50.1 1.0
O2 A:POP1007 4.0 50.1 1.0
NZ A:LYS73 4.2 83.0 1.0
P1 A:POP1007 4.2 50.1 1.0
O A:ASP218 4.7 58.5 1.0
CA A:ASP218 4.7 58.5 1.0
CA A:GLY220 4.7 65.6 1.0
N A:GLY220 4.8 65.6 1.0
OD1 A:ASN209 4.8 44.1 1.0
C A:ASP218 4.9 58.5 1.0

Magnesium binding site 4 out of 4 in 7dok

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Magnesium binding site 4 out of 4 in the Structure of Covid-19 Rna-Dependent Rna Polymerase (Extended Conformation) Bound to Penciclovir


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 (Extended Conformation) Bound to Penciclovir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1006

b:30.0
occ:1.00
 O2 A:POP1007 1.9 50.1 1.0
OD1 A:ASN209 2.1 44.1 1.0
OD2 A:ASP218 2.3 58.5 1.0
O5 A:POP1007 2.5 50.1 1.0
CG A:ASN209 3.3 44.1 1.0
CG A:ASP218 3.3 58.5 1.0
P1 A:POP1007 3.3 50.1 1.0
P2 A:POP1007 3.6 50.1 1.0
O A:POP1007 3.7 50.1 1.0
CB A:ASP218 3.8 58.5 1.0
MG A:MG1005 3.8 30.0 1.0
O A:ASP208 3.9 36.3 1.0
O6 A:POP1007 4.0 50.1 1.0
ND2 A:ASN209 4.0 44.1 1.0
OD2 A:ASP208 4.0 36.3 1.0
O1 A:POP1007 4.2 50.1 1.0
OD1 A:ASP218 4.4 58.5 1.0
O3 A:POP1007 4.4 50.1 1.0
C A:ASP208 4.4 36.3 1.0
CG A:ASP208 4.4 36.3 1.0
CB A:ASN209 4.4 44.1 1.0
CA A:ASN209 4.5 44.1 1.0
N A:ASN209 4.6 44.1 1.0
CB A:ASP208 4.9 36.3 1.0
OD1 A:ASP208 4.9 36.3 1.0
O4 A:POP1007 4.9 50.1 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 Aug 14 04:13:06 2025

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