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Zinc in PDB 8gwm: Sars-Cov-2 E-Rtc Bound with Mmp-NSP9 and Gmppnp

Enzymatic activity of Sars-Cov-2 E-Rtc Bound with Mmp-NSP9 and Gmppnp

All present enzymatic activity of Sars-Cov-2 E-Rtc Bound with Mmp-NSP9 and Gmppnp:
2.7.7.48;

Other elements in 8gwm:

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

Fluorine (F) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 E-Rtc Bound with Mmp-NSP9 and Gmppnp (pdb code 8gwm). 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 E-Rtc Bound with Mmp-NSP9 and Gmppnp, PDB code: 8gwm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8gwm

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Zinc binding site 1 out of 8 in the Sars-Cov-2 E-Rtc Bound with Mmp-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 E-Rtc Bound with Mmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:16.7
occ:1.00
 ND1 A:HIS295 2.1 15.7 1.0
SG A:CYS301 2.3 13.1 1.0
SG A:CYS306 2.3 14.5 1.0
SG A:CYS310 2.3 16.8 1.0
CE1 A:HIS295 2.9 12.6 1.0
CG A:HIS295 3.2 11.3 1.0
O A:CYS306 3.4 13.5 1.0
CB A:CYS301 3.5 15.9 1.0
CB A:CYS310 3.6 18.3 1.0
CB A:HIS295 3.6 19.0 1.0
CB A:CYS306 3.7 16.9 1.0
CA A:CYS301 3.9 16.8 1.0
C A:CYS306 3.9 22.0 1.0
NE2 A:HIS295 4.1 13.2 1.0
N A:HIS295 4.2 12.3 1.0
CA A:CYS306 4.2 12.7 1.0
CD2 A:HIS295 4.3 14.2 1.0
CA A:HIS295 4.5 14.3 1.0
O A:THR293 4.7 11.5 1.0
N A:CYS301 4.7 12.2 1.0
N A:ILE307 4.7 14.4 1.0
CA A:CYS310 4.8 37.8 1.0
N A:CYS310 4.9 39.0 1.0
N A:LEU302 5.0 14.5 1.0

Zinc binding site 2 out of 8 in 8gwm

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Zinc binding site 2 out of 8 in the Sars-Cov-2 E-Rtc Bound with Mmp-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 E-Rtc Bound with Mmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:100.9
occ:1.00
 ND1 A:HIS642 2.1 19.7 1.0
SG A:CYS487 2.3 20.7 1.0
SG A:CYS646 2.3 21.5 1.0
SG A:CYS645 2.3 21.5 1.0
CE1 A:HIS642 3.1 18.4 1.0
CG A:HIS642 3.1 18.4 1.0
CB A:HIS642 3.4 17.9 1.0
CB A:CYS645 3.6 20.5 1.0
CB A:CYS487 3.7 18.1 1.0
CB A:CYS646 3.8 18.5 1.0
N A:CYS487 4.0 18.3 1.0
N A:CYS646 4.0 18.7 1.0
NE2 A:HIS642 4.2 17.4 1.0
C A:CYS645 4.2 19.3 1.0
CD2 A:HIS642 4.2 17.5 1.0
CE1 A:PHE571 4.2 16.4 1.0
CA A:HIS642 4.3 17.5 1.0
CA A:CYS487 4.4 17.7 1.0
CA A:CYS646 4.5 18.7 1.0
CA A:CYS645 4.5 19.6 1.0
C A:GLY486 4.7 17.0 1.0
O A:CYS645 4.7 20.0 1.0
CA A:GLY486 4.8 17.2 1.0
O A:HIS642 4.8 17.0 1.0
CD1 A:PHE571 4.8 16.5 1.0
NZ A:LYS532 4.9 14.9 1.0
CZ A:PHE571 5.0 16.3 1.0
C A:HIS642 5.0 17.4 1.0

