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Zinc in PDB 8gwo: A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors

Enzymatic activity of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors

All present enzymatic activity of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors:
2.7.7.48;

Zinc Binding Sites:

The binding sites of Zinc atom in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors (pdb code 8gwo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors, PDB code: 8gwo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8gwo

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Zinc binding site 1 out of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:103.2
occ:1.00
 CE1 A:HIS295 0.9 67.4 1.0
ND1 A:HIS295 1.8 67.4 1.0
NE2 A:HIS295 2.1 67.4 1.0
SG A:CYS301 2.3 64.6 1.0
SG A:CYS310 2.3 63.7 1.0
SG A:CYS306 2.3 64.6 1.0
CG A:HIS295 3.0 67.4 1.0
CD2 A:HIS295 3.1 67.4 1.0
O A:CYS306 3.3 64.6 1.0
CB A:CYS310 3.6 63.7 1.0
CB A:CYS301 3.6 64.6 1.0
CB A:CYS306 3.7 64.6 1.0
C A:CYS306 3.8 64.6 1.0
CA A:CYS301 4.0 64.6 1.0
CA A:CYS306 4.3 64.6 1.0
CB A:HIS295 4.3 67.4 1.0
N A:HIS295 4.4 67.4 1.0
O A:HIS295 4.5 67.4 1.0
N A:ILE307 4.6 59.1 1.0
N A:CYS301 4.8 64.6 1.0
CA A:CYS310 4.8 63.7 1.0
N A:CYS310 4.8 63.7 1.0
CA A:HIS295 4.8 67.4 1.0

Zinc binding site 2 out of 8 in 8gwo

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Zinc binding site 2 out of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:135.6
occ:1.00
 ND1 A:HIS642 2.1 81.1 1.0
CE1 A:HIS642 2.2 81.1 1.0
SG A:CYS646 2.3 97.7 1.0
SG A:CYS487 2.3 84.9 1.0
SG A:CYS645 2.3 102.9 1.0
CG A:HIS642 3.2 81.1 1.0
NE2 A:HIS642 3.3 81.1 1.0
CB A:CYS646 3.3 97.7 1.0
CB A:CYS645 3.5 102.9 1.0
CB A:CYS487 3.7 84.9 1.0
CD2 A:HIS642 3.7 81.1 1.0
CE1 A:PHE571 3.8 63.7 1.0
N A:CYS646 3.8 97.7 1.0
CB A:HIS642 4.1 81.1 1.0
C A:CYS645 4.1 102.9 1.0
CA A:CYS646 4.2 97.7 1.0
NZ A:LYS532 4.2 62.3 1.0
N A:CYS487 4.3 84.9 1.0
CD1 A:PHE571 4.3 63.7 1.0
CA A:CYS645 4.4 102.9 1.0
CA A:CYS487 4.5 84.9 1.0
O A:CYS645 4.7 102.9 1.0
CZ A:PHE571 4.7 63.7 1.0

Zinc binding site 3 out of 8 in 8gwo

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Zinc binding site 3 out of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn701

b:268.0
occ:1.00
 CE1 F:HIS39 1.4 207.1 1.0
ND1 F:HIS39 2.1 207.1 1.0
NE2 F:HIS33 2.1 202.3 1.0
SG F:CYS16 2.3 191.2 1.0
SG F:CYS19 2.3 207.7 1.0
NE2 F:HIS39 2.5 207.1 1.0
CB F:CYS19 2.7 207.7 1.0
CE1 F:HIS33 3.0 202.3 1.0
CD2 F:HIS33 3.1 202.3 1.0
CG F:HIS39 3.2 207.1 1.0
CD2 F:HIS39 3.4 207.1 1.0
CB F:CYS16 3.4 191.2 1.0
CA F:CYS19 3.6 207.7 1.0
CB F:ALA110 4.0 230.9 1.0
ND1 F:HIS33 4.2 202.3 1.0
N F:CYS19 4.2 207.7 1.0
CG F:HIS33 4.2 202.3 1.0
CB F:HIS39 4.5 207.1 1.0
CZ F:PHE106 4.7 219.5 1.0
CA F:CYS16 4.8 191.2 1.0
CE2 F:PHE106 4.9 219.5 1.0
C F:CYS19 4.9 207.7 1.0
C F:ALA18 5.0 198.3 1.0

