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Zinc in PDB 8gwb: 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;

Other elements in 8gwb:

The structure of A Mechanism For Sars-Cov-2 Rna Capping and Its Inhibition By Nucleotide Analogue Inhibitors also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

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 8gwb). 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: 8gwb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8gwb

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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:91.1
occ:1.00
 CD2 A:HIS295 2.2 43.8 1.0
NE2 A:HIS295 2.3 37.8 1.0
SG A:CYS301 2.3 31.4 1.0
SG A:CYS306 2.3 42.6 1.0
SG A:CYS310 2.3 52.0 1.0
CG A:HIS295 2.6 42.5 1.0
CE1 A:HIS295 2.7 43.8 1.0
ND1 A:HIS295 2.8 46.7 1.0
CB A:HIS295 3.5 38.5 1.0
CB A:CYS301 3.5 32.0 1.0
O A:CYS306 3.6 50.3 1.0
CB A:CYS310 3.7 55.8 1.0
CB A:CYS306 3.8 37.8 1.0
CA A:CYS301 3.9 31.2 1.0
N A:HIS295 3.9 31.9 1.0
C A:CYS306 4.2 40.6 1.0
O A:THR293 4.2 37.0 1.0
CA A:HIS295 4.3 36.5 1.0
CA A:CYS306 4.5 36.0 1.0
C A:TYR294 4.7 26.8 1.0
N A:CYS301 4.8 32.0 1.0
CA A:TYR294 4.8 25.5 1.0
N A:LEU302 4.9 33.6 1.0
ND1 A:HIS309 4.9 43.4 1.0
C A:THR293 4.9 31.5 1.0
CA A:CYS310 4.9 50.4 1.0
C A:CYS301 5.0 33.2 1.0
N A:ILE307 5.0 35.7 1.0

Zinc binding site 2 out of 8 in 8gwb

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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:84.3
occ:1.00
 ND1 A:HIS642 2.0 29.7 1.0
SG A:CYS487 2.3 35.7 1.0
SG A:CYS646 2.3 53.1 1.0
SG A:CYS645 2.3 53.6 1.0
CE1 A:HIS642 2.4 29.4 1.0
CG A:HIS642 3.1 27.7 1.0
CB A:CYS646 3.4 51.5 1.0
NE2 A:HIS642 3.5 28.1 1.0
CB A:CYS487 3.5 38.0 1.0
CB A:CYS645 3.7 44.5 1.0
CE1 A:PHE571 3.7 36.2 1.0
CD2 A:HIS642 3.8 27.0 1.0
N A:CYS646 3.9 52.2 1.0
N A:CYS487 3.9 40.8 1.0
CB A:HIS642 3.9 31.3 1.0
C A:CYS645 4.1 50.3 1.0
CD1 A:PHE571 4.1 36.6 1.0
CA A:CYS646 4.1 50.4 1.0
CA A:CYS487 4.2 38.5 1.0
CA A:CYS645 4.5 46.8 1.0
O A:CYS645 4.5 51.3 1.0
NZ A:LYS532 4.5 43.3 1.0
CZ A:PHE571 4.8 29.4 1.0
C A:GLY486 4.9 32.5 1.0
CA A:HIS642 4.9 28.3 1.0

Zinc binding site 3 out of 8 in 8gwb

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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:237.5
occ:1.00
 CE1 F:HIS39 1.6 162.3 1.0
NE2 F:HIS33 2.1 180.8 1.0
ND1 F:HIS39 2.1 162.6 1.0
SG F:CYS16 2.3 180.6 1.0
SG F:CYS19 2.3 182.1 1.0
CB F:CYS19 2.5 180.8 1.0
NE2 F:HIS39 2.6 160.9 1.0
CE1 F:HIS33 3.0 180.0 1.0
CD2 F:HIS33 3.2 180.5 1.0
CG F:HIS39 3.2 161.4 1.0
CD2 F:HIS39 3.4 160.5 1.0
CB F:CYS16 3.5 176.8 1.0
CA F:CYS19 3.5 180.9 1.0
ND1 F:HIS33 4.2 180.2 1.0
CB F:ALA110 4.2 173.1 1.0
N F:CYS19 4.2 180.3 1.0
CG F:HIS33 4.3 180.8 1.0
CB F:HIS39 4.4 159.8 1.0
C F:CYS19 4.8 181.2 1.0
CA F:CYS16 4.8 177.0 1.0
N F:ILE20 5.0 178.2 1.0
CD F:PRO23 5.0 182.7 1.0

