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Zinc in PDB 8gwk: Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp

Enzymatic activity of Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp

All present enzymatic activity of Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp:
2.7.7.48;

Other elements in 8gwk:

The structure of Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp (pdb code 8gwk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp, PDB code: 8gwk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8gwk

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Zinc binding site 1 out of 8 in the Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:115.9
occ:1.00
 ND1 A:HIS295 2.1 94.2 1.0
SG A:CYS301 2.3 67.8 1.0
SG A:CYS306 2.3 79.2 1.0
SG A:CYS310 2.3 79.5 1.0
CE1 A:HIS295 3.0 90.1 1.0
CG A:HIS295 3.2 92.0 1.0
CB A:CYS301 3.5 72.3 1.0
O A:CYS306 3.5 75.8 1.0
CB A:HIS295 3.6 90.8 1.0
CB A:CYS310 3.6 88.4 1.0
CB A:CYS306 3.7 65.0 1.0
CA A:CYS301 3.9 68.7 1.0
C A:CYS306 4.0 65.5 1.0
NE2 A:HIS295 4.2 87.9 1.0
N A:HIS295 4.2 91.1 1.0
CD2 A:HIS295 4.3 95.0 1.0
CA A:CYS306 4.3 68.7 1.0
CA A:HIS295 4.5 89.2 1.0
O A:THR293 4.7 71.5 1.0
N A:CYS301 4.7 68.9 1.0
N A:ILE307 4.8 50.4 1.0
CA A:CYS310 4.9 87.5 1.0
N A:LEU302 4.9 73.4 1.0
N A:CYS310 4.9 94.8 1.0
O A:HIS295 5.0 92.2 1.0
C A:CYS301 5.0 75.4 1.0

Zinc binding site 2 out of 8 in 8gwk

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Zinc binding site 2 out of 8 in the Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:111.4
occ:1.00
 ND1 A:HIS642 2.1 79.7 1.0
SG A:CYS645 2.3 72.6 1.0
SG A:CYS487 2.3 70.8 1.0
SG A:CYS646 2.3 77.0 1.0
CE1 A:HIS642 3.0 78.9 1.0
CG A:HIS642 3.1 77.0 1.0
CB A:HIS642 3.5 74.5 1.0
CB A:CYS645 3.6 69.3 1.0
CB A:CYS646 3.6 70.9 1.0
CB A:CYS487 3.8 67.3 1.0
CE1 A:PHE571 4.0 76.5 1.0
N A:CYS487 4.0 57.8 1.0
N A:CYS646 4.0 75.1 1.0
NE2 A:HIS642 4.2 77.1 1.0
CD2 A:HIS642 4.2 77.0 1.0
C A:CYS645 4.3 75.5 1.0
CA A:CYS646 4.4 72.1 1.0
CA A:CYS487 4.4 60.3 1.0
CA A:HIS642 4.4 76.2 1.0
CA A:CYS645 4.5 70.5 1.0
CD1 A:PHE571 4.6 83.0 1.0
C A:GLY486 4.6 57.6 1.0
CZ A:PHE571 4.7 67.9 1.0
CA A:GLY486 4.8 50.4 1.0
O A:HIS642 4.9 87.6 1.0
O A:CYS645 4.9 79.0 1.0

Zinc binding site 3 out of 8 in 8gwk

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Zinc binding site 3 out of 8 in the Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn701

b:267.5
occ:1.00
 ND1 E:HIS39 2.0 185.6 1.0
NE2 E:HIS33 2.0 191.8 1.0
CB E:CYS16 2.2 200.2 1.0
SG E:CYS19 2.3 201.8 1.0
SG E:CYS16 2.3 201.5 1.0
CD2 E:HIS33 2.7 191.5 1.0
CG E:HIS39 2.8 184.6 1.0
CE1 E:HIS39 2.9 185.3 1.0
CB E:HIS39 3.1 183.4 1.0
CE1 E:HIS33 3.2 190.5 1.0
CA E:CYS16 3.7 199.3 1.0
CB E:CYS19 3.7 200.1 1.0
CD2 E:HIS39 3.8 184.2 1.0
NE2 E:HIS39 3.9 184.8 1.0
CG E:HIS33 3.9 191.1 1.0
ND1 E:HIS33 4.2 190.8 1.0
C E:CYS16 4.3 198.8 1.0
N E:CYS19 4.3 199.7 1.0
CA E:CYS19 4.5 199.9 1.0
CA E:HIS39 4.6 183.6 1.0
N E:CYS16 4.6 198.5 1.0
O E:CYS16 4.7 198.8 1.0
CG E:PRO23 4.9 183.0 1.0
N E:GLY17 5.0 172.9 1.0

Zinc binding site 4 out of 8 in 8gwk

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Zinc binding site 4 out of 8 in the Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn702

b:276.1
occ:1.00
 SG E:CYS8 2.3 199.8 1.0
SG E:CYS5 2.3 183.8 1.0
SG E:CYS26 2.3 183.2 1.0
SG E:CYS29 2.4 162.9 1.0
CB E:CYS8 3.0 197.8 1.0
CB E:CYS29 3.0 161.2 1.0
CB E:CYS26 3.2 179.1 1.0
CB E:CYS5 3.2 182.5 1.0
N E:CYS26 3.3 179.0 1.0
CA E:CYS26 3.8 178.5 1.0
N E:CYS8 3.9 196.6 1.0
CA E:CYS8 4.1 197.8 1.0
C E:LEU7 4.2 183.8 1.0
C E:LEU25 4.3 178.6 1.0
CB E:LEU7 4.3 185.2 1.0
N E:LEU7 4.4 185.9 1.0
CA E:LEU25 4.4 179.4 1.0
CA E:CYS29 4.5 162.7 1.0
CA E:LEU7 4.6 184.8 1.0
CA E:CYS5 4.7 182.1 1.0
CD1 E:LEU25 4.7 179.3 1.0
CD1 E:LEU7 4.8 184.9 1.0
O E:LEU7 4.8 183.3 1.0
C E:CYS26 4.9 178.1 1.0
O E:CYS26 4.9 178.3 1.0
CA E:GLY99 5.0 168.4 1.0

