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Zinc in PDB 9i51: Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Adp

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

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Adp:
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 Adp, PDB code: 9i51 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) 34.22 / 1.82
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.31, 70.504, 85.206, 103.1, 94.85, 112.74
R / Rfree (%) 17.3 / 20.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Adp (pdb code 9i51). 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 Adp, PDB code: 9i51:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 9i51

Go back to Zinc Binding Sites List in 9i51
Zinc binding site 1 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:40.4
occ:1.00
 ND1 A:HIS75 2.1 43.2 1.0
SG A:CYS55 2.3 42.6 1.0
SG A:CYS50 2.3 39.4 1.0
SG A:CYS72 2.4 39.0 1.0
CE1 A:HIS75 2.9 45.4 1.0
CB A:CYS55 3.1 40.6 1.0
CG A:HIS75 3.2 42.0 1.0
CB A:CYS50 3.2 35.6 1.0
CB A:CYS72 3.3 36.6 1.0
CB A:HIS75 3.7 37.0 1.0
N A:CYS72 3.8 39.7 1.0
NE2 A:HIS75 4.1 40.1 1.0
CA A:CYS72 4.1 43.2 1.0
CD2 A:HIS75 4.2 37.1 1.0
CB A:ALA52 4.5 39.3 1.0
CG2 A:VAL57 4.5 44.8 1.0
N A:HIS75 4.6 39.0 1.0
CA A:CYS55 4.6 53.5 1.0
CA A:CYS50 4.7 41.2 1.0
CB A:VAL57 4.7 49.2 1.0
CA A:HIS75 4.8 38.2 1.0
C A:CYS72 4.8 44.7 1.0

Zinc binding site 2 out of 6 in 9i51

Go back to Zinc Binding Sites List in 9i51
Zinc binding site 2 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:36.8
occ:1.00
 NE2 A:HIS33 2.0 34.7 1.0
ND1 A:HIS39 2.0 33.9 1.0
SG A:CYS16 2.3 39.5 1.0
SG A:CYS19 2.3 35.5 1.0
CE1 A:HIS39 2.9 37.2 1.0
CE1 A:HIS33 2.9 38.5 1.0
CD2 A:HIS33 3.0 39.2 1.0
CG A:HIS39 3.0 36.8 1.0
CB A:CYS16 3.3 44.6 1.0
N A:CYS19 3.4 38.9 1.0
CB A:HIS39 3.4 40.2 1.0
CB A:CYS19 3.4 36.1 1.0
CA A:CYS19 3.8 35.6 1.0
NE2 A:HIS39 4.0 38.5 1.0
ND1 A:HIS33 4.1 44.0 1.0
CD2 A:HIS39 4.1 42.0 1.0
CG A:HIS33 4.1 41.4 1.0
C A:ALA18 4.2 42.1 1.0
CB A:ALA18 4.4 37.7 1.0
CB A:ALA110 4.6 40.2 1.0
CA A:ALA18 4.7 36.9 1.0
CA A:CYS16 4.7 41.2 1.0
N A:ALA18 4.7 37.9 1.0
CA A:HIS39 4.9 35.4 1.0
C A:CYS16 5.0 43.5 1.0

Zinc binding site 3 out of 6 in 9i51

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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 Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:61.0
occ:1.00
 SG A:CYS29 2.3 54.7 1.0
SG A:CYS26 2.3 58.6 1.0
SG A:CYS8 2.3 70.5 1.0
SG A:CYS5 2.4 61.5 1.0
CB A:CYS29 3.1 53.0 1.0
CB A:CYS5 3.3 66.5 1.0
CB A:CYS26 3.4 58.5 1.0
CB A:CYS8 3.6 75.5 1.0
N A:CYS26 3.7 55.9 1.0
N A:CYS8 3.9 74.8 1.0
CA A:CYS26 4.1 55.5 1.0
N A:CYS29 4.2 58.2 1.0
CA A:CYS29 4.3 53.2 1.0
CA A:CYS8 4.3 71.7 1.0
CB A:LEU7 4.3 69.3 1.0
CA A:GLY99 4.4 73.4 1.0
N A:GLY99 4.5 80.2 1.0
C A:GLY99 4.6 82.0 1.0
O A:GLY99 4.6 92.1 1.0
CA A:CYS5 4.7 67.0 1.0
C A:LEU7 4.8 70.8 1.0
C A:LEU25 4.8 52.7 1.0
C A:CYS26 4.8 55.1 1.0
N A:LEU7 4.9 61.0 1.0
CA A:LEU7 4.9 68.7 1.0
O A:CYS26 4.9 52.1 1.0
C A:CYS8 5.0 75.0 1.0
CB A:SER10 5.0 78.9 1.0

