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

Zinc binding site 1 out of 8 in 8gwn

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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:83.0
occ:1.00
 CE1 A:HIS295 0.9 61.5 1.0
ND1 A:HIS295 1.9 61.5 1.0
NE2 A:HIS295 2.1 61.5 1.0
SG A:CYS301 2.3 61.0 1.0
SG A:CYS306 2.3 52.0 1.0
SG A:CYS310 2.3 54.6 1.0
CG A:HIS295 3.0 61.5 1.0
CD2 A:HIS295 3.1 61.5 1.0
O A:CYS306 3.2 52.0 1.0
CB A:CYS306 3.2 52.0 1.0
CB A:CYS310 3.7 54.6 1.0
C A:CYS306 3.7 52.0 1.0
CB A:CYS301 3.8 61.0 1.0
CA A:CYS306 3.9 52.0 1.0
CA A:CYS301 4.1 61.0 1.0
CB A:HIS295 4.4 61.5 1.0
N A:HIS295 4.4 61.5 1.0
N A:ILE307 4.7 48.4 1.0
ND1 A:HIS309 4.8 52.4 1.0
N A:CYS310 4.8 54.6 1.0
CA A:CYS310 4.8 54.6 1.0
O A:HIS295 4.9 61.5 1.0
CA A:HIS295 5.0 61.5 1.0
N A:CYS301 5.0 61.0 1.0

Zinc binding site 2 out of 8 in 8gwn

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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:157.4
occ:1.00
 ND1 A:HIS642 2.0 85.5 1.0
SG A:CYS645 2.3 97.1 1.0
SG A:CYS487 2.3 81.6 1.0
CE1 A:HIS642 2.3 85.5 1.0
SG A:CYS646 2.3 93.9 1.0
CB A:CYS487 3.2 81.6 1.0
CG A:HIS642 3.3 85.5 1.0
CB A:CYS646 3.5 93.9 1.0
NE2 A:HIS642 3.6 85.5 1.0
CB A:CYS645 3.9 97.1 1.0
CE1 A:PHE571 3.9 65.1 1.0
N A:CYS487 4.0 81.6 1.0
N A:CYS646 4.0 93.9 1.0
CA A:CYS487 4.0 81.6 1.0
CD2 A:HIS642 4.1 85.5 1.0
CB A:HIS642 4.2 85.5 1.0
CA A:CYS646 4.3 93.9 1.0
C A:CYS645 4.3 97.1 1.0
CD1 A:PHE571 4.4 65.1 1.0
CZ A:PHE571 4.5 65.1 1.0
NZ A:LYS532 4.6 65.0 1.0
O A:CYS645 4.7 97.1 1.0
CA A:CYS645 4.7 97.1 1.0
C A:GLY486 5.0 80.5 1.0

Zinc binding site 3 out of 8 in 8gwn

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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:362.2
occ:1.00
 CE1 F:HIS39 1.6 202.8 1.0
ND1 F:HIS39 2.1 202.8 1.0
NE2 F:HIS33 2.2 190.7 1.0
SG F:CYS19 2.3 216.2 1.0
SG F:CYS16 2.3 184.2 1.0
NE2 F:HIS39 2.6 202.8 1.0
CE1 F:HIS33 2.8 190.7 1.0
CD2 F:HIS33 3.0 190.7 1.0
CG F:HIS39 3.1 202.8 1.0
CB F:CYS16 3.2 184.2 1.0
CD2 F:HIS39 3.3 202.8 1.0
ND1 F:HIS33 3.7 190.7 1.0
CG F:HIS33 3.9 190.7 1.0
CB F:CYS19 3.9 216.2 1.0
O F:ALA18 4.2 207.0 1.0
CB F:HIS39 4.3 202.8 1.0
CD F:PRO23 4.6 180.3 1.0
CA F:CYS16 4.6 184.2 1.0
CG F:PRO23 4.7 180.3 1.0
CA F:CYS19 4.8 216.2 1.0
CD1 F:LEU25 4.8 157.6 1.0
C F:ALA18 4.8 207.0 1.0
N F:CYS19 5.0 216.2 1.0

Zinc binding site 4 out of 8 in 8gwn

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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:329.5
occ:1.00
 CB F:CYS29 2.2 173.4 1.0
SG F:CYS8 2.3 207.3 1.0
SG F:CYS26 2.3 170.9 1.0
SG F:CYS5 2.3 195.6 1.0
SG F:CYS29 2.3 173.4 1.0
CB F:CYS26 3.0 170.9 1.0
CB F:CYS8 3.0 207.3 1.0
CB F:CYS5 3.3 195.6 1.0
CA F:CYS29 3.8 173.4 1.0
N F:CYS26 3.9 170.9 1.0
OG F:SER10 3.9 179.2 1.0
CA F:CYS26 4.0 170.9 1.0
CA F:CYS8 4.3 207.3 1.0
N F:CYS8 4.3 207.3 1.0
O F:CYS26 4.3 170.9 1.0
N F:CYS29 4.4 173.4 1.0
C F:CYS29 4.5 173.4 1.0
C F:CYS26 4.6 170.9 1.0
C F:LEU7 4.7 204.2 1.0
N F:GLY99 4.7 193.4 1.0
CA F:GLY99 4.7 193.4 1.0
CA F:CYS5 4.7 195.6 1.0
N F:CYS30 4.8 165.7 1.0
O F:LEU7 4.9 204.2 1.0
C F:LEU25 5.0 157.6 1.0

