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Zinc in PDB 7kro: Structure of Sars-Cov-2 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc

Enzymatic activity of Structure of Sars-Cov-2 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc

All present enzymatic activity of Structure of Sars-Cov-2 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc:
2.7.7.48; 3.6.4.12; 3.6.4.13;

Other elements in 7kro:

The structure of Structure of Sars-Cov-2 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Sars-Cov-2 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc (pdb code 7kro). 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 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc, PDB code: 7kro:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7kro

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


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 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:59.7
occ:1.00
 CE1 A:HIS295 0.9 41.0 1.0
ND1 A:HIS295 1.9 41.0 1.0
NE2 A:HIS295 2.1 41.0 1.0
SG A:CYS310 2.3 44.3 1.0
SG A:CYS306 2.3 31.5 1.0
SG A:CYS301 2.3 38.2 1.0
O A:CYS306 2.9 31.5 1.0
CG A:HIS295 3.0 41.0 1.0
CD2 A:HIS295 3.1 41.0 1.0
CB A:CYS306 3.5 31.5 1.0
CB A:CYS310 3.5 44.3 1.0
CB A:CYS301 3.6 38.2 1.0
C A:CYS306 3.8 31.5 1.0
CA A:CYS301 4.0 38.2 1.0
CA A:CYS306 4.2 31.5 1.0
CB A:HIS295 4.3 41.0 1.0
N A:HIS295 4.4 41.0 1.0
O A:HIS295 4.4 41.0 1.0
N A:CYS310 4.7 44.3 1.0
CA A:CYS310 4.7 44.3 1.0
N A:ILE307 4.8 28.9 1.0
N A:CYS301 4.9 38.2 1.0
CA A:HIS295 4.9 41.0 1.0

Zinc binding site 2 out of 8 in 7kro

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


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 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:69.4
occ:1.00
 ND1 A:HIS642 2.0 38.2 1.0
SG A:CYS645 2.3 45.4 1.0
SG A:CYS487 2.3 38.6 1.0
SG A:CYS646 2.3 43.8 1.0
CG A:HIS642 2.9 38.2 1.0
CE1 A:HIS642 3.0 38.2 1.0
CB A:HIS642 3.2 38.2 1.0
CB A:CYS646 3.4 43.8 1.0
CB A:CYS487 3.5 38.6 1.0
N A:CYS487 3.7 38.6 1.0
CB A:CYS645 3.7 45.4 1.0
N A:CYS646 3.8 43.8 1.0
CE1 A:PHE571 3.8 28.9 1.0
CD2 A:HIS642 4.1 38.2 1.0
NE2 A:HIS642 4.1 38.2 1.0
NZ A:LYS532 4.1 27.2 1.0
CA A:CYS487 4.1 38.6 1.0
CA A:CYS646 4.2 43.8 1.0
C A:CYS645 4.2 45.4 1.0
CA A:HIS642 4.3 38.2 1.0
CD1 A:PHE571 4.4 28.9 1.0
CA A:CYS645 4.5 45.4 1.0
CZ A:PHE571 4.6 28.9 1.0
C A:GLY486 4.6 37.1 1.0
CE A:LYS532 4.7 27.2 1.0
CA A:GLY486 4.8 37.1 1.0
N A:CYS645 4.9 45.4 1.0
O A:CYS645 4.9 45.4 1.0

Zinc binding site 3 out of 8 in 7kro

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


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 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn701

b:74.7
occ:1.00
 SG E:CYS26 2.3 57.3 1.0
SG E:CYS8 2.3 57.9 1.0
SG E:CYS29 2.3 62.7 1.0
SG E:CYS5 2.3 53.2 1.0
CB E:CYS26 2.7 57.3 1.0
CB E:CYS29 2.9 62.7 1.0
CB E:CYS5 3.4 53.2 1.0
N E:CYS26 3.6 57.3 1.0
CA E:CYS26 3.7 57.3 1.0
CB E:CYS8 3.7 57.9 1.0
N E:CYS8 3.9 57.9 1.0
CA E:CYS29 4.1 62.7 1.0
N E:CYS29 4.1 62.7 1.0
CB E:LEU7 4.3 54.2 1.0
O E:VAL98 4.3 68.1 1.0
C E:CYS26 4.4 57.3 1.0
CA E:CYS8 4.4 57.9 1.0
O E:CYS26 4.6 57.3 1.0
C E:LEU7 4.6 54.2 1.0
CA E:CYS5 4.8 53.2 1.0
C E:LEU25 4.8 48.1 1.0
CA E:LEU7 4.8 54.2 1.0
N E:LEU7 4.9 54.2 1.0

