Zinc in PDB 7nio: Crystal Structure of the Sars-Cov-2 Helicase Apo Form

Enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase Apo Form

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase Apo Form:
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 Apo Form, PDB code: 7nio was solved by J.A.Newman, Y.Yosaatmadja, A.Douangamath, C.Bountra, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.24 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.699, 70.118, 83.998, 104.31, 93.3, 112.16
R / Rfree (%) 23 / 28.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Helicase Apo Form (pdb code 7nio). 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 Apo Form, PDB code: 7nio:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7nio

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Zinc binding site 1 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase Apo Form


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

b:33.0
occ:1.00
 ND1 A:HIS39 2.0 26.9 1.0
NE2 A:HIS33 2.1 38.3 1.0
SG A:CYS16 2.3 29.4 1.0
SG A:CYS19 2.3 33.1 1.0
CE1 A:HIS39 3.0 28.1 1.0
CD2 A:HIS33 3.0 35.2 1.0
CG A:HIS39 3.0 36.1 1.0
CE1 A:HIS33 3.1 35.9 1.0
CB A:CYS16 3.4 30.8 1.0
CB A:HIS39 3.4 32.0 1.0
CB A:CYS19 3.4 24.9 1.0
N A:CYS19 3.6 38.2 1.0
CA A:CYS19 3.9 32.3 1.0
NE2 A:HIS39 4.1 33.1 1.0
CD2 A:HIS39 4.2 33.8 1.0
CG A:HIS33 4.2 30.9 1.0
ND1 A:HIS33 4.2 26.2 1.0
C A:ALA18 4.3 35.9 1.0
CB A:ALA18 4.5 35.5 1.0
CB A:ALA110 4.6 34.7 1.0
CA A:CYS16 4.7 29.8 1.0
CA A:ALA18 4.8 27.6 1.0
N A:ALA18 4.9 31.9 1.0
CA A:HIS39 4.9 41.5 1.0
C A:CYS16 5.0 34.6 1.0
O A:CYS16 5.0 31.9 1.0

Zinc binding site 2 out of 6 in 7nio

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Zinc binding site 2 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase Apo Form


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

b:41.7
occ:1.00
 SG A:CYS29 2.3 36.4 1.0
SG A:CYS8 2.3 51.5 1.0
SG A:CYS26 2.3 47.2 1.0
SG A:CYS5 2.3 39.5 1.0
CB A:CYS29 3.0 36.2 1.0
CB A:CYS26 3.1 33.0 1.0
CB A:CYS5 3.5 41.4 1.0
CB A:CYS8 3.6 36.4 1.0
N A:CYS26 3.7 33.0 1.0
N A:CYS8 3.8 46.7 1.0
CA A:CYS26 3.9 43.9 1.0
N A:CYS29 4.0 40.7 1.0
CA A:CYS29 4.1 30.0 1.0
CA A:GLY99 4.2 45.5 1.0
N A:GLY99 4.2 47.1 1.0
CA A:CYS8 4.3 49.9 1.0
CB A:LEU7 4.5 43.7 1.0
C A:GLY99 4.5 46.7 1.0
C A:CYS26 4.7 32.2 1.0
C A:LEU7 4.8 44.4 1.0
C A:LEU25 4.8 36.7 1.0
C A:CYS8 4.9 48.9 1.0
CA A:CYS5 4.9 43.9 1.0
N A:SER100 4.9 41.3 1.0
N A:LEU7 4.9 47.2 1.0
O A:GLY99 5.0 51.0 1.0
CA A:LEU7 5.0 44.6 1.0

Zinc binding site 3 out of 6 in 7nio

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Zinc binding site 3 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase Apo Form


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

b:42.9
occ:1.00
 ND1 A:HIS75 2.1 43.4 1.0
SG A:CYS50 2.3 47.3 1.0
SG A:CYS55 2.3 38.3 1.0
SG A:CYS72 2.3 35.5 1.0
CE1 A:HIS75 2.8 44.6 1.0
CB A:CYS55 3.1 43.3 1.0
CB A:CYS72 3.3 39.7 1.0
CG A:HIS75 3.3 48.8 1.0
CB A:CYS50 3.4 40.3 1.0
CB A:HIS75 3.8 48.9 1.0
N A:CYS72 3.9 41.8 1.0
NE2 A:HIS75 4.0 46.3 1.0
CA A:CYS72 4.1 40.6 1.0
CB A:ALA52 4.2 48.3 1.0
CD2 A:HIS75 4.3 41.2 1.0
CA A:CYS55 4.6 43.4 1.0
N A:HIS75 4.6 32.1 1.0
CG2 A:VAL57 4.7 37.1 1.0
CB A:VAL57 4.7 36.9 1.0
CA A:CYS50 4.8 37.0 1.0
CA A:HIS75 4.8 41.3 1.0
C A:CYS72 4.9 43.0 1.0