Zinc binding site 4 out of 8 in 8gwo

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Zinc binding site 4 out of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn702

b:294.9
occ:1.00
 SG F:CYS26 2.3 177.3 1.0
SG F:CYS8 2.3 193.9 1.0
SG F:CYS5 2.3 172.8 1.0
SG F:CYS29 2.3 184.4 1.0
CB F:CYS8 2.9 193.9 1.0
CB F:CYS26 3.0 177.3 1.0
CB F:CYS29 3.2 184.4 1.0
N F:CYS26 3.3 177.3 1.0
CB F:CYS5 3.6 172.8 1.0
CA F:CYS26 3.6 177.3 1.0
N F:CYS8 3.8 193.9 1.0
CA F:CYS8 4.0 193.9 1.0
C F:CYS26 4.2 177.3 1.0
O F:CYS26 4.2 177.3 1.0
N F:CYS29 4.3 184.4 1.0
CA F:CYS29 4.3 184.4 1.0
C F:LEU7 4.5 179.1 1.0
C F:LEU25 4.5 161.5 1.0
OG F:SER10 4.7 168.0 1.0
CB F:LEU7 4.8 179.1 1.0
N F:LEU7 4.8 179.1 1.0
CA F:LEU25 4.9 161.5 1.0
C F:CYS8 4.9 193.9 1.0
CA F:CYS5 4.9 172.8 1.0
CA F:LEU7 4.9 179.1 1.0

Zinc binding site 5 out of 8 in 8gwo

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Zinc binding site 5 out of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn703

b:334.3
occ:1.00
 CB F:CYS50 1.9 225.1 1.0
ND1 F:HIS75 2.1 224.5 1.0
SG F:CYS50 2.3 225.1 1.0
SG F:CYS55 2.3 221.2 1.0
SG F:CYS72 2.3 223.8 1.0
CB F:CYS72 2.5 223.8 1.0
CE1 F:HIS75 2.7 224.5 1.0
CG2 F:VAL57 3.3 234.1 1.0
CA F:CYS50 3.4 225.1 1.0
CG F:HIS75 3.4 224.5 1.0
CB F:CYS55 3.4 221.2 1.0
N F:CYS72 3.6 223.8 1.0
CA F:CYS72 3.6 223.8 1.0
CG1 F:VAL57 3.8 234.1 1.0
NE2 F:HIS75 3.9 224.5 1.0
N F:CYS50 4.0 225.1 1.0
CB F:HIS75 4.1 224.5 1.0
CB F:VAL57 4.1 234.1 1.0
C F:TYR71 4.2 197.8 1.0
C F:CYS50 4.2 225.1 1.0
CD2 F:HIS75 4.3 224.5 1.0
O F:CYS50 4.4 225.1 1.0
C F:CYS72 4.5 223.8 1.0
OG F:SER74 4.7 226.4 1.0
CA F:CYS55 4.7 221.2 1.0
N F:VAL57 4.7 234.1 1.0
O F:TYR71 4.7 197.8 1.0
O F:CYS72 4.8 223.8 1.0
CA F:TYR71 4.8 197.8 1.0
N F:ASP56 4.8 230.8 1.0
N F:HIS75 5.0 224.5 1.0

Zinc binding site 6 out of 8 in 8gwo

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Zinc binding site 6 out of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn701

b:257.0
occ:1.00
 NE2 E:HIS33 2.0 172.5 1.0
ND1 E:HIS39 2.0 175.2 1.0
CE1 E:HIS39 2.1 175.2 1.0
SG E:CYS16 2.3 141.2 1.0
SG E:CYS19 2.3 152.9 1.0
CE1 E:HIS33 2.6 172.5 1.0
NE2 E:HIS39 3.0 175.2 1.0
CG E:HIS39 3.0 175.2 1.0
CD2 E:HIS33 3.2 172.5 1.0
CB E:CYS16 3.4 141.2 1.0
CD2 E:HIS39 3.5 175.2 1.0
CB E:CYS19 3.7 152.9 1.0
ND1 E:HIS33 3.8 172.5 1.0
CB E:HIS39 4.0 175.2 1.0
N E:CYS19 4.1 152.9 1.0
CG E:HIS33 4.1 172.5 1.0
CB E:ALA110 4.4 184.0 1.0
CA E:CYS19 4.4 152.9 1.0
CE1 E:PHE106 4.5 170.9 1.0
C E:ALA18 4.7 155.6 1.0
CA E:CYS16 4.7 141.2 1.0
O E:CYS16 4.8 141.2 1.0
C E:CYS16 4.9 141.2 1.0

