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Zinc in PDB 8gw1: 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; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

Other elements in 8gw1:

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 8gw1). 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: 8gw1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8gw1

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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:69.9
occ:1.00
 ND1 A:HIS295 2.1 66.2 1.0
SG A:CYS310 2.3 48.5 1.0
SG A:CYS301 2.3 60.2 1.0
SG A:CYS306 2.3 48.1 1.0
CE1 A:HIS295 2.8 65.6 1.0
CG A:HIS295 3.3 63.7 1.0
O A:CYS306 3.3 50.2 1.0
CB A:CYS301 3.6 61.1 1.0
CB A:CYS306 3.6 49.9 1.0
CB A:CYS310 3.7 42.1 1.0
CB A:HIS295 3.8 61.9 1.0
C A:CYS306 3.8 45.6 1.0
CA A:CYS301 4.0 62.7 1.0
NE2 A:HIS295 4.0 61.5 1.0
CA A:CYS306 4.2 46.4 1.0
CD2 A:HIS295 4.3 63.1 1.0
N A:HIS295 4.3 65.3 1.0
N A:ILE307 4.6 40.4 1.0
CA A:HIS295 4.7 62.5 1.0
O A:THR293 4.7 69.8 1.0
N A:CYS301 4.7 61.5 1.0
N A:CYS310 4.9 41.1 1.0
CA A:CYS310 4.9 40.2 1.0

Zinc binding site 2 out of 8 in 8gw1

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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:155.2
occ:1.00
 ND1 A:HIS642 2.1 73.0 1.0
SG A:CYS487 2.3 65.5 1.0
SG A:CYS646 2.3 90.5 1.0
SG A:CYS645 2.3 84.8 1.0
CE1 A:HIS642 2.9 74.7 1.0
CG A:HIS642 3.2 71.8 1.0
CB A:CYS646 3.5 88.5 1.0
CB A:CYS487 3.6 69.4 1.0
CB A:CYS645 3.6 85.8 1.0
CB A:HIS642 3.6 72.1 1.0
CE1 A:PHE571 3.9 65.0 1.0
N A:CYS646 4.0 91.3 1.0
NE2 A:HIS642 4.0 73.2 1.0
NZ A:LYS532 4.1 57.9 1.0
N A:CYS487 4.1 69.3 1.0
C A:CYS645 4.1 87.1 1.0
CD2 A:HIS642 4.2 70.7 1.0
CA A:CYS646 4.3 89.7 1.0
CD1 A:PHE571 4.4 66.0 1.0
CA A:CYS487 4.4 69.9 1.0
CA A:CYS645 4.5 85.7 1.0
O A:CYS645 4.5 86.3 1.0
CA A:HIS642 4.8 71.5 1.0
CE A:LYS532 4.8 56.2 1.0

Zinc binding site 3 out of 8 in 8gw1

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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
E:Zn701

b:239.8
occ:1.00
 ND1 E:HIS39 2.1 156.1 1.0
NE2 E:HIS33 2.1 164.1 1.0
SG E:CYS16 2.3 189.9 1.0
SG E:CYS19 2.3 164.1 1.0
CB E:CYS19 2.3 164.3 1.0
CE1 E:HIS39 2.8 155.6 1.0
CE1 E:HIS33 3.0 163.3 1.0
CD2 E:HIS33 3.1 163.7 1.0
CG E:HIS39 3.2 155.0 1.0
CA E:CYS19 3.4 163.8 1.0
CB E:CYS16 3.5 189.7 1.0
CB E:ALA110 3.7 144.5 1.0
CB E:HIS39 3.8 154.8 1.0
NE2 E:HIS39 4.0 154.8 1.0
N E:CYS19 4.1 163.9 1.0
ND1 E:HIS33 4.1 163.0 1.0
CD2 E:HIS39 4.2 154.7 1.0
CG E:HIS33 4.2 163.2 1.0
CD E:PRO23 4.6 160.5 1.0
C E:CYS19 4.7 164.2 1.0
CG E:PRO23 4.8 159.6 1.0
CA E:CYS16 4.9 189.7 1.0
CA E:ALA110 5.0 144.7 1.0

Zinc binding site 4 out of 8 in 8gw1

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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
E:Zn702

b:261.0
occ:1.00
 CB E:CYS26 2.0 149.9 1.0
SG E:CYS8 2.3 161.3 1.0
SG E:CYS5 2.4 156.1 1.0
SG E:CYS26 2.4 149.1 1.0
SG E:CYS29 2.4 160.9 1.0
CB E:CYS29 2.6 159.8 1.0
CB E:CYS8 3.1 160.2 1.0
CA E:CYS26 3.4 148.7 1.0
N E:CYS26 3.8 148.5 1.0
CB E:CYS5 3.8 155.1 1.0
N E:CYS8 3.9 159.2 1.0
C E:CYS26 4.1 148.2 1.0
CA E:CYS29 4.1 158.9 1.0
CA E:CYS8 4.1 159.8 1.0
O E:CYS26 4.3 148.2 1.0
N E:CYS29 4.7 158.5 1.0
OG E:SER10 4.7 155.1 1.0
CA E:GLY99 4.7 143.9 1.0
CB E:LEU7 4.7 141.8 1.0
C E:CYS29 4.9 158.8 1.0
C E:LEU7 4.9 142.8 1.0
N E:GLY99 4.9 144.0 1.0
C E:GLY99 4.9 144.4 1.0

