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Zinc in PDB 7re3: Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer

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

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

Other elements in 7re3:

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

Fluorine (F) 12 atoms
Aluminium (Al) 4 atoms
Magnesium (Mg) 6 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer (pdb code 7re3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer, PDB code: 7re3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 7re3

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Zinc binding site 1 out of 16 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer


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 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2000

b:55.1
occ:1.00
ND1 A:HIS295 2.1 44.9 1.0
SG A:CYS310 2.3 42.0 1.0
SG A:CYS301 2.3 48.1 1.0
SG A:CYS306 2.3 44.5 1.0
CE1 A:HIS295 2.9 44.9 1.0
O A:CYS306 3.1 44.5 1.0
CG A:HIS295 3.2 44.9 1.0
CB A:CYS301 3.3 48.1 1.0
CA A:CYS301 3.5 48.1 1.0
CB A:CYS310 3.6 42.0 1.0
CB A:CYS306 3.6 44.5 1.0
CB A:HIS295 3.7 44.9 1.0
C A:CYS306 3.8 44.5 1.0
NE2 A:HIS295 4.1 44.9 1.0
N A:HIS295 4.1 44.9 1.0
CA A:CYS306 4.2 44.5 1.0
CD2 A:HIS295 4.2 44.9 1.0
N A:CYS301 4.4 48.1 1.0
CA A:HIS295 4.5 44.9 1.0
N A:LEU302 4.6 48.0 1.0
C A:CYS301 4.6 48.1 1.0
N A:ILE307 4.7 42.5 1.0
O A:HIS295 4.7 44.9 1.0
CA A:CYS310 4.8 42.0 1.0
N A:CYS310 4.8 42.0 1.0
O A:THR293 4.9 46.0 1.0

Zinc binding site 2 out of 16 in 7re3

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Zinc binding site 2 out of 16 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer


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 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:59.8
occ:1.00
ND1 A:HIS642 2.1 46.7 1.0
SG A:CYS487 2.3 49.5 1.0
SG A:CYS646 2.3 49.4 1.0
SG A:CYS645 2.3 53.0 1.0
CE1 A:HIS642 3.0 46.7 1.0
CG A:HIS642 3.0 46.7 1.0
CB A:CYS646 3.4 49.4 1.0
CB A:CYS487 3.4 49.5 1.0
CB A:HIS642 3.4 46.7 1.0
CE1 A:PHE571 3.6 42.2 1.0
N A:CYS487 3.8 49.5 1.0
CB A:CYS645 3.9 53.0 1.0
N A:CYS646 3.9 49.4 1.0
NE2 A:HIS642 4.0 46.7 1.0
CD2 A:HIS642 4.1 46.7 1.0
CD1 A:PHE571 4.1 42.2 1.0
CA A:CYS487 4.1 49.5 1.0
CA A:CYS646 4.2 49.4 1.0
C A:CYS645 4.3 53.0 1.0
CA A:HIS642 4.5 46.7 1.0
C A:GLY486 4.6 48.2 1.0
CZ A:PHE571 4.7 42.2 1.0
CA A:CYS645 4.7 53.0 1.0
O A:CYS645 4.9 53.0 1.0
CA A:GLY486 5.0 48.2 1.0

Zinc binding site 3 out of 16 in 7re3

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Zinc binding site 3 out of 16 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer


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

b:228.7
occ:1.00
CB E:CYS26 2.0 217.0 1.0
SG E:CYS8 2.3 216.5 1.0
SG E:CYS5 2.3 214.3 1.0
SG E:CYS29 2.3 221.1 1.0
SG E:CYS26 2.3 217.0 1.0
CB E:CYS5 3.2 214.3 1.0
CB E:CYS29 3.3 221.1 1.0
CA E:CYS26 3.4 217.0 1.0
CB E:CYS8 3.7 216.5 1.0
N E:CYS26 3.9 217.0 1.0
O E:VAL98 4.0 203.8 1.0
N E:CYS29 4.5 221.1 1.0
C E:CYS26 4.5 217.0 1.0
N E:CYS8 4.5 216.5 1.0
CA E:CYS29 4.5 221.1 1.0
N E:CYS27 4.6 215.4 1.0
CA E:CYS5 4.6 214.3 1.0
CA E:CYS8 4.7 216.5 1.0
CB E:SER10 5.0 204.9 1.0
CD1 E:LEU7 5.0 223.3 1.0

Zinc binding site 4 out of 16 in 7re3

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Zinc binding site 4 out of 16 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer


