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Zinc in PDB 9i1s: Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Myricetin

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

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Myricetin:
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 Myricetin, PDB code: 9i1s 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) 35.63 / 2.09
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.327, 70.632, 86.149, 103.11, 96.1, 112.15
R / Rfree (%) 21.5 / 24.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Myricetin (pdb code 9i1s). 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 Myricetin, PDB code: 9i1s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 9i1s

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Zinc binding site 1 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 in Complex with Myricetin


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

b:57.5
occ:1.00
 ND1 A:HIS75 2.1 65.7 1.0
SG A:CYS55 2.3 63.1 1.0
SG A:CYS72 2.3 62.1 1.0
SG A:CYS50 2.3 60.3 1.0
CE1 A:HIS75 3.0 60.1 1.0
CG A:HIS75 3.1 62.2 1.0
CB A:CYS55 3.2 65.6 1.0
CB A:CYS72 3.3 63.0 1.0
CB A:CYS50 3.4 65.6 1.0
CB A:HIS75 3.5 59.4 1.0
N A:CYS72 3.8 60.2 1.0
NE2 A:HIS75 4.1 65.9 1.0
CA A:CYS72 4.2 66.0 1.0
CB A:ALA52 4.2 67.5 1.0
CD2 A:HIS75 4.2 65.8 1.0
CG2 A:VAL57 4.6 75.2 1.0
N A:HIS75 4.6 64.1 1.0
CA A:CYS55 4.7 69.1 1.0
CA A:HIS75 4.7 65.8 1.0
CA A:CYS50 4.8 70.1 1.0
CB A:VAL57 4.8 67.3 1.0
C A:CYS72 4.9 67.6 1.0
C A:TYR71 5.0 62.8 1.0

Zinc binding site 2 out of 6 in 9i1s

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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 Myricetin


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

b:72.4
occ:1.00
 NE2 A:HIS33 2.0 72.1 1.0
ND1 A:HIS39 2.0 73.4 1.0
SG A:CYS19 2.3 75.5 1.0
SG A:CYS16 2.3 74.0 1.0
CE1 A:HIS39 2.9 69.8 1.0
N A:CYS19 2.9 73.3 1.0
CE1 A:HIS33 2.9 71.6 1.0
CD2 A:HIS33 3.0 73.5 1.0
CG A:HIS39 3.1 71.5 1.0
CB A:CYS19 3.2 76.3 1.0
CB A:CYS16 3.4 77.3 1.0
CA A:CYS19 3.4 77.5 1.0
CB A:HIS39 3.5 69.9 1.0
C A:ALA18 3.8 75.4 1.0
CB A:ALA18 3.9 75.6 1.0
NE2 A:HIS39 4.1 74.6 1.0
ND1 A:HIS33 4.1 72.8 1.0
CG A:HIS33 4.1 74.0 1.0
CD2 A:HIS39 4.2 72.1 1.0
CA A:ALA18 4.2 80.0 1.0
N A:ALA18 4.3 73.8 1.0
O A:ALA18 4.6 78.7 1.0
CA A:CYS16 4.7 80.0 1.0
CB A:ALA110 4.7 75.3 1.0
C A:CYS16 4.9 79.9 1.0
C A:CYS19 4.9 75.8 1.0
CA A:HIS39 4.9 70.4 1.0

Zinc binding site 3 out of 6 in 9i1s

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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 Myricetin


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

b:119.3
occ:1.00
 SG A:CYS26 2.3 123.5 1.0
SG A:CYS5 2.3 108.4 1.0
SG A:CYS8 2.3 127.2 1.0
SG A:CYS29 2.3 117.3 1.0
CB A:CYS5 3.2 113.3 1.0
CB A:CYS29 3.4 104.2 1.0
CB A:CYS8 3.4 126.2 1.0
N A:CYS8 3.6 119.7 1.0
CB A:CYS26 3.7 111.2 1.0
CB A:LEU7 4.1 105.7 1.0
CA A:CYS8 4.1 126.5 1.0
N A:CYS26 4.2 109.1 1.0
C A:LEU7 4.4 118.5 1.0
N A:CYS29 4.4 110.0 1.0
CA A:CYS29 4.5 102.6 1.0
CA A:CYS26 4.5 109.8 1.0
CA A:LEU7 4.6 112.8 1.0
CA A:CYS5 4.6 117.5 1.0
N A:LEU7 4.7 113.7 1.0
C A:CYS8 4.8 131.4 1.0
N A:ASN9 5.0 128.9 1.0

Zinc binding site 4 out of 6 in 9i1s

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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 Myricetin