Zinc binding site 3 out of 8 in 8gwm

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Zinc binding site 3 out of 8 in the Sars-Cov-2 E-Rtc Bound with Mmp-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 E-Rtc Bound with Mmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn701

b:217.3
occ:1.00
 ND1 E:HIS39 2.0 112.0 1.0
NE2 E:HIS33 2.1 115.6 1.0
SG E:CYS19 2.3 110.1 1.0
SG E:CYS16 2.3 128.8 1.0
CB E:CYS19 2.6 108.9 1.0
CE1 E:HIS39 2.7 108.8 1.0
CD2 E:HIS33 2.8 113.5 1.0
CB E:CYS16 3.0 122.6 1.0
CE1 E:HIS33 3.2 114.0 1.0
CG E:HIS39 3.2 106.5 1.0
CB E:HIS39 3.8 106.1 1.0
NE2 E:HIS39 3.9 106.3 1.0
CA E:CYS19 3.9 103.5 1.0
CG E:HIS33 4.0 111.7 1.0
CD2 E:HIS39 4.1 102.5 1.0
ND1 E:HIS33 4.1 113.2 1.0
CA E:CYS16 4.5 118.9 1.0
N E:CYS19 4.5 100.9 1.0
CB E:ALA110 4.6 108.0 1.0

Zinc binding site 4 out of 8 in 8gwm

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Zinc binding site 4 out of 8 in the Sars-Cov-2 E-Rtc Bound with Mmp-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 E-Rtc Bound with Mmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn702

b:125.2
occ:1.00
 CB E:CYS8 1.6 129.7 1.0
SG E:CYS26 2.3 127.8 1.0
SG E:CYS5 2.3 117.5 1.0
SG E:CYS8 2.4 133.1 1.0
SG E:CYS29 2.4 118.3 1.0
CA E:CYS8 3.1 123.5 1.0
CB E:CYS29 3.1 113.5 1.0
CB E:CYS26 3.3 128.0 1.0
N E:CYS8 3.5 113.2 1.0
N E:CYS26 3.7 123.0 1.0
CB E:CYS5 3.8 114.4 1.0
C E:CYS8 3.9 120.8 1.0
CA E:CYS26 4.2 123.3 1.0
N E:ASN9 4.3 106.7 1.0
O E:CYS8 4.5 127.9 1.0
CA E:CYS29 4.6 105.5 1.0
N E:SER10 4.6 105.5 1.0
C E:LEU7 4.6 98.4 1.0
C E:LEU25 4.8 117.5 1.0
CD2 E:LEU7 4.8 96.0 1.0
O E:SER10 4.9 107.4 1.0
CB E:SER10 4.9 102.6 1.0
CD2 E:LEU25 4.9 118.1 1.0
CA E:LEU25 4.9 115.7 1.0

Zinc binding site 5 out of 8 in 8gwm

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Zinc binding site 5 out of 8 in the Sars-Cov-2 E-Rtc Bound with Mmp-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 E-Rtc Bound with Mmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn703

b:220.2
occ:1.00
 CB E:CYS72 2.2 139.8 1.0
ND1 E:HIS75 2.2 143.3 1.0
SG E:CYS55 2.3 122.0 1.0
SG E:CYS50 2.3 107.3 1.0
SG E:CYS72 2.3 140.8 1.0
CE1 E:HIS75 2.5 143.6 1.0
CB E:CYS55 3.4 103.7 1.0
CG E:HIS75 3.5 141.8 1.0
CA E:CYS72 3.6 131.6 1.0
CB E:CYS50 3.6 98.8 1.0
NE2 E:HIS75 3.8 145.5 1.0
N E:CYS72 4.0 126.1 1.0
CB E:ALA52 4.0 86.2 1.0
CB E:HIS75 4.3 138.5 1.0
CD2 E:HIS75 4.3 145.2 1.0
CG2 E:VAL57 4.6 142.9 1.0
C E:CYS72 4.7 128.8 1.0
CA E:CYS55 4.8 101.8 1.0
CA E:CYS50 4.9 90.2 1.0
N E:ASP56 5.0 127.6 1.0
O E:CYS50 5.0 84.2 1.0
CB E:VAL57 5.0 139.8 1.0