Zinc binding site 4 out of 8 in 7kro

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


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 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn702

b:201.1
occ:1.00
 ND1 E:HIS75 2.1 110.5 1.0
SG E:CYS72 2.3 106.8 1.0
SG E:CYS55 2.3 111.1 1.0
SG E:CYS50 2.3 97.3 1.0
CE1 E:HIS75 2.5 110.5 1.0
CB E:CYS55 2.7 111.1 1.0
CG E:HIS75 3.2 110.5 1.0
CB E:CYS72 3.4 106.8 1.0
CB E:CYS50 3.4 97.3 1.0
NE2 E:HIS75 3.6 110.5 1.0
N E:CYS72 3.9 106.8 1.0
CB E:HIS75 4.0 110.5 1.0
CD2 E:HIS75 4.0 110.5 1.0
CA E:CYS55 4.2 111.1 1.0
CA E:CYS72 4.2 106.8 1.0
N E:HIS75 4.4 110.5 1.0
CB E:ALA52 4.5 111.4 1.0
CA E:CYS50 4.8 97.3 1.0
CA E:HIS75 4.9 110.5 1.0
C E:CYS55 5.0 111.1 1.0
CB E:SER74 5.0 111.7 1.0
C E:CYS72 5.0 106.8 1.0

Zinc binding site 5 out of 8 in 7kro

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


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 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn703

b:90.7
occ:1.00
 NE2 E:HIS33 2.0 59.7 1.0
ND1 E:HIS39 2.0 64.9 1.0
SG E:CYS19 2.3 62.8 1.0
SG E:CYS16 2.3 52.9 1.0
CE1 E:HIS39 2.4 64.9 1.0
CE1 E:HIS33 2.8 59.7 1.0
CD2 E:HIS33 2.9 59.7 1.0
CB E:CYS16 3.2 52.9 1.0
CG E:HIS39 3.4 64.9 1.0
NE2 E:HIS39 3.7 64.9 1.0
CB E:CYS19 3.8 62.8 1.0
ND1 E:HIS33 3.8 59.7 1.0
CG E:HIS33 3.9 59.7 1.0
CD2 E:HIS39 4.1 64.9 1.0
CB E:HIS39 4.2 64.9 1.0
O E:CYS16 4.2 52.9 1.0
N E:CYS19 4.2 62.8 1.0
CZ E:PHE106 4.3 61.9 1.0
CB E:ALA110 4.4 60.1 1.0
CA E:CYS19 4.4 62.8 1.0
CE2 E:PHE106 4.5 61.9 1.0
CA E:CYS16 4.5 52.9 1.0
C E:CYS16 4.7 52.9 1.0
CD E:PRO23 5.0 47.6 1.0
CG E:PRO23 5.0 47.6 1.0

Zinc binding site 6 out of 8 in 7kro

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


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 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1000