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

b:47.2
occ:1.00
 ND1 B:HIS39 2.0 50.8 1.0
NE2 B:HIS33 2.1 47.1 1.0
SG B:CYS16 2.3 51.6 1.0
SG B:CYS19 2.3 52.3 1.0
CD2 B:HIS33 2.9 52.8 1.0
CE1 B:HIS39 3.0 54.5 1.0
CG B:HIS39 3.0 51.3 1.0
CE1 B:HIS33 3.1 48.5 1.0
CB B:HIS39 3.4 52.6 1.0
CB B:CYS16 3.4 52.6 1.0
CB B:CYS19 3.4 53.9 1.0
N B:CYS19 3.6 59.1 1.0
CA B:CYS19 3.9 51.4 1.0
NE2 B:HIS39 4.1 55.5 1.0
CD2 B:HIS39 4.1 56.1 1.0
CG B:HIS33 4.1 51.9 1.0
ND1 B:HIS33 4.2 50.7 1.0
C B:ALA18 4.4 57.6 1.0
CB B:ALA110 4.5 51.7 1.0
CB B:ALA18 4.6 52.7 1.0
CA B:CYS16 4.8 48.9 1.0
CE2 B:PHE106 4.9 52.2 1.0
CA B:HIS39 4.9 51.5 1.0
CA B:ALA18 4.9 58.0 1.0

Zinc binding site 5 out of 6 in 9i1s

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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 Myricetin


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

b:62.5
occ:1.00
 SG B:CYS26 2.3 66.0 1.0
SG B:CYS29 2.3 61.8 1.0
SG B:CYS8 2.3 84.2 1.0
SG B:CYS5 2.3 64.9 1.0
CB B:CYS29 3.2 53.8 1.0
CB B:CYS5 3.3 75.0 1.0
CB B:CYS8 3.6 72.4 1.0
CB B:CYS26 3.8 66.8 1.0
N B:CYS8 4.0 74.6 1.0
N B:CYS26 4.0 54.4 1.0
N B:CYS29 4.2 56.9 1.0
CA B:CYS8 4.3 74.5 1.0
CA B:CYS29 4.4 52.8 1.0
CB B:LEU7 4.4 65.8 1.0
CA B:GLY99 4.5 76.0 1.0
CA B:CYS26 4.5 61.7 1.0
N B:GLY99 4.6 81.6 1.0
C B:LEU7 4.7 76.8 1.0
CA B:CYS5 4.8 74.4 1.0
C B:GLY99 4.8 79.1 1.0
CB B:SER10 4.8 80.5 1.0
OG B:SER10 4.9 83.9 1.0
N B:LEU7 4.9 73.8 1.0
CA B:LEU7 4.9 71.0 1.0
C B:CYS8 4.9 79.1 1.0
O B:GLY99 4.9 75.1 1.0

Zinc binding site 6 out of 6 in 9i1s

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


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

b:84.3
occ:1.00
 ND1 B:HIS75 2.1 95.4 1.0
SG B:CYS55 2.3 89.6 1.0
SG B:CYS72 2.3 87.7 1.0
SG B:CYS50 2.3 89.5 1.0
CE1 B:HIS75 3.1 94.3 1.0
CG B:HIS75 3.1 95.4 1.0
CB B:CYS55 3.1 95.8 1.0
CB B:CYS50 3.3 78.3 1.0
CB B:HIS75 3.4 93.3 1.0
CB B:CYS72 3.5 77.3 1.0
N B:CYS72 4.0 81.4 1.0
NE2 B:HIS75 4.1 101.5 1.0
CD2 B:HIS75 4.2 100.9 1.0
CB B:ALA52 4.2 98.4 1.0
CA B:CYS72 4.3 81.3 1.0
N B:HIS75 4.4 87.9 1.0
CA B:HIS75 4.5 95.4 1.0
CA B:CYS55 4.5 97.6 1.0
CG2 B:VAL57 4.6 79.5 1.0
CA B:CYS50 4.7 84.5 1.0
CB B:VAL57 4.8 78.1 1.0

Reference:

P.Kloskowski, P.Neumann, P.Kumar, A.Berndt, M.Dobbelstein, R.Ficner. Myricetin-Bound Crystal Structure of the Sars-Cov-2 Helicase NSP13 Facilitates the Discovery of Novel Natural Inhibitors. Acta Crystallogr D Struct V. 81 310 2025BIOL.
ISSN: ISSN 2059-7983
PubMed: 40421686
DOI: 10.1107/S2059798325004498
Page generated: Fri Aug 22 18:08:30 2025

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