Zinc binding site 4 out of 6 in 7nio

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Zinc binding site 4 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn701

b:32.5
occ:1.00
 ND1 E:HIS39 2.0 38.2 1.0
NE2 E:HIS33 2.1 22.6 1.0
SG E:CYS16 2.3 35.9 1.0
SG E:CYS19 2.3 34.0 1.0
CD2 E:HIS33 2.9 23.2 1.0
CE1 E:HIS39 3.0 28.1 1.0
CG E:HIS39 3.0 27.7 1.0
CE1 E:HIS33 3.1 24.5 1.0
CB E:HIS39 3.4 33.8 1.0
N E:CYS19 3.4 32.1 1.0
CB E:CYS16 3.4 32.3 1.0
CB E:CYS19 3.4 29.2 1.0
CA E:CYS19 3.8 32.4 1.0
CG E:HIS33 4.1 24.4 1.0
NE2 E:HIS39 4.1 33.7 1.0
CD2 E:HIS39 4.2 30.1 1.0
ND1 E:HIS33 4.2 23.6 1.0
C E:ALA18 4.3 33.7 1.0
CB E:ALA18 4.5 32.1 1.0
CB E:ALA110 4.6 27.4 1.0
CA E:ALA18 4.8 35.1 1.0
CA E:CYS16 4.8 33.6 1.0
N E:ALA18 4.9 33.1 1.0
CA E:HIS39 4.9 30.1 1.0

Zinc binding site 5 out of 6 in 7nio

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Zinc binding site 5 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn702

b:42.4
occ:1.00
 SG E:CYS29 2.3 48.5 1.0
SG E:CYS26 2.3 44.3 1.0
SG E:CYS8 2.3 50.4 1.0
SG E:CYS5 2.3 47.8 1.0
CB E:CYS29 3.1 32.6 1.0
CB E:CYS5 3.4 42.6 1.0
CB E:CYS26 3.4 37.1 1.0
CB E:CYS8 3.7 43.1 1.0
N E:CYS26 3.8 39.3 1.0
N E:CYS8 4.0 42.9 1.0
CA E:CYS26 4.2 42.9 1.0
N E:CYS29 4.2 42.5 1.0
CA E:CYS29 4.3 36.8 1.0
CA E:CYS8 4.4 44.1 1.0
CB E:LEU7 4.5 47.4 1.0
CA E:GLY99 4.5 48.8 1.0
N E:GLY99 4.5 56.9 1.0
C E:GLY99 4.7 50.6 1.0
CB E:SER10 4.8 42.2 1.0
CA E:CYS5 4.8 44.1 1.0
C E:LEU7 4.9 43.0 1.0
C E:CYS26 4.9 41.8 1.0
OG E:SER10 4.9 56.9 1.0
N E:LEU7 5.0 39.3 1.0
C E:CYS8 5.0 39.9 1.0
C E:LEU25 5.0 35.1 1.0

Zinc binding site 6 out of 6 in 7nio

Go back to Zinc Binding Sites List in 7nio
Zinc binding site 6 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn703

b:50.7
occ:1.00
 ND1 E:HIS75 2.1 56.4 1.0
SG E:CYS50 2.3 54.0 1.0
SG E:CYS55 2.3 46.5 1.0
SG E:CYS72 2.3 48.7 1.0
CE1 E:HIS75 2.9 53.0 1.0
CB E:CYS55 3.1 48.8 1.0
CG E:HIS75 3.3 48.9 1.0
CB E:CYS50 3.3 45.7 1.0
CB E:CYS72 3.4 49.8 1.0
CB E:HIS75 3.7 49.6 1.0
N E:CYS72 4.0 44.3 1.0
CB E:ALA52 4.0 53.5 1.0
NE2 E:HIS75 4.1 46.3 1.0
CA E:CYS72 4.3 44.9 1.0
CD2 E:HIS75 4.3 43.2 1.0
CA E:CYS55 4.6 52.8 1.0
CG2 E:VAL57 4.6 41.5 1.0
CB E:VAL57 4.6 49.6 1.0
N E:HIS75 4.7 40.1 1.0
CA E:CYS50 4.7 46.0 1.0
CA E:HIS75 4.8 38.0 1.0
C E:CYS72 4.9 42.6 1.0
N E:ALA52 4.9 57.2 1.0

Reference:

J.A.Newman, Y.Yosaatmadja, A.Douangamath, C.Bountra, O.Gileadi. Crystal Structure of the Sars-Cov-2 Helicase Apo Form To Be Published.
Page generated: Sat Apr 3 18:40:17 2021

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