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

b:233.2
occ:1.00
ND1 E:HIS75 2.1 223.2 1.0
SG E:CYS55 2.3 227.1 1.0
SG E:CYS72 2.3 224.6 1.0
SG E:CYS50 2.3 222.7 1.0
CE1 E:HIS75 2.7 223.2 1.0
CB E:CYS55 2.9 227.1 1.0
CB E:CYS72 3.0 224.6 1.0
CG E:HIS75 3.3 223.2 1.0
CB E:CYS50 3.5 222.7 1.0
CB E:ALA52 3.6 221.7 1.0
CB E:HIS75 3.9 223.2 1.0
NE2 E:HIS75 3.9 223.2 1.0
N E:CYS72 4.0 224.6 1.0
CA E:CYS72 4.1 224.6 1.0
OG E:SER74 4.1 223.1 1.0
CD2 E:HIS75 4.2 223.2 1.0
CA E:CYS55 4.4 227.1 1.0
N E:ALA52 4.7 221.7 1.0
N E:HIS75 4.7 223.2 1.0
CA E:ALA52 4.8 221.7 1.0
CA E:CYS50 4.9 222.7 1.0
CA E:HIS75 5.0 223.2 1.0

Zinc binding site 5 out of 16 in 7re3

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Zinc binding site 5 out of 16 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer


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

b:235.1
occ:1.00
NE2 E:HIS33 2.0 230.1 1.0
ND1 E:HIS39 2.1 234.3 1.0
SG E:CYS19 2.3 236.8 1.0
SG E:CYS16 2.3 231.5 1.0
CG E:HIS39 2.6 234.3 1.0
CB E:HIS39 2.7 234.3 1.0
CE1 E:HIS33 2.9 230.1 1.0
CD2 E:HIS33 3.1 230.1 1.0
CE1 E:HIS39 3.2 234.3 1.0
N E:CYS19 3.2 236.8 1.0
CB E:CYS19 3.5 236.8 1.0
CB E:CYS16 3.5 231.5 1.0
CA E:CYS19 3.7 236.8 1.0
CD2 E:HIS39 3.8 234.3 1.0
C E:ALA18 3.9 234.5 1.0
ND1 E:HIS33 4.1 230.1 1.0
NE2 E:HIS39 4.1 234.3 1.0
CA E:HIS39 4.2 234.3 1.0
CG E:HIS33 4.2 230.1 1.0
N E:ALA18 4.2 234.5 1.0
CA E:ALA18 4.4 234.5 1.0
CB E:ALA18 4.5 234.5 1.0
O E:ALA18 4.6 234.5 1.0
CA E:CYS16 4.7 231.5 1.0
N E:GLY17 4.8 232.7 1.0
C E:HIS39 4.9 234.3 1.0
C E:CYS16 4.9 231.5 1.0

Zinc binding site 6 out of 16 in 7re3

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Zinc binding site 6 out of 16 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer


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

b:118.5
occ:1.00
SG F:CYS8 2.3 112.9 1.0
SG F:CYS26 2.3 115.3 1.0
SG F:CYS29 2.3 114.8 1.0
SG F:CYS5 2.3 112.8 1.0
CB F:CYS29 3.1 114.8 1.0
CB F:CYS26 3.3 115.3 1.0
CB F:CYS5 3.3 112.8 1.0
N F:CYS26 3.6 115.3 1.0
OG F:SER10 3.8 115.7 1.0
CB F:CYS8 3.9 112.9 1.0
CA F:CYS26 4.0 115.3 1.0
CD2 F:LEU7 4.1 113.2 1.0
N F:CYS29 4.2 114.8 1.0
CA F:CYS29 4.3 114.8 1.0
O F:VAL98 4.3 116.9 1.0
N F:CYS8 4.4 112.9 1.0
CG F:LEU7 4.6 113.2 1.0
C F:CYS26 4.7 115.3 1.0
CA F:CYS8 4.8 112.9 1.0
CA F:CYS5 4.8 112.8 1.0
O F:CYS26 4.8 115.3 1.0
C F:LEU25 4.8 110.6 1.0

Zinc binding site 7 out of 16 in 7re3

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Zinc binding site 7 out of 16 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer


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

b:143.8
occ:1.00
NE2 F:HIS75 2.1 126.5 1.0
SG F:CYS55 2.3 126.8 1.0
SG F:CYS72 2.3 126.9 1.0
SG F:CYS50 2.3 122.5 1.0
CE1 F:HIS75 2.5 126.5 1.0
CB F:CYS50 3.1 122.5 1.0
CG2 F:VAL57 3.1 121.7 1.0
CB F:CYS55 3.3 126.8 1.0
CB F:CYS72 3.4 126.9 1.0
CD2 F:HIS75 3.4 126.5 1.0
CB F:VAL57 3.5 121.7 1.0
ND1 F:HIS75 3.8 126.5 1.0
N F:CYS72 4.0 126.9 1.0
CG F:HIS75 4.2 126.5 1.0
CA F:CYS72 4.3 126.9 1.0
CG1 F:VAL57 4.5 121.7 1.0
N F:VAL57 4.5 121.7 1.0
CA F:CYS50 4.6 122.5 1.0
CA F:VAL57 4.6 121.7 1.0
CA F:CYS55 4.7 126.8 1.0
CB F:ALA52 4.7 125.1 1.0
N F:ASP56 4.8 123.7 1.0
C F:CYS55 4.9 126.8 1.0
C F:ASP56 5.0 123.7 1.0