Zinc binding site 5 out of 8 in 8gwn

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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:321.0
occ:1.00
 ND1 F:HIS75 2.1 177.8 1.0
CB F:CYS50 2.3 170.3 1.0
SG F:CYS55 2.3 174.1 1.0
SG F:CYS72 2.3 173.2 1.0
SG F:CYS50 2.3 170.3 1.0
CB F:CYS72 2.4 173.2 1.0
CE1 F:HIS75 2.7 177.8 1.0
CG1 F:VAL57 3.0 175.0 1.0
CG F:HIS75 3.3 177.8 1.0
CG2 F:VAL57 3.4 175.0 1.0
CB F:CYS55 3.5 174.1 1.0
CA F:CYS72 3.7 173.2 1.0
CA F:CYS50 3.7 170.3 1.0
CB F:VAL57 3.8 175.0 1.0
N F:CYS72 3.8 173.2 1.0
NE2 F:HIS75 3.9 177.8 1.0
CB F:HIS75 4.0 177.8 1.0
C F:TYR71 4.2 146.8 1.0
CD2 F:HIS75 4.2 177.8 1.0
O F:CYS50 4.2 170.3 1.0
C F:CYS50 4.3 170.3 1.0
O F:TYR71 4.4 146.8 1.0
N F:CYS50 4.4 170.3 1.0
C F:CYS72 4.5 173.2 1.0
O F:CYS72 4.8 173.2 1.0
N F:ASP56 4.8 176.8 1.0
CA F:CYS55 4.9 174.1 1.0
CA F:TYR71 4.9 146.8 1.0
N F:VAL57 5.0 175.0 1.0

Zinc binding site 6 out of 8 in 8gwn

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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:277.9
occ:1.00
 CE1 E:HIS39 1.6 191.2 1.0
ND1 E:HIS39 2.0 191.2 1.0
NE2 E:HIS33 2.1 195.4 1.0
NE2 E:HIS39 2.2 191.2 1.0
SG E:CYS16 2.3 158.6 1.0
SG E:CYS19 2.3 176.1 1.0
CD2 E:HIS33 2.6 195.4 1.0
CG E:HIS39 2.7 191.2 1.0
CD2 E:HIS39 2.8 191.2 1.0
CE1 E:HIS33 3.3 195.4 1.0
CB E:CYS16 3.6 158.6 1.0
CE1 E:PHE106 3.8 192.7 1.0
CB E:ALA110 3.9 195.8 1.0
CG E:HIS33 3.9 195.4 1.0
CB E:CYS19 3.9 176.1 1.0
CB E:HIS39 3.9 191.2 1.0
O E:CYS16 4.2 158.6 1.0
ND1 E:HIS33 4.2 195.4 1.0
N E:CYS19 4.2 176.1 1.0
CZ E:PHE106 4.3 192.7 1.0
CA E:CYS19 4.5 176.1 1.0
CA E:CYS16 4.9 158.6 1.0
CD1 E:PHE106 4.9 192.7 1.0
C E:ALA18 4.9 171.4 1.0
CB E:ALA18 5.0 171.4 1.0
C E:CYS16 5.0 158.6 1.0

Zinc binding site 7 out of 8 in 8gwn

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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:248.4
occ:1.00
 CB E:CYS26 1.6 171.2 1.0
SG E:CYS8 2.3 188.4 1.0
SG E:CYS29 2.3 180.8 1.0
SG E:CYS26 2.3 171.2 1.0
SG E:CYS5 2.4 167.7 1.0
CB E:CYS8 2.6 188.4 1.0
OG E:SER10 2.9 167.8 1.0
CA E:CYS26 3.1 171.2 1.0
N E:CYS26 3.5 171.2 1.0
CB E:CYS5 3.7 167.7 1.0
N E:CYS8 3.7 188.4 1.0
CA E:CYS8 3.7 188.4 1.0
CB E:CYS29 3.9 180.8 1.0
C E:CYS26 3.9 171.2 1.0
CB E:SER10 4.2 167.8 1.0
O E:CYS26 4.4 171.2 1.0
N E:CYS29 4.5 180.8 1.0
C E:CYS8 4.6 188.4 1.0
N E:CYS27 4.7 169.7 1.0
C E:LEU7 4.8 179.6 1.0
CA E:CYS29 4.8 180.8 1.0
C E:LEU25 4.8 148.1 1.0
N E:SER10 4.9 167.8 1.0
CB E:LEU7 4.9 179.6 1.0
O E:SER10 5.0 167.8 1.0
N E:GLY99 5.0 198.0 1.0

Zinc binding site 8 out of 8 in 8gwn

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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:342.7
occ:1.00
 CE1 E:HIS75 1.6 219.2 1.0
NE2 E:HIS75 1.8 219.2 1.0
ND1 E:HIS75 2.1 219.2 1.0
SG E:CYS50 2.3 196.9 1.0
CD2 E:HIS75 2.3 219.2 1.0
SG E:CYS55 2.3 214.4 1.0
SG E:CYS72 2.3 205.1 1.0
CG E:HIS75 2.5 219.2 1.0
CB E:CYS50 3.1 196.9 1.0
CB E:CYS55 3.4 214.4 1.0
CB E:HIS75 3.8 219.2 1.0
N E:CYS72 3.9 205.1 1.0
CB E:CYS72 4.0 205.1 1.0
O E:CYS50 4.4 196.9 1.0
CB E:ALA52 4.4 211.8 1.0
CG2 E:VAL57 4.4 192.5 1.0
CA E:CYS72 4.5 205.1 1.0
CA E:CYS50 4.5 196.9 1.0
OG E:SER74 4.8 215.1 1.0
CA E:CYS55 4.8 214.4 1.0
C E:CYS50 4.8 196.9 1.0
C E:TYR71 4.9 186.3 1.0
CB E:VAL57 4.9 192.5 1.0
CA E:TYR71 4.9 186.3 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 06:49:47 2024

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