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Zinc in PDB 7rdy: Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class

Enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class

All present enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class:
2.7.7.48; 3.6.4.12; 3.6.4.13;

Other elements in 7rdy:

The structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Magnesium (Mg) 3 atoms
Aluminium (Al) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class (pdb code 7rdy). 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 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class, PDB code: 7rdy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7rdy

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Zinc binding site 1 out of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:55.6
occ:1.00
 ND1 A:HIS295 2.1 36.3 1.0
SG A:CYS310 2.3 32.9 1.0
SG A:CYS306 2.3 37.2 1.0
SG A:CYS301 2.3 41.2 1.0
O A:CYS306 2.8 37.2 1.0
CE1 A:HIS295 3.0 36.3 1.0
CG A:HIS295 3.2 36.3 1.0
CB A:CYS301 3.5 41.2 1.0
CB A:CYS306 3.5 37.2 1.0
CB A:HIS295 3.6 36.3 1.0
CB A:CYS310 3.7 32.9 1.0
C A:CYS306 3.8 37.2 1.0
CA A:CYS301 4.0 41.2 1.0
N A:HIS295 4.0 36.3 1.0
NE2 A:HIS295 4.1 36.3 1.0
CA A:CYS306 4.1 37.2 1.0
CD2 A:HIS295 4.3 36.3 1.0
CA A:HIS295 4.4 36.3 1.0
N A:CYS310 4.8 32.9 1.0
O A:HIS295 4.8 36.3 1.0
N A:CYS301 4.8 41.2 1.0
CA A:CYS310 4.8 32.9 1.0
O A:THR293 4.8 38.5 1.0
N A:ILE307 4.9 34.6 1.0
N A:LEU302 5.0 40.8 1.0

Zinc binding site 2 out of 8 in 7rdy

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Zinc binding site 2 out of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:65.2
occ:1.00
 ND1 A:HIS642 2.0 42.8 1.0
SG A:CYS487 2.3 43.0 1.0
SG A:CYS646 2.3 47.2 1.0
SG A:CYS645 2.3 50.0 1.0
CE1 A:HIS642 2.9 42.8 1.0
CG A:HIS642 3.2 42.8 1.0
CB A:CYS487 3.4 43.0 1.0
CB A:CYS646 3.4 47.2 1.0
CB A:HIS642 3.6 42.8 1.0
N A:CYS487 3.7 43.0 1.0
CB A:CYS645 3.9 50.0 1.0
CE1 A:PHE571 3.9 38.0 1.0
N A:CYS646 4.0 47.2 1.0
NE2 A:HIS642 4.0 42.8 1.0
CA A:CYS487 4.1 43.0 1.0
CA A:CYS646 4.2 47.2 1.0
C A:CYS645 4.2 50.0 1.0
CD2 A:HIS642 4.2 42.8 1.0
CD1 A:PHE571 4.3 38.0 1.0
NZ A:LYS532 4.5 37.8 1.0
C A:GLY486 4.6 41.5 1.0
O A:CYS645 4.6 50.0 1.0
CA A:CYS645 4.7 50.0 1.0
CE A:LYS532 4.7 37.8 1.0
CA A:HIS642 4.7 42.8 1.0
CZ A:PHE571 4.8 38.0 1.0

Zinc binding site 3 out of 8 in 7rdy

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Zinc binding site 3 out of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1000

b:89.6
occ:1.00
 SG E:CYS8 2.3 79.5 1.0
SG E:CYS26 2.3 77.3 1.0
SG E:CYS5 2.3 74.7 1.0
SG E:CYS29 2.3 81.7 1.0
CB E:CYS29 2.9 81.7 1.0
CB E:CYS26 3.0 77.3 1.0
CB E:CYS5 3.4 74.7 1.0
N E:CYS26 3.7 77.3 1.0
CB E:CYS8 3.8 79.5 1.0
CA E:CYS26 3.9 77.3 1.0
O E:VAL98 4.0 83.8 1.0
CA E:CYS29 4.1 81.7 1.0
N E:CYS29 4.2 81.7 1.0
N E:CYS8 4.3 79.5 1.0
C E:CYS26 4.5 77.3 1.0
CG E:LEU7 4.6 79.9 1.0
CA E:CYS8 4.6 79.5 1.0
O E:CYS26 4.7 77.3 1.0
CA E:CYS5 4.8 74.7 1.0
C E:LEU25 4.9 71.2 1.0
C E:LEU7 5.0 79.9 1.0

