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Magnesium in PDB 7doi: Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Penciclovir.

Enzymatic activity of Structure of Covid-19 Rna-Dependent Rna Polymerase Bound to Penciclovir.

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

Other elements in 7doi:

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

Magnesium binding site 1 out of 4 in 7doi

Go back to Magnesium Binding Sites List in 7doi
Magnesium binding site 1 out of 4 in the Structure of Covid-19 Rna-Dependent Rna Polymerase 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 Bound to Penciclovir. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:62.0
occ:1.00
O A:TYR619 3.4 33.1 1.0
O5 P:HCU1201 3.4 0.5 1.0
O A:POP1003 3.5 71.2 1.0
O P:HOH1302 3.5 46.6 1.0
O4 A:POP1003 3.8 71.2 1.0
C9 P:HCU1201 3.8 0.5 1.0
OD2 A:ASP760 3.9 33.4 1.0
CB A:CYS622 4.0 37.2 1.0
O1 A:POP1003 4.2 71.2 1.0
OD1 A:ASP760 4.3 33.4 1.0
O3 P:HCU1201 4.3 0.5 1.0
P2 A:POP1003 4.3 71.2 1.0
CG A:ASP760 4.4 33.4 1.0
O P:HOH1301 4.4 48.2 1.0
P1 P:HCU1201 4.5 0.5 1.0
O A:HOH1101 4.5 30.0 1.0
OD1 A:ASP618 4.5 38.0 1.0
C A:TYR619 4.6 33.1 1.0
P1 A:POP1003 4.6 71.2 1.0
N A:CYS622 4.6 37.2 1.0
CB A:TYR619 4.9 33.1 1.0
N A:TYR619 5.0 33.1 1.0

Magnesium binding site 2 out of 4 in 7doi

Go back to Magnesium Binding Sites List in 7doi
Magnesium binding site 2 out of 4 in the Structure of Covid-19 Rna-Dependent Rna Polymerase 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 Bound to Penciclovir. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1005

b:34.0
occ:1.00
OD2 A:ASP761 2.7 28.6 1.0
OE2 A:GLU811 3.3 33.4 1.0
N A:SER814 3.5 32.0 1.0
CG A:ASP761 3.6 28.6 1.0
OP1 P:U20 3.6 46.3 1.0
OD1 A:ASP761 3.7 28.6 1.0
O P:HOH1301 3.7 48.2 1.0
N A:CYS813 3.8 33.1 1.0
CA A:CYS813 4.1 33.1 1.0
CG A:GLU811 4.1 33.4 1.0
CD A:GLU811 4.2 33.4 1.0
CA A:SER814 4.2 32.0 1.0
C A:CYS813 4.2 33.1 1.0
CB A:SER814 4.7 32.0 1.0
C A:PHE812 4.7 29.0 1.0
CA A:PHE812 4.9 29.0 1.0
CB A:ASP761 5.0 28.6 1.0

Magnesium binding site 3 out of 4 in 7doi

Go back to Magnesium Binding Sites List in 7doi
Magnesium binding site 3 out of 4 in the Structure of Covid-19 Rna-Dependent Rna Polymerase 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 Bound to Penciclovir. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1006

b:30.0
occ:1.00
OD2 A:ASP218 2.0 40.9 1.0
O4 A:POP1008 2.1 50.1 1.0
CG A:ASP218 3.0 40.9 1.0
P2 A:POP1008 3.0 50.1 1.0
O6 A:POP1008 3.1 50.1 1.0
OD1 A:ASP218 3.2 40.9 1.0
O2 A:POP1008 4.1 50.1 1.0
O5 A:POP1008 4.1 50.1 1.0
O A:POP1008 4.2 50.1 1.0
MG A:MG1007 4.2 30.0 1.0
CB A:ASP218 4.3 40.9 1.0
NZ A:LYS73 4.6 57.4 1.0
N A:GLY220 4.7 46.9 1.0
CA A:GLY220 4.7 46.9 1.0
P1 A:POP1008 4.9 50.1 1.0
OD2 A:ASP221 5.0 49.3 1.0

Magnesium binding site 4 out of 4 in 7doi

Go back to Magnesium Binding Sites List in 7doi
Magnesium binding site 4 out of 4 in the Structure of Covid-19 Rna-Dependent Rna Polymerase 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 Bound to Penciclovir. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1007

b:30.0
occ:1.00
OD1 A:ASN209 2.1 32.2 1.0
O6 A:POP1008 2.2 50.1 1.0
O2 A:POP1008 2.5 50.1 1.0
CG A:ASN209 3.3 32.2 1.0
OD2 A:ASP218 3.3 40.9 1.0
P1 A:POP1008 3.5 50.1 1.0
O3 A:POP1008 3.6 50.1 1.0
P2 A:POP1008 3.6 50.1 1.0
ND2 A:ASN209 3.8 32.2 1.0
OD2 A:ASP208 3.9 31.7 1.0
CG A:ASP218 4.0 40.9 1.0
O A:POP1008 4.0 50.1 1.0
MG A:MG1006 4.2 30.0 1.0
CB A:ASP218 4.2 40.9 1.0
O A:ASP208 4.2 31.7 1.0
CG A:ASP208 4.3 31.7 1.0
O4 A:POP1008 4.4 50.1 1.0
CB A:ASN209 4.5 32.2 1.0
C A:ASP208 4.6 31.7 1.0
CA A:ASN209 4.6 32.2 1.0
O5 A:POP1008 4.7 50.1 1.0
OD1 A:ASP208 4.7 31.7 1.0
N A:ASN209 4.8 32.2 1.0
O1 A:POP1008 4.8 50.1 1.0
OD1 A:ASP218 5.0 40.9 1.0
CB A:ASP208 5.0 31.7 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: Wed Oct 2 15:56:34 2024

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