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Zinc in PDB 9i53: Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp

Enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp:
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp, PDB code: 9i53 was solved by P.Kloskowski, P.Neumann, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.81 / 1.92
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.577, 70.643, 85.885, 102.99, 95.29, 112.53
R / Rfree (%) 18.7 / 22.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp (pdb code 9i53). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp, PDB code: 9i53:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 9i53

Go back to Zinc Binding Sites List in 9i53
Zinc binding site 1 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:38.4
occ:1.00
 ND1 A:HIS75 2.1 38.1 1.0
SG A:CYS55 2.3 40.8 1.0
SG A:CYS50 2.3 34.5 1.0
SG A:CYS72 2.3 33.5 1.0
CE1 A:HIS75 3.0 39.2 1.0
CG A:HIS75 3.2 39.3 1.0
CB A:CYS55 3.2 40.1 1.0
CB A:CYS50 3.3 31.7 1.0
CB A:CYS72 3.4 31.4 1.0
CB A:HIS75 3.6 33.5 1.0
N A:CYS72 3.8 32.4 1.0
NE2 A:HIS75 4.2 40.8 1.0
CA A:CYS72 4.2 35.4 1.0
CD2 A:HIS75 4.3 42.5 1.0
CG2 A:VAL57 4.5 41.9 1.0
CB A:ALA52 4.5 35.2 1.0
N A:HIS75 4.5 40.7 1.0
CA A:CYS55 4.7 46.2 1.0
CA A:HIS75 4.7 39.4 1.0
CA A:CYS50 4.7 40.8 1.0
CB A:VAL57 4.7 46.7 1.0
C A:CYS72 4.8 36.5 1.0
C A:TYR71 5.0 39.9 1.0

Zinc binding site 2 out of 6 in 9i53

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Zinc binding site 2 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp


Mono view


Stereo pair view

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

b:36.1
occ:1.00
 ND1 A:HIS39 2.0 35.5 1.0
NE2 A:HIS33 2.0 32.5 1.0
SG A:CYS19 2.3 37.7 1.0
SG A:CYS16 2.3 39.1 1.0
CE1 A:HIS39 2.9 40.2 1.0
CE1 A:HIS33 2.9 35.2 1.0
CG A:HIS39 3.0 35.7 1.0
CD2 A:HIS33 3.1 33.2 1.0
N A:CYS19 3.3 33.7 1.0
CB A:CYS16 3.3 35.1 1.0
CB A:CYS19 3.4 34.2 1.0
CB A:HIS39 3.4 35.9 1.0
CA A:CYS19 3.7 34.4 1.0
NE2 A:HIS39 4.0 36.3 1.0
ND1 A:HIS33 4.1 38.5 1.0
CD2 A:HIS39 4.1 42.9 1.0
CG A:HIS33 4.2 41.5 1.0
C A:ALA18 4.2 34.9 1.0
CB A:ALA18 4.3 34.0 1.0
CA A:ALA18 4.6 37.6 1.0
CB A:ALA110 4.6 37.0 1.0
N A:ALA18 4.7 34.8 1.0
CA A:CYS16 4.7 39.5 1.0
CA A:HIS39 4.9 37.2 1.0

Zinc binding site 3 out of 6 in 9i53

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Zinc binding site 3 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:52.2
occ:1.00
 SG A:CYS8 2.3 65.9 1.0
SG A:CYS29 2.3 51.2 1.0
SG A:CYS26 2.3 55.8 1.0
SG A:CYS5 2.3 54.2 1.0
CB A:CYS29 3.1 52.2 1.0
CB A:CYS5 3.3 67.2 1.0
CB A:CYS26 3.4 58.2 1.0
CB A:CYS8 3.6 66.5 1.0
N A:CYS26 3.7 55.4 1.0
N A:CYS8 3.9 68.1 1.0
N A:CYS29 4.1 61.5 1.0
CA A:CYS26 4.2 59.9 1.0
CA A:CYS29 4.3 52.6 1.0
CA A:CYS8 4.3 69.7 1.0
CA A:GLY99 4.3 73.1 1.0
N A:GLY99 4.3 77.0 1.0
CB A:LEU7 4.4 59.9 1.0
C A:GLY99 4.6 72.4 1.0
CA A:CYS5 4.8 65.0 1.0
C A:LEU7 4.8 64.3 1.0
CB A:SER10 4.8 72.5 1.0
C A:CYS26 4.8 58.4 1.0
O A:GLY99 4.9 75.3 1.0
C A:LEU25 4.9 52.2 1.0
C A:CYS8 4.9 71.7 1.0
CA A:LEU7 5.0 63.6 1.0
N A:LEU7 5.0 59.5 1.0
OG A:SER10 5.0 72.7 1.0
O A:CYS26 5.0 54.3 1.0