Zinc binding site 4 out of 8 in 7rdy

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Zinc binding site 4 out of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:116.3
occ:1.00
 CE1 E:HIS75 1.7 97.3 1.0
ND1 E:HIS75 2.0 97.3 1.0
SG E:CYS72 2.3 94.2 1.0
SG E:CYS55 2.3 101.1 1.0
SG E:CYS50 2.3 92.1 1.0
CB E:CYS72 2.8 94.2 1.0
CB E:CYS55 3.0 101.1 1.0
NE2 E:HIS75 3.0 97.3 1.0
CG E:HIS75 3.3 97.3 1.0
CB E:CYS50 3.4 92.1 1.0
CD2 E:HIS75 3.8 97.3 1.0
N E:CYS72 3.8 94.2 1.0
CA E:CYS72 3.9 94.2 1.0
CB E:ALA52 3.9 100.5 1.0
OG E:SER74 4.4 96.7 1.0
CA E:CYS55 4.4 101.1 1.0
CB E:HIS75 4.5 97.3 1.0
C E:CYS72 4.7 94.2 1.0
CG2 E:VAL57 4.7 92.1 1.0
CA E:CYS50 4.8 92.1 1.0
CB E:VAL57 4.9 92.1 1.0
N E:HIS75 4.9 97.3 1.0
C E:CYS55 5.0 101.1 1.0

Zinc binding site 5 out of 8 in 7rdy

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Zinc binding site 5 out of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1002

b:94.8
occ:1.00
 NE2 E:HIS33 2.0 80.2 1.0
ND1 E:HIS39 2.0 84.0 1.0
SG E:CYS19 2.3 81.0 1.0
SG E:CYS16 2.3 76.8 1.0
CG E:HIS39 2.7 84.0 1.0
CE1 E:HIS33 2.8 80.2 1.0
CB E:HIS39 2.8 84.0 1.0
CE1 E:HIS39 3.1 84.0 1.0
CD2 E:HIS33 3.1 80.2 1.0
CB E:CYS16 3.5 76.8 1.0
N E:CYS19 3.5 81.0 1.0
CB E:CYS19 3.6 81.0 1.0
CD2 E:HIS39 3.9 84.0 1.0
ND1 E:HIS33 4.0 80.2 1.0
NE2 E:HIS39 4.0 84.0 1.0
CA E:CYS19 4.1 81.0 1.0
CG E:HIS33 4.2 80.2 1.0
C E:ALA18 4.3 82.0 1.0
CA E:HIS39 4.3 84.0 1.0
N E:ALA18 4.4 82.0 1.0
CB E:ALA18 4.4 82.0 1.0
CA E:ALA18 4.6 82.0 1.0
CA E:CYS16 4.7 76.8 1.0
C E:CYS16 4.9 76.8 1.0
N E:GLY17 4.9 79.1 1.0
O E:HIS39 4.9 84.0 1.0

Zinc binding site 6 out of 8 in 7rdy

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Zinc binding site 6 out of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1000

b:126.5
occ:1.00
 SG F:CYS26 2.3 114.4 1.0
SG F:CYS8 2.3 115.4 1.0
SG F:CYS29 2.3 119.0 1.0
SG F:CYS5 2.3 111.8 1.0
CB F:CYS29 3.1 119.0 1.0
CB F:CYS5 3.2 111.8 1.0
CB F:CYS8 3.3 115.4 1.0
CB F:CYS26 3.5 114.4 1.0
N F:CYS26 3.7 114.4 1.0
N F:CYS8 3.9 115.4 1.0
OG F:SER10 4.1 110.0 1.0
CA F:CYS26 4.2 114.4 1.0
CA F:CYS8 4.2 115.4 1.0
CA F:CYS29 4.4 119.0 1.0
N F:CYS29 4.5 119.0 1.0
C F:LEU7 4.6 117.9 1.0
O F:VAL98 4.6 117.3 1.0
CA F:GLY99 4.6 121.3 1.0
CG F:LEU7 4.6 117.9 1.0
CA F:CYS5 4.6 111.8 1.0
C F:LEU25 4.8 109.7 1.0
CD1 F:LEU7 4.9 117.9 1.0
N F:LEU7 4.9 117.9 1.0
CA F:LEU25 4.9 109.7 1.0
C F:CYS26 4.9 114.4 1.0
C F:CYS8 5.0 115.4 1.0

