Zinc in PDB 6xez: Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc

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

All present enzymatic activity of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc:
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

Other elements in 6xez:

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

Zinc binding site 1 out of 8 in 6xez

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:92.2
occ:1.00
 SG A:CYS301 2.2 68.2 1.0
SG A:CYS310 2.3 60.9 1.0
SG A:CYS306 2.3 63.5 1.0
ND1 A:HIS295 2.3 63.6 1.0
CE1 A:HIS295 2.8 63.6 1.0
CB A:CYS310 3.6 60.9 1.0
CG A:HIS295 3.6 63.6 1.0
O A:CYS306 3.7 63.5 1.0
CB A:CYS301 3.7 68.2 1.0
CB A:CYS306 3.9 63.5 1.0
N A:HIS295 4.0 63.6 1.0
NE2 A:HIS295 4.1 63.6 1.0
CB A:HIS295 4.2 63.6 1.0
C A:CYS306 4.3 63.5 1.0
CA A:CYS301 4.4 68.2 1.0
CD2 A:HIS295 4.5 63.6 1.0
CA A:CYS306 4.6 63.5 1.0
O A:HIS295 4.7 63.6 1.0
CA A:HIS295 4.7 63.6 1.0
CA A:CYS310 4.7 60.9 1.0
N A:CYS310 4.8 60.9 1.0
CA A:TYR294 4.9 62.9 1.0
O A:ASN300 4.9 65.6 1.0
C A:TYR294 5.0 62.9 1.0

Zinc binding site 2 out of 8 in 6xez

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:0.0
occ:1.00
 SG A:CYS646 2.3 83.9 1.0
ND1 A:HIS642 2.4 76.3 1.0
SG A:CYS487 2.4 80.7 1.0
SG A:CYS645 2.4 88.5 1.0
CB A:HIS642 2.4 76.3 1.0
CG A:HIS642 2.7 76.3 1.0
N A:CYS487 3.3 80.7 1.0
CB A:CYS645 3.3 88.5 1.0
CB A:CYS487 3.3 80.7 1.0
CE1 A:HIS642 3.6 76.3 1.0
CA A:HIS642 3.7 76.3 1.0
CE1 A:PHE571 3.7 69.2 1.0
CA A:CYS487 3.8 80.7 1.0
C A:GLY486 3.9 77.3 1.0
CD2 A:HIS642 4.0 76.3 1.0
CB A:CYS646 4.0 83.9 1.0
N A:CYS646 4.2 83.9 1.0
CA A:GLY486 4.2 77.3 1.0
NE2 A:HIS642 4.4 76.3 1.0
CD1 A:PHE571 4.4 69.2 1.0
CA A:CYS645 4.4 88.5 1.0
C A:CYS645 4.5 88.5 1.0
N A:HIS642 4.5 76.3 1.0
CZ A:PHE571 4.6 69.2 1.0
C A:HIS642 4.7 76.3 1.0
O A:GLY486 4.7 77.3 1.0
O A:HIS642 4.7 76.3 1.0
CA A:CYS646 4.8 83.9 1.0
N A:CYS645 4.9 88.5 1.0

Zinc binding site 3 out of 8 in 6xez

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn701

b:0.4
occ:1.00
 SG E:CYS26 2.3 0.2 1.0
SG E:CYS8 2.3 0.1 1.0
SG E:CYS5 2.3 0.5 1.0
SG E:CYS29 2.4 0.6 1.0
CB E:CYS8 2.5 0.1 1.0
CB E:CYS26 3.1 0.2 1.0
N E:CYS8 3.2 0.1 1.0
CB E:CYS29 3.2 0.6 1.0
CA E:CYS8 3.4 0.1 1.0
CA E:GLY99 3.7 0.8 1.0
CB E:CYS5 3.8 0.5 1.0
C E:LEU7 3.9 0.3 1.0
CB E:LEU7 3.9 0.3 1.0
N E:CYS26 4.1 0.2 1.0
N E:GLY99 4.2 0.8 1.0
CA E:CYS26 4.2 0.2 1.0
N E:SER100 4.3 0.4 1.0
CA E:LEU7 4.3 0.3 1.0
CA E:CYS29 4.4 0.6 1.0
C E:GLY99 4.5 0.8 1.0
OG E:SER100 4.5 0.4 1.0
C E:CYS8 4.6 0.1 1.0
N E:CYS29 4.6 0.6 1.0
O E:LEU7 4.6 0.3 1.0
N E:LEU7 4.6 0.3 1.0
C E:CYS26 4.9 0.2 1.0
CG E:LEU7 5.0 0.3 1.0

