Zinc in PDB 7re1: Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc (Composite)

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

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

Other elements in 7re1:

The structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc (Composite) 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 (Composite) (pdb code 7re1). 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 (Composite), PDB code: 7re1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7re1

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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 (Composite)


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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:79.1
occ:1.00
 ND1 A:HIS295 2.1 59.1 1.0
SG A:CYS306 2.3 65.1 1.0
SG A:CYS310 2.3 59.0 1.0
SG A:CYS301 2.3 65.7 1.0
CE1 A:HIS295 3.0 59.1 1.0
O A:CYS306 3.1 65.1 1.0
CG A:HIS295 3.2 59.1 1.0
CB A:CYS301 3.3 65.7 1.0
CB A:CYS310 3.5 59.0 1.0
CB A:HIS295 3.6 59.1 1.0
CA A:CYS301 3.6 65.7 1.0
CB A:CYS306 3.7 65.1 1.0
C A:CYS306 3.8 65.1 1.0
NE2 A:HIS295 4.1 59.1 1.0
N A:HIS295 4.2 59.1 1.0
CD2 A:HIS295 4.2 59.1 1.0
CA A:CYS306 4.2 65.1 1.0
N A:CYS301 4.3 65.7 1.0
O A:HOH1160 4.5 64.5 1.0
CA A:HIS295 4.5 59.1 1.0
N A:ILE307 4.6 61.9 1.0
O A:THR293 4.7 61.6 1.0
CA A:CYS310 4.8 59.0 1.0
C A:CYS301 4.8 65.7 1.0
N A:CYS310 4.8 59.0 1.0
N A:LEU302 4.8 66.8 1.0
O A:HIS295 4.9 59.1 1.0
C A:ASN300 5.0 64.5 1.0

Zinc binding site 2 out of 8 in 7re1

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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 (Composite)


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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:80.9
occ:1.00
 ND1 A:HIS642 2.1 66.3 1.0
SG A:CYS646 2.3 69.8 1.0
SG A:CYS487 2.3 66.1 1.0
SG A:CYS645 2.3 71.9 1.0
CG A:HIS642 3.0 66.3 1.0
CE1 A:HIS642 3.0 66.3 1.0
CB A:HIS642 3.3 66.3 1.0
CB A:CYS487 3.5 66.1 1.0
CB A:CYS645 3.6 71.9 1.0
N A:CYS487 3.6 66.1 1.0
CB A:CYS646 3.7 69.8 1.0
CE1 A:PHE571 3.8 63.7 1.0
N A:CYS646 4.1 69.8 1.0
CD2 A:HIS642 4.1 66.3 1.0
NE2 A:HIS642 4.1 66.3 1.0
CA A:CYS487 4.1 66.1 1.0
C A:CYS645 4.2 71.9 1.0
CD1 A:PHE571 4.2 63.7 1.0
CA A:HIS642 4.3 66.3 1.0
CA A:CYS646 4.4 69.8 1.0
C A:GLY486 4.4 66.0 1.0
CA A:CYS645 4.5 71.9 1.0
NZ A:LYS532 4.6 62.7 1.0
CA A:GLY486 4.6 66.0 1.0
O A:CYS645 4.7 71.9 1.0
CZ A:PHE571 4.7 63.7 1.0
CE A:LYS532 5.0 62.7 1.0

Zinc binding site 3 out of 8 in 7re1

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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 (Composite)


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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn701

b:90.2
occ:1.00
 SG E:CYS8 2.3 83.7 1.0
SG E:CYS26 2.3 81.8 1.0
SG E:CYS29 2.3 81.7 1.0
SG E:CYS5 2.3 82.0 1.0
CB E:CYS29 3.0 81.7 1.0
CB E:CYS26 3.1 81.8 1.0
CB E:CYS5 3.2 82.0 1.0
CB E:CYS8 3.6 83.7 1.0
N E:CYS26 3.7 81.8 1.0
O E:VAL98 3.9 89.5 1.0
CA E:CYS26 4.0 81.8 1.0
CA E:CYS29 4.2 81.7 1.0
N E:CYS29 4.2 81.7 1.0
N E:CYS8 4.3 83.7 1.0
CA E:CYS8 4.5 83.7 1.0
C E:CYS26 4.6 81.8 1.0
CG E:LEU7 4.6 82.3 1.0
CA E:CYS5 4.7 82.0 1.0
CA E:GLY99 4.7 91.0 1.0
O E:CYS26 4.8 81.8 1.0
C E:VAL98 4.9 89.5 1.0
C E:LEU25 4.9 77.0 1.0

Zinc binding site 4 out of 8 in 7re1

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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 (Composite)


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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn702

b:104.2
occ:1.00
 ND1 E:HIS75 2.1 86.9 1.0
SG E:CYS50 2.3 86.3 1.0
SG E:CYS72 2.3 83.2 1.0
SG E:CYS55 2.3 90.5 1.0
CE1 E:HIS75 2.5 86.9 1.0
CG E:HIS75 2.6 86.9 1.0
CB E:CYS72 2.8 83.2 1.0
CB E:CYS55 3.1 90.5 1.0
NE2 E:HIS75 3.1 86.9 1.0
CD2 E:HIS75 3.2 86.9 1.0
CB E:CYS50 3.4 86.3 1.0
CB E:HIS75 3.4 86.9 1.0
N E:CYS72 3.8 83.2 1.0
CA E:CYS72 3.9 83.2 1.0
CB E:ALA52 4.2 87.0 1.0
CA E:CYS55 4.5 90.5 1.0
CA E:HIS75 4.6 86.9 1.0
N E:HIS75 4.7 86.9 1.0
C E:CYS72 4.7 83.2 1.0
CG2 E:VAL57 4.7 86.0 1.0
CA E:CYS50 4.8 86.3 1.0
CB E:VAL57 4.9 86.0 1.0