Zinc binding site 7 out of 8 in 8gwo

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Zinc binding site 7 out of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn702

b:245.1
occ:1.00
 CB E:CYS26 1.6 163.8 1.0
SG E:CYS8 2.3 162.7 1.0
SG E:CYS29 2.3 171.7 1.0
SG E:CYS26 2.3 163.8 1.0
SG E:CYS5 2.3 145.3 1.0
CB E:CYS8 3.0 162.7 1.0
CA E:CYS26 3.1 163.8 1.0
N E:CYS26 3.6 163.8 1.0
CB E:CYS5 3.7 145.3 1.0
N E:CYS8 3.7 162.7 1.0
C E:CYS26 3.9 163.8 1.0
CA E:CYS8 4.0 162.7 1.0
CB E:CYS29 4.0 171.7 1.0
O E:CYS26 4.3 163.8 1.0
CB E:SER10 4.6 136.6 1.0
N E:CYS29 4.6 171.7 1.0
OG E:SER10 4.7 136.6 1.0
N E:CYS27 4.8 156.9 1.0
C E:LEU7 4.8 152.9 1.0
CB E:LEU7 4.8 152.9 1.0
C E:CYS8 4.8 162.7 1.0
N E:GLY99 4.8 199.2 1.0
CA E:GLY99 4.9 199.2 1.0
C E:LEU25 4.9 131.7 1.0
N E:LEU7 4.9 152.9 1.0
CA E:CYS29 4.9 171.7 1.0
N E:SER10 5.0 136.6 1.0

Zinc binding site 8 out of 8 in 8gwo

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Zinc binding site 8 out of 8 in the A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn703

b:349.5
occ:1.00
 ND1 E:HIS75 2.1 217.8 1.0
SG E:CYS55 2.3 236.6 1.0
SG E:CYS50 2.3 209.1 1.0
SG E:CYS72 2.3 208.9 1.0
CE1 E:HIS75 2.6 217.8 1.0
OG E:SER74 3.1 214.1 1.0
CG E:HIS75 3.3 217.8 1.0
CB E:CYS55 3.3 236.6 1.0
CB E:CYS50 3.5 209.1 1.0
NE2 E:HIS75 3.8 217.8 1.0
CB E:CYS72 3.8 208.9 1.0
N E:CYS72 4.0 208.9 1.0
CB E:HIS75 4.0 217.8 1.0
CD2 E:HIS75 4.1 217.8 1.0
CG2 E:VAL57 4.2 207.2 1.0
CB E:ALA52 4.3 227.0 1.0
N E:HIS75 4.4 217.8 1.0
CB E:SER74 4.4 214.1 1.0
CA E:CYS72 4.4 208.9 1.0
CG1 E:VAL57 4.7 207.2 1.0
CA E:CYS55 4.8 236.6 1.0
C E:SER74 4.8 214.1 1.0
CA E:CYS50 4.8 209.1 1.0
CA E:HIS75 4.9 217.8 1.0
C E:CYS72 4.9 208.9 1.0
O E:CYS50 4.9 209.1 1.0
N E:SER74 5.0 214.1 1.0
CA E:SER74 5.0 214.1 1.0

Reference:

L.Yan, Y.Huang, J.Ge, Z.Liu, P.Lu, B.Huang, S.Gao, J.Wang, L.Tan, S.Ye, F.Yu, W.Lan, S.Xu, F.Zhou, L.Shi, L.W.Guddat, Y.Gao, Z.Rao, Z.Lou. A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analog Inhibitors. Cell V. 185 4347 2022.
ISSN: ISSN 1097-4172
PubMed: 36335936
DOI: 10.1016/J.CELL.2022.09.037
Page generated: Thu Oct 31 06:49:46 2024

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