Zinc binding site 5 out of 8 in 8gwk

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Zinc binding site 5 out of 8 in the Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn703

b:260.8
occ:1.00
 CE1 E:HIS75 2.1 187.1 1.0
ND1 E:HIS75 2.1 187.8 1.0
SG E:CYS50 2.3 165.7 1.0
SG E:CYS72 2.3 181.4 1.0
SG E:CYS55 2.3 168.4 1.0
CB E:CYS50 2.8 166.9 1.0
NE2 E:HIS75 3.2 185.6 1.0
CB E:CYS55 3.2 168.6 1.0
CB E:CYS72 3.3 181.8 1.0
CG E:HIS75 3.3 187.2 1.0
CD2 E:HIS75 3.8 186.2 1.0
CG1 E:VAL57 4.1 174.5 1.0
N E:CYS72 4.2 180.8 1.0
CB E:HIS75 4.3 186.9 1.0
CA E:CYS72 4.3 181.9 1.0
CA E:CYS50 4.3 166.4 1.0
CA E:CYS55 4.7 169.2 1.0
N E:CYS50 4.8 165.3 1.0
C E:TYR71 4.9 161.7 1.0

Zinc binding site 6 out of 8 in 8gwk

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Zinc binding site 6 out of 8 in the Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn701

b:262.4
occ:1.00
 NE2 F:HIS33 2.0 184.9 1.0
ND1 F:HIS39 2.1 183.1 1.0
SG F:CYS19 2.3 166.9 1.0
SG F:CYS16 2.3 170.8 1.0
CB F:CYS16 2.5 168.5 1.0
CD2 F:HIS33 2.6 184.7 1.0
CG F:HIS39 2.7 182.6 1.0
CB F:HIS39 3.0 181.2 1.0
CE1 F:HIS39 3.0 182.4 1.0
CE1 F:HIS33 3.3 184.8 1.0
CB F:CYS19 3.7 166.5 1.0
CD2 F:HIS39 3.7 182.6 1.0
NE2 F:HIS39 3.9 182.3 1.0
CG F:HIS33 3.9 184.8 1.0
CA F:CYS16 4.0 167.2 1.0
N F:CYS19 4.2 167.8 1.0
ND1 F:HIS33 4.2 184.9 1.0
CA F:CYS19 4.4 166.5 1.0
CA F:HIS39 4.5 181.8 1.0
C F:CYS16 4.7 167.3 1.0
N F:CYS16 4.9 166.5 1.0
C F:ALA18 5.0 165.3 1.0

Zinc binding site 7 out of 8 in 8gwk

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Zinc binding site 7 out of 8 in the Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn702

b:224.4
occ:1.00
 SG F:CYS26 2.3 182.6 1.0
SG F:CYS8 2.3 171.3 1.0
SG F:CYS5 2.3 169.0 1.0
SG F:CYS29 2.4 187.5 1.0
CB F:CYS29 2.6 184.8 1.0
CB F:CYS8 2.9 168.5 1.0
CB F:CYS26 3.5 179.0 1.0
N F:CYS26 3.5 179.0 1.0
N F:CYS8 3.7 167.7 1.0
CB F:CYS5 3.8 166.4 1.0
CA F:CYS8 3.9 167.8 1.0
C F:LEU7 4.0 160.2 1.0
CA F:CYS26 4.1 178.7 1.0
CA F:CYS29 4.2 184.9 1.0
CB F:LEU7 4.3 159.0 1.0
N F:LEU7 4.5 160.9 1.0
CA F:LEU7 4.5 160.7 1.0
O F:LEU7 4.6 159.1 1.0
C F:LEU25 4.6 169.6 1.0
CA F:LEU25 4.7 169.5 1.0
CA F:GLY99 4.7 161.7 1.0
O F:CYS26 4.8 180.2 1.0
C F:CYS26 4.8 179.6 1.0
N F:CYS29 4.8 185.5 1.0
CD2 F:LEU25 4.8 170.0 1.0
N F:GLY99 4.9 162.0 1.0
CG F:LEU7 5.0 159.3 1.0
C F:CYS29 5.0 184.9 1.0

Zinc binding site 8 out of 8 in 8gwk

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Zinc binding site 8 out of 8 in the Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Sars-Cov-2 Rna E-Rtc Complex with Rmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn703

b:316.3
occ:1.00
 ND1 F:HIS75 2.1 197.1 1.0
SG F:CYS50 2.3 183.6 1.0
SG F:CYS72 2.3 189.6 1.0
SG F:CYS55 2.3 184.6 1.0
CE1 F:HIS75 2.5 196.8 1.0
CB F:CYS50 2.5 181.8 1.0
CG F:HIS75 3.0 195.9 1.0
CB F:CYS72 3.3 190.1 1.0
NE2 F:HIS75 3.4 196.3 1.0
CB F:CYS55 3.4 185.0 1.0
CD2 F:HIS75 3.7 195.8 1.0
CB F:HIS75 3.8 195.2 1.0
N F:CYS72 3.9 189.4 1.0
CA F:CYS50 4.1 180.6 1.0
CA F:CYS72 4.2 189.8 1.0
N F:CYS50 4.7 180.5 1.0
CA F:CYS55 4.9 185.1 1.0
C F:CYS50 4.9 181.0 1.0
C F:TYR71 4.9 180.3 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: Fri Aug 22 10:30:21 2025

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