Zinc in PDB 7re0: Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Swiveled Class

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

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

Other elements in 7re0:

The structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc - Swiveled 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 - Swiveled Class (pdb code 7re0). 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 - Swiveled Class, PDB code: 7re0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7re0

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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 - Swiveled 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 - Swiveled Class within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2000

b:80.7
occ:1.00
 ND1 A:HIS295 2.1 59.9 1.0
SG A:CYS310 2.3 59.6 1.0
SG A:CYS306 2.3 65.7 1.0
SG A:CYS301 2.3 66.4 1.0
CE1 A:HIS295 3.0 59.9 1.0
O A:CYS306 3.1 65.7 1.0
CG A:HIS295 3.2 59.9 1.0
CB A:CYS301 3.3 66.4 1.0
CB A:CYS310 3.5 59.6 1.0
CB A:HIS295 3.6 59.9 1.0
CA A:CYS301 3.6 66.4 1.0
CB A:CYS306 3.7 65.7 1.0
C A:CYS306 3.8 65.7 1.0
NE2 A:HIS295 4.1 59.9 1.0
N A:HIS295 4.2 59.9 1.0
CA A:CYS306 4.2 65.7 1.0
CD2 A:HIS295 4.2 59.9 1.0
N A:CYS301 4.4 66.4 1.0
CA A:HIS295 4.5 59.9 1.0
N A:ILE307 4.7 62.4 1.0
O A:THR293 4.7 62.1 1.0
CA A:CYS310 4.8 59.6 1.0
C A:CYS301 4.8 66.4 1.0
N A:CYS310 4.8 59.6 1.0
N A:LEU302 4.8 67.6 1.0
O A:HIS295 4.9 59.9 1.0
C A:ASN300 5.0 65.2 1.0

Zinc binding site 2 out of 8 in 7re0

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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 - Swiveled 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 - Swiveled Class within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:81.4
occ:1.00
 ND1 A:HIS642 2.1 66.7 1.0
SG A:CYS487 2.3 66.7 1.0
SG A:CYS646 2.3 69.9 1.0
SG A:CYS645 2.3 71.9 1.0
CG A:HIS642 3.0 66.7 1.0
CE1 A:HIS642 3.0 66.7 1.0
CB A:HIS642 3.3 66.7 1.0
CB A:CYS487 3.5 66.7 1.0
CB A:CYS646 3.6 69.9 1.0
N A:CYS487 3.7 66.7 1.0
CB A:CYS645 3.8 71.9 1.0
CE1 A:PHE571 3.8 64.2 1.0
N A:CYS646 4.0 69.9 1.0
NE2 A:HIS642 4.1 66.7 1.0
CD2 A:HIS642 4.1 66.7 1.0
CA A:CYS487 4.1 66.7 1.0
CD1 A:PHE571 4.2 64.2 1.0
C A:CYS645 4.2 71.9 1.0
CA A:CYS646 4.3 69.9 1.0
CA A:HIS642 4.4 66.7 1.0
C A:GLY486 4.5 66.6 1.0
NZ A:LYS532 4.5 63.2 1.0
CA A:CYS645 4.6 71.9 1.0
O A:CYS645 4.7 71.9 1.0
CA A:GLY486 4.7 66.6 1.0
CZ A:PHE571 4.7 64.2 1.0
CE A:LYS532 4.9 63.2 1.0

Zinc binding site 3 out of 8 in 7re0

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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 - Swiveled 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 - Swiveled Class within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1000

b:90.7
occ:1.00
 SG E:CYS8 2.3 83.8 1.0
SG E:CYS26 2.3 81.9 1.0
SG E:CYS5 2.3 82.0 1.0
SG E:CYS29 2.3 82.0 1.0
CB E:CYS29 3.0 82.0 1.0
CB E:CYS26 3.1 81.9 1.0
CB E:CYS5 3.2 82.0 1.0
CB E:CYS8 3.6 83.8 1.0
N E:CYS26 3.8 81.9 1.0
CA E:CYS26 4.0 81.9 1.0
CA E:CYS29 4.2 82.0 1.0
N E:CYS29 4.2 82.0 1.0
N E:CYS8 4.2 83.8 1.0
CA E:CYS8 4.5 83.8 1.0
CA E:GLY99 4.5 91.4 1.0
CG E:LEU7 4.6 82.4 1.0
C E:CYS26 4.6 81.9 1.0
CA E:CYS5 4.7 82.0 1.0
O E:CYS26 4.8 81.9 1.0
N E:GLY99 4.9 91.4 1.0
C E:LEU25 4.9 77.1 1.0
O E:VAL98 5.0 90.0 1.0
C E:LEU7 5.0 82.4 1.0

Zinc binding site 4 out of 8 in 7re0

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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 - Swiveled 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 - Swiveled Class within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:103.8
occ:1.00
 ND1 E:HIS75 2.1 86.4 1.0
SG E:CYS50 2.3 85.9 1.0
SG E:CYS72 2.3 82.7 1.0
SG E:CYS55 2.3 90.0 1.0
CE1 E:HIS75 2.4 86.4 1.0
CG E:HIS75 2.7 86.4 1.0
CB E:CYS72 2.8 82.7 1.0
CB E:CYS55 3.1 90.0 1.0
NE2 E:HIS75 3.1 86.4 1.0
CD2 E:HIS75 3.3 86.4 1.0
CB E:CYS50 3.3 85.9 1.0
CB E:HIS75 3.5 86.4 1.0
N E:CYS72 3.8 82.7 1.0
CA E:CYS72 3.9 82.7 1.0
CB E:ALA52 4.2 86.5 1.0
CA E:CYS55 4.6 90.0 1.0
C E:CYS72 4.7 82.7 1.0
CA E:HIS75 4.7 86.4 1.0
N E:HIS75 4.7 86.4 1.0
CA E:CYS50 4.7 85.9 1.0
CG2 E:VAL57 4.8 85.6 1.0
CB E:VAL57 4.9 85.6 1.0