Zinc binding site 4 out of 6 in 9i53

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Zinc binding site 4 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:32.3
occ:1.00
 NE2 B:HIS33 2.1 41.9 1.0
ND1 B:HIS39 2.1 31.3 1.0
SG B:CYS16 2.3 31.8 1.0
SG B:CYS19 2.3 35.6 1.0
CD2 B:HIS33 3.0 27.5 1.0
CG B:HIS39 3.1 31.4 1.0
CE1 B:HIS39 3.1 32.7 1.0
CE1 B:HIS33 3.1 31.9 1.0
CB B:HIS39 3.4 32.9 1.0
CB B:CYS19 3.4 35.5 1.0
N B:CYS19 3.4 30.2 1.0
CB B:CYS16 3.4 36.9 1.0
CA B:CYS19 3.8 35.8 1.0
CG B:HIS33 4.2 36.1 1.0
NE2 B:HIS39 4.2 33.4 1.0
ND1 B:HIS33 4.2 27.9 1.0
CD2 B:HIS39 4.2 34.7 1.0
C B:ALA18 4.2 43.4 1.0
CB B:ALA18 4.6 32.2 1.0
CB B:ALA110 4.6 35.6 1.0
CA B:ALA18 4.8 37.2 1.0
CA B:CYS16 4.8 30.0 1.0
N B:ALA18 4.8 34.2 1.0
CA B:HIS39 4.9 33.7 1.0
O B:ALA18 4.9 41.3 1.0

Zinc binding site 5 out of 6 in 9i53

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Zinc binding site 5 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:44.5
occ:1.00
 SG B:CYS26 2.3 53.5 1.0
SG B:CYS29 2.3 47.7 1.0
SG B:CYS8 2.3 52.1 1.0
SG B:CYS5 2.4 45.1 1.0
CB B:CYS29 3.1 38.1 1.0
CB B:CYS5 3.3 51.6 1.0
CB B:CYS8 3.5 57.4 1.0
CB B:CYS26 3.6 55.4 1.0
N B:CYS8 3.8 58.3 1.0
N B:CYS26 3.9 41.4 1.0
N B:CYS29 4.1 35.6 1.0
CA B:CYS8 4.2 53.1 1.0
CA B:CYS29 4.3 40.0 1.0
CA B:CYS26 4.3 43.2 1.0
N B:GLY99 4.5 63.5 1.0
CA B:GLY99 4.5 53.9 1.0
CB B:LEU7 4.6 45.8 1.0
C B:LEU7 4.7 54.9 1.0
CA B:CYS5 4.7 44.8 1.0
OG B:SER10 4.7 60.4 1.0
C B:GLY99 4.8 53.9 1.0
C B:CYS8 4.8 53.4 1.0
CB B:SER10 4.8 61.2 1.0
C B:CYS26 5.0 40.1 1.0

Zinc binding site 6 out of 6 in 9i53

Go back to Zinc Binding Sites List in 9i53
Zinc binding site 6 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:52.2
occ:1.00
 ND1 B:HIS75 2.1 50.9 1.0
SG B:CYS50 2.3 51.8 1.0
SG B:CYS55 2.3 59.0 1.0
SG B:CYS72 2.3 60.1 1.0
CE1 B:HIS75 3.0 53.5 1.0
CB B:CYS55 3.1 62.3 1.0
CG B:HIS75 3.2 53.5 1.0
CB B:CYS50 3.4 53.0 1.0
CB B:CYS72 3.5 48.8 1.0
CB B:HIS75 3.6 60.0 1.0
N B:CYS72 3.9 52.6 1.0
NE2 B:HIS75 4.2 65.3 1.0
CD2 B:HIS75 4.3 66.5 1.0
CB B:ALA52 4.3 61.9 1.0
CA B:CYS72 4.3 56.7 1.0
CG2 B:VAL57 4.5 44.8 1.0
N B:HIS75 4.5 55.9 1.0
CA B:CYS55 4.6 69.0 1.0
CA B:HIS75 4.7 62.4 1.0
CB B:VAL57 4.8 57.2 1.0
CA B:CYS50 4.8 57.3 1.0
C B:CYS72 4.9 59.9 1.0

Reference:

P.Kloskowski, P.Neumann, A.Berndt, R.Ficner. Nucleotide-Bound Crystal Structures of the Sars-Cov-2 Helicase NSP13. Acta Crystallogr.,Sect.F 2025.
ISSN: ESSN 2053-230X
PubMed: 40638074
DOI: 10.1107/S2053230X25005266
Page generated: Fri Aug 22 18:09:59 2025

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