Zinc binding site 7 out of 8 in 7rdy

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Zinc binding site 7 out of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:150.0
occ:1.00
 ND1 F:HIS75 2.1 133.5 1.0
SG F:CYS55 2.3 134.1 1.0
SG F:CYS72 2.3 132.9 1.0
SG F:CYS50 2.3 127.7 1.0
CE1 F:HIS75 2.4 133.5 1.0
CB F:CYS55 2.5 134.1 1.0
CG F:HIS75 3.2 133.5 1.0
CB F:CYS72 3.3 132.9 1.0
CB F:CYS50 3.4 127.7 1.0
NE2 F:HIS75 3.5 133.5 1.0
N F:CYS72 3.8 132.9 1.0
CD2 F:HIS75 3.9 133.5 1.0
CB F:HIS75 4.0 133.5 1.0
CA F:CYS55 4.1 134.1 1.0
CA F:CYS72 4.2 132.9 1.0
O F:GLY54 4.7 134.3 1.0
N F:HIS75 4.7 133.5 1.0
CB F:ALA52 4.8 130.5 1.0
C F:CYS55 4.8 134.1 1.0
CA F:CYS50 4.8 127.7 1.0
C F:TYR71 4.9 128.4 1.0
N F:CYS55 4.9 134.1 1.0
CG2 F:VAL57 4.9 128.9 1.0
N F:ASP56 5.0 131.6 1.0
CA F:HIS75 5.0 133.5 1.0

Zinc binding site 8 out of 8 in 7rdy

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Zinc binding site 8 out of 8 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class


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 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Engaged Class within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1002

b:138.2
occ:1.00
 NE2 F:HIS33 2.0 124.9 1.0
ND1 F:HIS39 2.0 126.3 1.0
SG F:CYS19 2.3 123.5 1.0
SG F:CYS16 2.3 113.9 1.0
CE1 F:HIS39 2.6 126.3 1.0
CD2 F:HIS33 2.8 124.9 1.0
CB F:CYS16 3.0 113.9 1.0
CE1 F:HIS33 3.1 124.9 1.0
CG F:HIS39 3.2 126.3 1.0
CB F:CYS19 3.6 123.5 1.0
NE2 F:HIS39 3.7 126.3 1.0
N F:CYS19 3.8 123.5 1.0
CB F:HIS39 3.8 126.3 1.0
CG F:HIS33 4.0 124.9 1.0
CD2 F:HIS39 4.0 126.3 1.0
ND1 F:HIS33 4.1 124.9 1.0
CA F:CYS19 4.2 123.5 1.0
CB F:ALA110 4.4 139.5 1.0
CA F:CYS16 4.4 113.9 1.0
O F:CYS16 4.6 113.9 1.0
C F:ALA18 4.6 121.4 1.0
CE2 F:PHE106 4.6 135.1 1.0
C F:CYS16 4.8 113.9 1.0
CZ F:PHE106 4.9 135.1 1.0
CB F:ALA18 4.9 121.4 1.0

Reference:

J.Chen, Q.Wang, B.Malone, E.Llewellyn, Y.Pechersky, K.Maruthi, E.T.Eng, J.K.Perry, E.A.Campbell, D.E.Shaw, S.A.Darst. Ensemble Cryo-Electron Microscopy Reveals Conformational States of the NSP13 Helicase in the Sars-Cov-2 Helicase Replication-Transcription Complex Biorxiv 2021.
DOI: 10.1101/2021.11.10.468168
Page generated: Wed Oct 30 10:15:00 2024

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