Zinc binding site 6 out of 8 in 8gwm

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Zinc binding site 6 out of 8 in the Sars-Cov-2 E-Rtc Bound with Mmp-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 E-Rtc Bound with Mmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn701

b:157.9
occ:1.00
 NE2 F:HIS33 2.1 162.7 1.0
CG F:HIS39 2.3 115.7 1.0
CD2 F:HIS39 2.3 113.8 1.0
SG F:CYS16 2.4 105.9 1.0
SG F:CYS19 2.4 108.7 1.0
CB F:CYS19 2.4 102.9 1.0
ND1 F:HIS39 2.6 116.5 1.0
NE2 F:HIS39 2.7 111.8 1.0
CE1 F:HIS39 2.9 112.2 1.0
CE1 F:HIS33 3.0 161.9 1.0
CB F:HIS39 3.0 112.1 1.0
CD2 F:HIS33 3.2 165.1 1.0
CA F:CYS19 3.4 94.8 1.0
CB F:CYS16 3.9 80.7 1.0
N F:CYS19 3.9 89.3 1.0
ND1 F:HIS33 4.1 163.6 1.0
CG F:HIS33 4.3 169.7 1.0
CB F:ALA110 4.3 88.9 1.0
CA F:HIS39 4.5 108.1 1.0
C F:CYS19 4.7 92.0 1.0
C F:ALA18 4.8 86.8 1.0
N F:HIS39 4.9 106.3 1.0

Zinc binding site 7 out of 8 in 8gwm

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Zinc binding site 7 out of 8 in the Sars-Cov-2 E-Rtc Bound with Mmp-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 E-Rtc Bound with Mmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn702

b:337.5
occ:1.00
 CB F:CYS8 1.6 158.0 1.0
SG F:CYS26 2.3 126.3 1.0
SG F:CYS29 2.3 107.5 1.0
SG F:CYS5 2.4 123.5 1.0
SG F:CYS8 2.4 145.9 1.0
CA F:CYS8 3.0 147.0 1.0
CB F:CYS26 3.2 113.8 1.0
N F:CYS8 3.4 134.0 1.0
CB F:CYS29 3.7 93.8 1.0
CB F:CYS5 3.8 105.9 1.0
N F:CYS26 3.9 89.2 1.0
C F:CYS8 4.0 153.7 1.0
OG F:SER10 4.1 157.1 1.0
CA F:CYS26 4.2 99.0 1.0
C F:LEU7 4.3 114.3 1.0
N F:ASN9 4.5 155.3 1.0
O F:CYS8 4.8 158.3 1.0
N F:SER10 4.8 158.8 1.0
CB F:LEU7 4.9 99.9 1.0
CA F:GLY99 4.9 94.2 1.0
O F:LEU7 4.9 109.4 1.0
CA F:CYS29 5.0 96.6 1.0
N F:GLY99 5.0 98.9 1.0
SG F:CYS97 5.0 155.4 1.0
CB F:SER10 5.0 160.5 1.0
CA F:LEU7 5.0 105.2 1.0

Zinc binding site 8 out of 8 in 8gwm

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Zinc binding site 8 out of 8 in the Sars-Cov-2 E-Rtc Bound with Mmp-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 E-Rtc Bound with Mmp-NSP9 and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn703

b:244.6
occ:1.00
 CB F:CYS72 2.0 156.5 1.0
SG F:CYS55 2.3 136.7 1.0
SG F:CYS72 2.3 155.9 1.0
SG F:CYS50 2.4 137.1 1.0
ND1 F:HIS75 2.9 153.8 1.0
CE1 F:HIS75 3.4 155.3 1.0
CB F:CYS50 3.5 132.2 1.0
CA F:CYS72 3.5 147.9 1.0
CG F:HIS75 3.6 153.2 1.0
CB F:CYS55 3.7 120.6 1.0
CB F:ALA52 3.9 99.7 1.0
N F:CYS72 4.0 144.2 1.0
NE2 F:HIS75 4.2 157.7 1.0
CB F:HIS75 4.2 151.2 1.0
CD2 F:HIS75 4.4 157.3 1.0
C F:CYS72 4.4 140.2 1.0
CG2 F:VAL57 4.8 121.3 1.0
CA F:CYS50 4.9 124.2 1.0
CA F:CYS55 5.0 116.0 1.0
N F:LYS73 5.0 126.3 1.0
O F:CYS72 5.0 136.7 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 06:47:14 2024

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