b:109.1
occ:1.00
 SG F:CYS26 2.3 83.7 1.0
SG F:CYS8 2.3 81.5 1.0
SG F:CYS29 2.3 92.9 1.0
SG F:CYS5 2.3 81.4 1.0
CB F:CYS26 2.7 83.7 1.0
CB F:CYS29 2.9 92.9 1.0
CB F:CYS5 3.4 81.4 1.0
N F:CYS26 3.6 83.7 1.0
CA F:CYS26 3.7 83.7 1.0
CB F:CYS8 3.7 81.5 1.0
N F:CYS8 3.9 81.5 1.0
CA F:CYS29 4.1 92.9 1.0
N F:CYS29 4.1 92.9 1.0
CB F:LEU7 4.3 84.5 1.0
O F:VAL98 4.3 92.2 1.0
C F:CYS26 4.4 83.7 1.0
CA F:CYS8 4.4 81.5 1.0
O F:CYS26 4.6 83.7 1.0
C F:LEU7 4.6 84.5 1.0
CA F:CYS5 4.8 81.4 1.0
C F:LEU25 4.8 70.9 1.0
CA F:LEU7 4.8 84.5 1.0
N F:LEU7 4.9 84.5 1.0

Zinc binding site 7 out of 8 in 7kro

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


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 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:224.3
occ:1.00
 ND1 F:HIS75 2.1 130.9 1.0
SG F:CYS72 2.3 127.6 1.0
SG F:CYS55 2.3 143.4 1.0
SG F:CYS50 2.3 125.8 1.0
CE1 F:HIS75 2.5 130.9 1.0
CB F:CYS55 2.7 143.4 1.0
CG F:HIS75 3.2 130.9 1.0
CB F:CYS72 3.4 127.6 1.0
CB F:CYS50 3.4 125.8 1.0
NE2 F:HIS75 3.6 130.9 1.0
N F:CYS72 3.9 127.6 1.0
CB F:HIS75 4.0 130.9 1.0
CD2 F:HIS75 4.0 130.9 1.0
CA F:CYS55 4.2 143.4 1.0
CA F:CYS72 4.2 127.6 1.0
N F:HIS75 4.4 130.9 1.0
CB F:ALA52 4.5 131.4 1.0
CA F:CYS50 4.8 125.8 1.0
CA F:HIS75 4.9 130.9 1.0
C F:CYS55 5.0 143.4 1.0
CB F:SER74 5.0 123.0 1.0
C F:CYS72 5.0 127.6 1.0

Zinc binding site 8 out of 8 in 7kro

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


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 Backtracked Complex Complex Bound to NSP13 Helicase - NSP13(2)-Btc within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1002

b:143.4
occ:1.00
 NE2 F:HIS33 2.0 97.6 1.0
ND1 F:HIS39 2.0 95.9 1.0
SG F:CYS19 2.3 86.7 1.0
SG F:CYS16 2.3 68.3 1.0
CE1 F:HIS39 2.4 95.9 1.0
CE1 F:HIS33 2.8 97.6 1.0
CD2 F:HIS33 2.9 97.6 1.0
CB F:CYS16 3.2 68.3 1.0
CG F:HIS39 3.4 95.9 1.0
NE2 F:HIS39 3.7 95.9 1.0
CB F:CYS19 3.8 86.7 1.0
ND1 F:HIS33 3.8 97.6 1.0
CG F:HIS33 3.9 97.6 1.0
CD2 F:HIS39 4.1 95.9 1.0
CB F:HIS39 4.2 95.9 1.0
O F:CYS16 4.2 68.3 1.0
N F:CYS19 4.2 86.7 1.0
CZ F:PHE106 4.3 101.8 1.0
CB F:ALA110 4.4 104.8 1.0
CA F:CYS19 4.4 86.7 1.0
CE2 F:PHE106 4.5 101.8 1.0
CA F:CYS16 4.5 68.3 1.0
C F:CYS16 4.7 68.3 1.0
CD F:PRO23 5.0 65.4 1.0
CG F:PRO23 5.0 65.4 1.0

Reference:

B.Malone, J.Chen, Q.Wang, E.C.Llewellyn, Y.J.Choi, P.D.B.Olinares, X.Cao, C.Hernandez, E.Eng, B.T.Chait, D.E.Shaw, R.Landick, S.A.Darst, E.A.Campbell. Structural Basis For Backtracking By the Sars-Cov-2 Replication-Transcription Complex Proc.Natl.Acad.Sci.Usa 2021.
ISSN: ESSN 1091-6490
Page generated: Tue Oct 29 22:26:34 2024

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