Zinc binding site 4 out of 6 in 9i51

Go back to Zinc Binding Sites List in 9i51
Zinc binding site 4 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Adp


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

b:33.9
occ:1.00
 ND1 B:HIS39 2.0 29.4 1.0
NE2 B:HIS33 2.1 37.1 1.0
SG B:CYS19 2.3 36.2 1.0
SG B:CYS16 2.4 36.8 1.0
CD2 B:HIS33 2.9 32.5 1.0
CE1 B:HIS39 3.0 32.0 1.0
CG B:HIS39 3.0 32.5 1.0
CE1 B:HIS33 3.1 36.9 1.0
CB B:CYS19 3.4 34.9 1.0
CB B:HIS39 3.4 28.5 1.0
CB B:CYS16 3.4 34.8 1.0
N B:CYS19 3.4 31.9 1.0
CA B:CYS19 3.8 34.4 1.0
NE2 B:HIS39 4.1 31.8 1.0
CG B:HIS33 4.1 34.7 1.0
CD2 B:HIS39 4.1 36.4 1.0
ND1 B:HIS33 4.2 37.8 1.0
C B:ALA18 4.2 38.6 1.0
CB B:ALA18 4.6 31.6 1.0
CB B:ALA110 4.6 39.4 1.0
CA B:ALA18 4.8 34.0 1.0
CA B:CYS16 4.8 34.8 1.0
CA B:HIS39 4.9 31.8 1.0
N B:ALA18 4.9 30.8 1.0
O B:ALA18 5.0 36.4 1.0

Zinc binding site 5 out of 6 in 9i51

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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 Adp


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

b:51.9
occ:1.00
 SG B:CYS26 2.2 61.2 1.0
SG B:CYS29 2.3 57.6 1.0
SG B:CYS5 2.3 51.5 1.0
SG B:CYS8 2.5 60.8 1.0
CB B:CYS29 3.1 45.5 1.0
CB B:CYS5 3.3 59.6 1.0
CB B:CYS26 3.5 58.9 1.0
CB B:CYS8 3.7 65.9 1.0
N B:CYS26 3.8 44.7 1.0
N B:CYS8 3.9 70.8 1.0
N B:CYS29 4.1 41.9 1.0
CA B:CYS29 4.3 41.7 1.0
CA B:CYS26 4.3 50.0 1.0
CA B:CYS8 4.3 68.4 1.0
CB B:LEU7 4.5 67.2 1.0
N B:GLY99 4.5 74.2 1.0
CA B:GLY99 4.5 57.5 1.0
OG B:SER100 4.6 87.7 1.0
OG B:SER10 4.6 76.9 1.0
CA B:CYS5 4.8 55.8 1.0
CB B:SER10 4.8 73.9 1.0
C B:CYS8 4.9 60.0 1.0
C B:LEU7 4.9 66.2 1.0
C B:GLY99 4.9 66.2 1.0
C B:CYS26 5.0 41.7 1.0
C B:LEU25 5.0 43.9 1.0

Zinc binding site 6 out of 6 in 9i51

Go back to Zinc Binding Sites List in 9i51
Zinc binding site 6 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Adp


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

b:50.3
occ:1.00
 ND1 B:HIS75 2.1 55.9 1.0
SG B:CYS50 2.2 48.4 1.0
SG B:CYS55 2.3 61.1 1.0
SG B:CYS72 2.4 52.9 1.0
CE1 B:HIS75 3.0 58.8 1.0
CG B:HIS75 3.1 61.4 1.0
CB B:CYS55 3.2 65.0 1.0
CB B:CYS50 3.4 45.0 1.0
CB B:HIS75 3.5 64.4 1.0
CB B:CYS72 3.5 50.8 1.0
N B:CYS72 4.0 50.3 1.0
NE2 B:HIS75 4.1 62.4 1.0
CD2 B:HIS75 4.2 66.4 1.0
CB B:ALA52 4.3 63.1 1.0
CA B:CYS72 4.3 54.0 1.0
CG2 B:VAL57 4.5 54.3 1.0
CA B:CYS55 4.6 76.6 1.0
N B:HIS75 4.7 57.0 1.0
CA B:HIS75 4.7 60.6 1.0
CA B:CYS50 4.8 53.2 1.0
CB B:VAL57 4.8 58.0 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 18:09:40 2025

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