Zinc binding site 8 out of 16 in 7re3

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Zinc binding site 8 out of 16 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer


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

b:123.2
occ:1.00
NE2 F:HIS33 2.0 115.2 1.0
ND1 F:HIS39 2.0 114.6 1.0
SG F:CYS19 2.3 112.7 1.0
SG F:CYS16 2.3 111.3 1.0
CD2 F:HIS33 2.7 115.2 1.0
CE1 F:HIS39 2.7 114.6 1.0
CB F:CYS16 3.1 111.3 1.0
CE1 F:HIS33 3.2 115.2 1.0
CG F:HIS39 3.2 114.6 1.0
CB F:HIS39 3.8 114.6 1.0
CB F:CYS19 3.8 112.7 1.0
CG F:HIS33 3.9 115.2 1.0
NE2 F:HIS39 3.9 114.6 1.0
N F:CYS19 4.0 112.7 1.0
ND1 F:HIS33 4.1 115.2 1.0
CD2 F:HIS39 4.2 114.6 1.0
CA F:CYS19 4.3 112.7 1.0
O F:CYS16 4.4 111.3 1.0
CA F:CYS16 4.4 111.3 1.0
C F:CYS16 4.6 111.3 1.0
C F:ALA18 4.7 112.3 1.0
CB F:ALA18 4.9 112.3 1.0
CB F:ALA110 5.0 121.0 1.0
N F:ALA18 5.0 112.3 1.0

Zinc binding site 9 out of 16 in 7re3

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Zinc binding site 9 out of 16 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2000

b:60.9
occ:1.00
ND1 G:HIS295 2.1 46.7 1.0
SG G:CYS310 2.3 45.2 1.0
SG G:CYS301 2.3 51.0 1.0
SG G:CYS306 2.3 48.5 1.0
CE1 G:HIS295 2.9 46.7 1.0
O G:CYS306 3.1 48.5 1.0
CG G:HIS295 3.2 46.7 1.0
CB G:CYS301 3.3 51.0 1.0
CA G:CYS301 3.5 51.0 1.0
CB G:CYS310 3.6 45.2 1.0
CB G:CYS306 3.6 48.5 1.0
CB G:HIS295 3.7 46.7 1.0
C G:CYS306 3.8 48.5 1.0
NE2 G:HIS295 4.1 46.7 1.0
N G:HIS295 4.1 46.7 1.0
CA G:CYS306 4.2 48.5 1.0
CD2 G:HIS295 4.2 46.7 1.0
N G:CYS301 4.4 51.0 1.0
CA G:HIS295 4.5 46.7 1.0
N G:LEU302 4.6 50.6 1.0
C G:CYS301 4.6 51.0 1.0
N G:ILE307 4.7 45.1 1.0
O G:HIS295 4.7 46.7 1.0
CA G:CYS310 4.8 45.2 1.0
N G:CYS310 4.8 45.2 1.0
O G:THR293 4.9 44.9 1.0

Zinc binding site 10 out of 16 in 7re3

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Zinc binding site 10 out of 16 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2001

b:61.6
occ:1.00
ND1 G:HIS642 2.1 49.2 1.0
SG G:CYS487 2.3 49.7 1.0
SG G:CYS646 2.3 50.8 1.0
SG G:CYS645 2.3 53.1 1.0
CE1 G:HIS642 3.0 49.2 1.0
CG G:HIS642 3.0 49.2 1.0
CB G:CYS646 3.4 50.8 1.0
CB G:CYS487 3.4 49.7 1.0
CB G:HIS642 3.4 49.2 1.0
CE1 G:PHE571 3.6 44.1 1.0
N G:CYS487 3.8 49.7 1.0
CB G:CYS645 3.9 53.1 1.0
N G:CYS646 3.9 50.8 1.0
NE2 G:HIS642 4.0 49.2 1.0
CD2 G:HIS642 4.1 49.2 1.0
CD1 G:PHE571 4.1 44.1 1.0
CA G:CYS487 4.1 49.7 1.0
CA G:CYS646 4.2 50.8 1.0
C G:CYS645 4.3 53.1 1.0
CA G:HIS642 4.5 49.2 1.0
C G:GLY486 4.6 50.5 1.0
CZ G:PHE571 4.7 44.1 1.0
CA G:CYS645 4.7 53.1 1.0
O G:CYS645 4.9 53.1 1.0
CA G:GLY486 5.0 50.5 1.0

Reference:

J.Chen, Q.Wang, B.Malone, E.C.Llewellyn, K.Maruthi, E.T.Eng, J.Perry, E.A.Campbell, D.E.Shaw, S.A.Darst. Ensemble Cryo-Electron Microscopy Reveals Conformational States of the Sars-Cov-2 Helicase Replication-Transcription Complex Biorxiv 2021.
DOI: 10.1101/2021.11.10.468168
Page generated: Thu Nov 25 10:57:23 2021

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