Zinc binding site 5 out of 8 in 8gw1

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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
E:Zn703

b:267.0
occ:1.00
 ND1 E:HIS75 2.1 173.0 1.0
SG E:CYS50 2.3 150.6 1.0
SG E:CYS72 2.3 156.1 1.0
SG E:CYS55 2.3 163.9 1.0
CE1 E:HIS75 2.3 172.9 1.0
CG E:HIS75 2.5 173.2 1.0
NE2 E:HIS75 2.8 173.0 1.0
CD2 E:HIS75 2.9 173.1 1.0
CB E:CYS50 3.1 149.3 1.0
CB E:HIS75 3.3 172.5 1.0
CB E:CYS55 3.6 163.0 1.0
CB E:CYS72 3.8 153.1 1.0
CG2 E:VAL57 4.2 163.4 1.0
N E:CYS72 4.3 150.8 1.0
CB E:ALA52 4.6 131.6 1.0
CA E:CYS50 4.6 148.8 1.0
CA E:CYS72 4.6 152.1 1.0
CA E:HIS75 4.7 172.6 1.0
CA E:CYS55 4.9 163.4 1.0
N E:HIS75 5.0 172.7 1.0
C E:CYS50 5.0 148.0 1.0

Zinc binding site 6 out of 8 in 8gw1

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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
F:Zn701

b:210.8
occ:1.00
 ND1 F:HIS39 2.1 161.7 1.0
NE2 F:HIS33 2.1 173.6 1.0
SG F:CYS16 2.3 158.1 1.0
SG F:CYS19 2.3 170.8 1.0
CB F:CYS19 2.4 170.1 1.0
CE1 F:HIS33 2.6 173.1 1.0
CE1 F:HIS39 2.8 161.2 1.0
CG F:HIS39 3.1 161.4 1.0
CD2 F:HIS33 3.3 173.4 1.0
CA F:CYS19 3.5 170.0 1.0
CB F:CYS16 3.5 156.9 1.0
CB F:HIS39 3.6 161.3 1.0
ND1 F:HIS33 3.8 173.4 1.0
CB F:ALA110 3.8 145.1 1.0
NE2 F:HIS39 3.9 161.0 1.0
N F:CYS19 4.0 169.6 1.0
CD2 F:HIS39 4.1 161.1 1.0
CG F:HIS33 4.2 173.6 1.0
C F:CYS19 4.8 170.3 1.0
CA F:CYS16 4.8 156.6 1.0
O F:CYS16 4.9 156.7 1.0
C F:ALA18 4.9 161.7 1.0

Zinc binding site 7 out of 8 in 8gw1

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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
F:Zn702

b:230.5
occ:1.00
 SG F:CYS8 2.3 157.2 1.0
SG F:CYS26 2.3 130.6 1.0
SG F:CYS5 2.3 166.7 1.0
SG F:CYS29 2.4 154.9 1.0
CB F:CYS29 2.4 153.7 1.0
CB F:CYS8 3.1 156.8 1.0
CB F:CYS26 3.3 130.5 1.0
N F:CYS8 3.5 157.5 1.0
CB F:CYS5 3.6 165.1 1.0
N F:CYS26 3.7 129.7 1.0
CA F:CYS29 3.8 153.3 1.0
CA F:CYS8 4.0 157.0 1.0
CA F:CYS26 4.0 129.8 1.0
CB F:LEU7 4.1 163.2 1.0
N F:CYS29 4.4 152.9 1.0
C F:LEU7 4.5 162.9 1.0
N F:LEU7 4.6 163.8 1.0
CA F:LEU7 4.6 163.3 1.0
OG F:SER10 4.7 160.4 1.0
C F:CYS26 4.7 130.6 1.0
CA F:GLY99 4.8 146.7 1.0
O F:CYS26 4.8 131.0 1.0
C F:CYS29 4.8 153.2 1.0
C F:LEU25 4.8 136.9 1.0
C F:GLY99 4.9 147.6 1.0
C F:CYS8 4.9 157.1 1.0
CD1 F:LEU7 4.9 163.2 1.0
CA F:CYS5 5.0 165.5 1.0

Zinc binding site 8 out of 8 in 8gw1

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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
F:Zn703

b:254.4
occ:1.00
 ND1 F:HIS75 2.1 174.3 1.0
SG F:CYS50 2.3 143.1 1.0
SG F:CYS55 2.3 183.8 1.0
SG F:CYS72 2.3 174.4 1.0
CG F:HIS75 2.4 174.0 1.0
CE1 F:HIS75 2.5 174.5 1.0
CD2 F:HIS75 2.8 173.8 1.0
NE2 F:HIS75 2.9 174.2 1.0
CB F:HIS75 3.1 173.4 1.0
CB F:CYS50 3.3 141.0 1.0
CB F:CYS55 3.5 182.7 1.0
CB F:CYS72 3.9 173.3 1.0
N F:CYS72 4.1 173.0 1.0
CA F:HIS75 4.5 173.2 1.0
CB F:ALA52 4.5 157.3 1.0
CA F:CYS72 4.6 173.4 1.0
N F:HIS75 4.7 172.9 1.0
CA F:CYS50 4.7 140.5 1.0
CG2 F:VAL57 4.7 146.7 1.0
CA F:CYS55 4.8 182.9 1.0
OG F:SER74 4.9 159.3 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 06:45:51 2024

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