Zinc binding site 4 out of 8 in 6xez

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn702

b:0.1
occ:1.00
 SG E:CYS55 2.3 0.7 1.0
ND1 E:HIS75 2.4 0.2 1.0
SG E:CYS50 2.4 0.4 1.0
SG E:CYS72 2.4 0.5 1.0
CB E:CYS72 2.7 0.5 1.0
CB E:CYS55 2.9 0.7 1.0
CG E:HIS75 2.9 0.2 1.0
CB E:HIS75 3.0 0.2 1.0
N E:CYS72 3.2 0.5 1.0
CE1 E:HIS75 3.4 0.2 1.0
CA E:CYS72 3.4 0.5 1.0
CB E:CYS50 3.6 0.4 1.0
CB E:ALA52 3.7 0.5 1.0
N E:HIS75 4.0 0.2 1.0
CD2 E:HIS75 4.0 0.2 1.0
CA E:HIS75 4.1 0.2 1.0
C E:CYS72 4.1 0.5 1.0
NE2 E:HIS75 4.2 0.2 1.0
O E:CYS72 4.3 0.5 1.0
CA E:CYS55 4.4 0.7 1.0
C E:TYR71 4.5 0.8 1.0
OG E:SER74 4.5 0.1 1.0
C E:HIS75 4.7 0.2 1.0
CB E:TYR71 4.8 0.8 1.0
CA E:ALA52 4.8 0.5 1.0
CA E:TYR71 4.9 0.8 1.0
N E:ALA52 4.9 0.5 1.0
CA E:CYS50 5.0 0.4 1.0
CD1 E:TYR71 5.0 0.8 1.0
N E:LYS73 5.0 0.1 1.0

Zinc binding site 5 out of 8 in 6xez

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn703

b:0.5
occ:1.00
 ND1 E:HIS39 2.2 0.0 1.0
SG E:CYS19 2.3 0.9 1.0
SG E:CYS16 2.3 0.3 1.0
NE2 E:HIS33 2.3 0.8 1.0
CB E:HIS39 2.6 0.0 1.0
CD2 E:HIS33 2.6 0.8 1.0
CG E:HIS39 2.7 0.0 1.0
CE1 E:HIS39 3.5 0.0 1.0
CE1 E:HIS33 3.5 0.8 1.0
CB E:CYS19 3.8 0.9 1.0
CB E:CYS16 3.8 0.3 1.0
CG E:HIS33 3.8 0.8 1.0
N E:CYS19 3.9 0.9 1.0
CD2 E:HIS39 4.0 0.0 1.0
CA E:HIS39 4.1 0.0 1.0
ND1 E:HIS33 4.2 0.8 1.0
CA E:CYS19 4.3 0.9 1.0
NE2 E:HIS39 4.3 0.0 1.0
O E:HIS33 4.6 0.8 1.0
CG2 E:THR37 4.7 0.4 1.0
C E:HIS39 4.7 0.0 1.0
CB E:ALA18 4.7 0.1 1.0
C E:ALA18 4.7 0.1 1.0
O E:HIS39 4.8 0.0 1.0
N E:HIS39 4.9 0.0 1.0

Zinc binding site 6 out of 8 in 6xez

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1000

b:0.9
occ:1.00
 CB F:CYS8 2.4 0.3 1.0
SG F:CYS5 2.4 0.7 1.0
SG F:CYS26 2.5 0.8 1.0
CB F:CYS26 2.5 0.8 1.0
SG F:CYS29 2.5 0.0 1.0
SG F:CYS8 2.6 0.3 1.0
N F:CYS8 3.1 0.3 1.0
CA F:CYS8 3.3 0.3 1.0
CB F:CYS29 3.5 0.0 1.0
CB F:CYS5 3.5 0.7 1.0
N F:CYS26 3.6 0.8 1.0
CA F:GLY99 3.6 0.9 1.0
CA F:CYS26 3.6 0.8 1.0
C F:LEU7 4.1 0.8 1.0
N F:GLY99 4.1 0.9 1.0
CB F:LEU7 4.4 0.8 1.0
C F:CYS8 4.4 0.3 1.0
C F:CYS26 4.5 0.8 1.0
C F:GLY99 4.5 0.9 1.0
CA F:LEU7 4.6 0.8 1.0
CA F:CYS29 4.7 0.0 1.0
N F:CYS29 4.7 0.0 1.0
N F:LEU7 4.7 0.8 1.0
O F:CYS26 4.8 0.8 1.0
N F:ASN9 4.8 0.8 1.0
C F:LEU25 4.9 0.7 1.0
N F:SER100 4.9 0.4 1.0
O F:LEU7 4.9 0.8 1.0
CA F:CYS5 5.0 0.7 1.0