Zinc binding site 4 out of 8 in 8gwb

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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:250.5
occ:1.00
 SG F:CYS26 2.3 188.6 1.0
SG F:CYS8 2.3 190.9 1.0
SG F:CYS29 2.3 193.4 1.0
SG F:CYS5 2.3 182.6 1.0
CB F:CYS8 2.9 189.8 1.0
CB F:CYS26 3.0 185.9 1.0
CB F:CYS29 3.2 191.9 1.0
N F:CYS26 3.3 186.3 1.0
CB F:CYS5 3.5 183.7 1.0
CA F:CYS26 3.6 185.8 1.0
N F:CYS8 3.8 189.2 1.0
CA F:CYS8 4.0 189.6 1.0
OG F:SER10 4.2 179.9 1.0
O F:CYS26 4.2 184.8 1.0
N F:CYS29 4.2 191.3 1.0
C F:CYS26 4.2 184.9 1.0
CA F:CYS29 4.3 191.1 1.0
C F:LEU25 4.4 184.9 1.0
C F:LEU7 4.5 202.9 1.0
CA F:LEU25 4.7 184.2 1.0
C F:CYS8 4.8 189.3 1.0
N F:GLY99 4.9 160.2 1.0
CA F:CYS5 4.9 183.9 1.0
CB F:LEU7 5.0 203.2 1.0

Zinc binding site 5 out of 8 in 8gwb

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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:221.6
occ:1.00
 ND1 F:HIS75 2.2 150.6 1.0
SG F:CYS50 2.3 163.8 1.0
SG F:CYS55 2.3 172.8 1.0
SG F:CYS72 2.3 160.5 1.0
CG F:HIS75 2.3 149.8 1.0
CB F:HIS75 2.6 149.6 1.0
CB F:CYS50 2.9 161.7 1.0
CB F:CYS55 3.0 171.4 1.0
CE1 F:HIS75 3.1 149.4 1.0
CD2 F:HIS75 3.3 148.7 1.0
NE2 F:HIS75 3.6 148.9 1.0
O F:HIS75 3.8 148.3 1.0
CA F:HIS75 3.9 149.3 1.0
CB F:CYS72 4.0 160.2 1.0
C F:HIS75 4.1 148.9 1.0
N F:CYS72 4.3 159.6 1.0
CA F:CYS55 4.4 170.6 1.0
CA F:CYS50 4.4 161.6 1.0
CG2 F:VAL57 4.5 167.6 1.0
CG1 F:VAL57 4.5 167.9 1.0
N F:HIS75 4.6 150.2 1.0
O F:CYS72 4.6 160.8 1.0
CA F:CYS72 4.6 159.6 1.0
C F:TYR71 5.0 142.2 1.0
C F:CYS72 5.0 159.6 1.0
N F:ASP56 5.0 166.8 1.0