Zinc binding site 5 out of 8 in 7re1

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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 (Composite)


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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn703

b:86.9
occ:1.00
 NE2 E:HIS33 2.0 76.7 1.0
ND1 E:HIS39 2.0 80.5 1.0
SG E:CYS19 2.3 83.1 1.0
SG E:CYS16 2.3 81.0 1.0
CE1 E:HIS39 2.9 80.5 1.0
CD2 E:HIS33 3.0 76.7 1.0
CE1 E:HIS33 3.0 76.7 1.0
CG E:HIS39 3.1 80.5 1.0
CB E:CYS16 3.3 81.0 1.0
CB E:HIS39 3.6 80.5 1.0
CB E:CYS19 3.7 83.1 1.0
N E:CYS19 4.1 83.1 1.0
NE2 E:HIS39 4.1 80.5 1.0
ND1 E:HIS33 4.1 76.7 1.0
CG E:HIS33 4.1 76.7 1.0
CD2 E:HIS39 4.2 80.5 1.0
CA E:CYS19 4.3 83.1 1.0
CB E:ALA110 4.5 81.5 1.0
CA E:CYS16 4.7 81.0 1.0
CE2 E:PHE106 4.7 80.3 1.0
CZ E:PHE106 4.9 80.3 1.0
C E:ALA18 4.9 81.1 1.0

Zinc binding site 6 out of 8 in 7re1

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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 (Composite)


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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1000

b:78.2
occ:1.00
 SG F:CYS26 2.3 77.5 1.0
SG F:CYS8 2.3 77.2 1.0
SG F:CYS29 2.3 78.8 1.0
SG F:CYS5 2.3 73.7 1.0
CB F:CYS26 2.8 77.5 1.0
CB F:CYS29 2.9 78.8 1.0
CB F:CYS5 3.2 73.7 1.0
CB F:CYS8 3.5 77.2 1.0
N F:CYS26 3.7 77.5 1.0
CA F:CYS26 3.8 77.5 1.0
O F:VAL98 3.9 82.3 1.0
CA F:CYS29 4.1 78.8 1.0
N F:CYS8 4.2 77.2 1.0
N F:CYS29 4.2 78.8 1.0
CA F:CYS8 4.4 77.2 1.0
C F:CYS26 4.4 77.5 1.0
O F:CYS26 4.6 77.5 1.0
CA F:CYS5 4.6 73.7 1.0
CG F:LEU7 4.7 77.6 1.0
CD2 F:LEU7 4.8 77.6 1.0
C F:LEU25 4.9 70.9 1.0
C F:LEU7 4.9 77.6 1.0

Zinc binding site 7 out of 8 in 7re1

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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 (Composite)


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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:105.1
occ:1.00
 ND1 F:HIS75 2.1 83.2 1.0
CE1 F:HIS75 2.1 83.2 1.0
SG F:CYS55 2.3 88.8 1.0
SG F:CYS72 2.3 78.6 1.0
SG F:CYS50 2.3 82.0 1.0
CB F:CYS55 2.7 88.8 1.0
NE2 F:HIS75 2.9 83.2 1.0
CG F:HIS75 2.9 83.2 1.0
CD2 F:HIS75 3.3 83.2 1.0
CB F:CYS50 3.6 82.0 1.0
CB F:HIS75 3.9 83.2 1.0
CB F:CYS72 3.9 78.6 1.0
N F:CYS72 4.1 78.6 1.0
CG2 F:VAL57 4.2 83.2 1.0
CA F:CYS55 4.2 88.8 1.0
CB F:ALA52 4.4 83.1 1.0
CA F:CYS72 4.6 78.6 1.0
C F:CYS55 4.6 88.8 1.0
N F:ASP56 4.9 89.6 1.0
N F:HIS75 5.0 83.2 1.0
CA F:CYS50 5.0 82.0 1.0

Zinc binding site 8 out of 8 in 7re1

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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 (Composite)


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 (Composite) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1002

b:84.1
occ:1.00
 NE2 F:HIS33 2.0 73.8 1.0
ND1 F:HIS39 2.0 75.1 1.0
SG F:CYS16 2.3 72.3 1.0
SG F:CYS19 2.3 75.1 1.0
CE1 F:HIS39 2.9 75.1 1.0
CE1 F:HIS33 2.9 73.8 1.0
CG F:HIS39 3.1 75.1 1.0
CD2 F:HIS33 3.1 73.8 1.0
CB F:CYS16 3.4 72.3 1.0
CB F:HIS39 3.5 75.1 1.0
CB F:CYS19 3.8 75.1 1.0
NE2 F:HIS39 4.0 75.1 1.0
ND1 F:HIS33 4.1 73.8 1.0
CD2 F:HIS39 4.1 75.1 1.0
N F:CYS19 4.2 75.1 1.0
CG F:HIS33 4.2 73.8 1.0
CA F:CYS19 4.3 75.1 1.0
CB F:ALA110 4.4 77.8 1.0
CA F:CYS16 4.7 72.3 1.0
O F:CYS16 4.8 72.3 1.0
C F:ALA18 4.9 72.9 1.0
C F:CYS16 5.0 72.3 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 10:15:53 2024

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