Zinc binding site 7 out of 8 in 6xez

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:0.4
occ:1.00
 SG F:CYS55 2.3 0.8 1.0
SG F:CYS50 2.3 0.9 1.0
SG F:CYS72 2.4 0.5 1.0
ND1 F:HIS75 2.4 0.8 1.0
CB F:CYS55 2.9 0.8 1.0
CB F:CYS72 3.0 0.5 1.0
CG F:HIS75 3.2 0.8 1.0
CB F:ALA52 3.3 0.9 1.0
N F:CYS72 3.3 0.5 1.0
CB F:HIS75 3.4 0.8 1.0
CE1 F:HIS75 3.4 0.8 1.0
CA F:CYS72 3.7 0.5 1.0
N F:HIS75 3.8 0.8 1.0
CB F:CYS50 3.8 0.9 1.0
CA F:HIS75 4.1 0.8 1.0
C F:CYS72 4.3 0.5 1.0
CD2 F:HIS75 4.3 0.8 1.0
O F:CYS72 4.4 0.5 1.0
NE2 F:HIS75 4.4 0.8 1.0
CA F:CYS55 4.4 0.8 1.0
C F:TYR71 4.4 0.8 1.0
CB F:TYR71 4.5 0.8 1.0
CA F:ALA52 4.5 0.9 1.0
CA F:TYR71 4.6 0.8 1.0
N F:ALA52 4.6 0.9 1.0
CB F:SER74 4.8 0.2 1.0
C F:HIS75 4.9 0.8 1.0
C F:SER74 4.9 0.2 1.0
N F:SER74 5.0 0.2 1.0
CD2 F:TYR71 5.0 0.8 1.0

Zinc binding site 8 out of 8 in 6xez

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP13 Helicase - NSP13(2)-Rtc within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1002

b:0.1
occ:1.00
 ND1 F:HIS39 2.4 0.3 1.0
SG F:CYS19 2.5 0.1 1.0
SG F:CYS16 2.5 0.2 1.0
ND1 F:HIS33 2.5 0.1 1.0
CE1 F:HIS33 2.7 0.1 1.0
CB F:CYS16 2.9 0.2 1.0
CE1 F:HIS39 3.2 0.3 1.0
CG F:HIS39 3.4 0.3 1.0
CB F:HIS39 3.7 0.3 1.0
CB F:CYS19 3.8 0.1 1.0
CG F:HIS33 3.9 0.1 1.0
NE2 F:HIS33 4.0 0.1 1.0
NE2 F:HIS39 4.3 0.3 1.0
CD2 F:HIS39 4.3 0.3 1.0
CA F:CYS16 4.4 0.2 1.0
N F:CYS19 4.4 0.1 1.0
CA F:CYS19 4.6 0.1 1.0
CD2 F:HIS33 4.6 0.1 1.0
CB F:HIS33 4.7 0.1 1.0
CZ F:PHE106 4.8 0.8 1.0
O F:CYS16 4.8 0.2 1.0
CE2 F:PHE106 4.9 0.8 1.0
C F:CYS16 5.0 0.2 1.0
CD1 F:LEU25 5.0 0.7 1.0

Reference:

J.Chen, B.Malone, E.Llewellyn, M.Grasso, P.M.M.Shelton, P.D.B.Olinares, K.Maruthi, E.T.Eng, H.Vatandaslar, B.T.Chait, T.M.Kapoor, S.A.Darst, E.A.Campbell. Structural Basis For Helicase-Polymerase Coupling in the Sars-Cov-2 Replication-Transcription Complex. Cell V. 182 1560 2020.
ISSN: ISSN 1097-4172
PubMed: 32783916
DOI: 10.1016/J.CELL.2020.07.033
Page generated: Wed Dec 16 13:10:22 2020

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