Zinc binding site 6 out of 8 in 8gwb

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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:228.4
occ:1.00
 CB E:CYS19 2.1 167.4 1.0
ND1 E:HIS39 2.1 168.1 1.0
NE2 E:HIS33 2.1 186.5 1.0
SG E:CYS16 2.3 161.7 1.0
SG E:CYS19 2.4 168.5 1.0
CE1 E:HIS39 2.5 168.1 1.0
CE1 E:HIS33 2.8 186.3 1.0
CB E:CYS16 3.1 162.0 1.0
CD2 E:HIS33 3.3 186.6 1.0
CG E:HIS39 3.4 167.0 1.0
CA E:CYS19 3.5 166.6 1.0
NE2 E:HIS39 3.7 167.2 1.0
ND1 E:HIS33 4.1 186.4 1.0
CD2 E:HIS39 4.1 166.7 1.0
N E:CYS19 4.2 166.6 1.0
CB E:HIS39 4.2 166.1 1.0
CG E:HIS33 4.3 186.8 1.0
CA E:CYS16 4.6 160.9 1.0
CB E:ALA110 4.6 160.0 1.0
C E:CYS19 4.6 165.6 1.0
C E:ALA18 4.8 160.6 1.0
C E:CYS16 4.9 160.6 1.0
O E:CYS16 4.9 161.5 1.0
CE1 E:PHE106 4.9 175.8 1.0

Zinc binding site 7 out of 8 in 8gwb

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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:257.2
occ:1.00
 CB E:CYS26 1.6 189.4 1.0
SG E:CYS8 2.3 200.9 1.0
SG E:CYS29 2.3 195.3 1.0
SG E:CYS26 2.3 189.2 1.0
SG E:CYS5 2.4 189.9 1.0
CB E:CYS8 3.0 199.3 1.0
CA E:CYS26 3.1 188.5 1.0
N E:CYS26 3.6 187.9 1.0
CB E:CYS5 3.6 188.2 1.0
N E:CYS8 3.7 199.4 1.0
C E:CYS26 3.9 188.2 1.0
CA E:CYS8 4.0 199.6 1.0
CB E:CYS29 4.0 194.2 1.0
O E:CYS26 4.3 188.3 1.0
CB E:SER10 4.4 171.9 1.0
OG E:SER10 4.6 172.2 1.0
N E:CYS29 4.6 193.8 1.0
C E:LEU7 4.6 195.3 1.0
N E:LEU7 4.7 194.9 1.0
N E:GLY99 4.7 177.7 1.0
N E:CYS27 4.7 189.4 1.0
CB E:LEU7 4.8 194.7 1.0
C E:CYS8 4.8 199.4 1.0
CA E:GLY99 4.9 177.5 1.0
C E:LEU25 4.9 176.3 1.0
N E:SER10 4.9 172.9 1.0
CA E:CYS29 4.9 193.8 1.0
CA E:LEU7 4.9 195.2 1.0

Zinc binding site 8 out of 8 in 8gwb

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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:228.7
occ:1.00
 ND1 E:HIS75 2.1 173.0 1.0
SG E:CYS55 2.3 154.8 1.0
SG E:CYS72 2.3 188.6 1.0
SG E:CYS50 2.3 167.6 1.0
CE1 E:HIS75 2.5 172.5 1.0
CG E:HIS75 3.3 172.5 1.0
CB E:CYS55 3.3 152.6 1.0
OG E:SER74 3.3 180.0 1.0
CB E:CYS50 3.4 166.6 1.0
NE2 E:HIS75 3.7 171.9 1.0
CB E:CYS72 3.8 187.3 1.0
N E:CYS72 3.9 187.0 1.0
CB E:HIS75 4.1 172.3 1.0
CD2 E:HIS75 4.1 171.7 1.0
CB E:ALA52 4.1 151.7 1.0
CG2 E:VAL57 4.2 165.3 1.0
CA E:CYS72 4.4 187.3 1.0
N E:HIS75 4.5 172.3 1.0
CB E:SER74 4.7 179.4 1.0
CA E:CYS55 4.8 151.8 1.0
CA E:CYS50 4.8 166.1 1.0
O E:CYS50 4.9 165.4 1.0
C E:SER74 4.9 179.0 1.0
C E:CYS72 4.9 186.5 1.0
CG1 E:VAL57 4.9 164.5 1.0
CA E:HIS75 4.9 171.9 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 06:45:51 2024

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