Zinc binding site 5 out of 8 in 7re0

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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 - Swiveled 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 - Swiveled Class within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1002

b:87.5
occ:1.00
 NE2 E:HIS33 2.0 77.0 1.0
ND1 E:HIS39 2.0 80.8 1.0
SG E:CYS19 2.3 83.4 1.0
SG E:CYS16 2.3 81.3 1.0
CE1 E:HIS39 2.9 80.8 1.0
CD2 E:HIS33 3.0 77.0 1.0
CE1 E:HIS33 3.0 77.0 1.0
CG E:HIS39 3.1 80.8 1.0
CB E:CYS16 3.3 81.3 1.0
CB E:HIS39 3.5 80.8 1.0
CB E:CYS19 3.7 83.4 1.0
NE2 E:HIS39 4.1 80.8 1.0
N E:CYS19 4.1 83.4 1.0
ND1 E:HIS33 4.1 77.0 1.0
CG E:HIS33 4.1 77.0 1.0
CD2 E:HIS39 4.2 80.8 1.0
CA E:CYS19 4.3 83.4 1.0
CA E:CYS16 4.7 81.3 1.0
CB E:ALA110 4.9 81.8 1.0
C E:ALA18 4.9 81.5 1.0
CB E:ALA18 5.0 81.5 1.0

Zinc binding site 6 out of 8 in 7re0

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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 - Swiveled 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 - Swiveled Class within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1000

b:79.2
occ:1.00
 SG F:CYS26 2.3 77.7 1.0
SG F:CYS8 2.3 77.6 1.0
SG F:CYS29 2.3 79.2 1.0
SG F:CYS5 2.3 74.0 1.0
CB F:CYS26 2.8 77.7 1.0
CB F:CYS29 2.9 79.2 1.0
CB F:CYS5 3.2 74.0 1.0
CB F:CYS8 3.4 77.6 1.0
N F:CYS26 3.7 77.7 1.0
CA F:CYS26 3.8 77.7 1.0
O F:VAL98 3.8 82.6 1.0
N F:CYS8 4.1 77.6 1.0
CA F:CYS29 4.1 79.2 1.0
N F:CYS29 4.2 79.2 1.0
CA F:CYS8 4.3 77.6 1.0
C F:CYS26 4.4 77.7 1.0
O F:CYS26 4.6 77.7 1.0
CA F:CYS5 4.6 74.0 1.0
CG F:LEU7 4.7 78.0 1.0
CD2 F:LEU7 4.9 78.0 1.0
C F:LEU7 4.9 78.0 1.0
C F:LEU25 4.9 71.1 1.0
C F:VAL98 5.0 82.6 1.0
C F:CYS8 5.0 77.6 1.0

Zinc binding site 7 out of 8 in 7re0

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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 - Swiveled 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 - Swiveled Class within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:106.3
occ:1.00
 ND1 F:HIS75 2.1 82.4 1.0
CE1 F:HIS75 2.1 82.4 1.0
SG F:CYS55 2.3 87.9 1.0
SG F:CYS72 2.3 78.0 1.0
SG F:CYS50 2.3 81.5 1.0
CB F:CYS55 2.6 87.9 1.0
NE2 F:HIS75 2.9 82.4 1.0
CG F:HIS75 2.9 82.4 1.0
CD2 F:HIS75 3.3 82.4 1.0
CB F:CYS50 3.6 81.5 1.0
CB F:HIS75 3.9 82.4 1.0
CB F:CYS72 3.9 78.0 1.0
CA F:CYS55 4.1 87.9 1.0
CG2 F:VAL57 4.1 82.6 1.0
N F:CYS72 4.1 78.0 1.0
CB F:ALA52 4.4 82.8 1.0
C F:CYS55 4.5 87.9 1.0
CA F:CYS72 4.6 78.0 1.0
N F:ASP56 4.8 89.1 1.0
CA F:CYS50 4.9 81.5 1.0

Zinc binding site 8 out of 8 in 7re0

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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 - Swiveled 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 - Swiveled Class within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1002

b:85.0
occ:1.00
 ND1 F:HIS39 2.0 75.2 1.0
NE2 F:HIS33 2.0 74.0 1.0
SG F:CYS19 2.3 75.2 1.0
SG F:CYS16 2.3 72.4 1.0
CE1 F:HIS39 2.9 75.2 1.0
CE1 F:HIS33 2.9 74.0 1.0
CD2 F:HIS33 3.1 74.0 1.0
CG F:HIS39 3.1 75.2 1.0
CB F:CYS16 3.4 72.4 1.0
CB F:HIS39 3.5 75.2 1.0
CB F:CYS19 3.7 75.2 1.0
NE2 F:HIS39 4.0 75.2 1.0
ND1 F:HIS33 4.1 74.0 1.0
CD2 F:HIS39 4.1 75.2 1.0
N F:CYS19 4.2 75.2 1.0
CG F:HIS33 4.2 74.0 1.0
CA F:CYS19 4.3 75.2 1.0
CB F:ALA110 4.5 78.0 1.0
CA F:CYS16 4.7 72.4 1.0
O F:CYS16 4.8 72.4 1.0
C F:CYS16 5.0 72.4 1.0
C F:ALA18 5.0 72.9 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 10:15:52 2024

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