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

Go back to Zinc Binding Sites List in 7nio
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

Go back to Zinc Binding Sites List in 7nio
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

Go back to Zinc Binding Sites List in 7nio
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

Go back to Zinc Binding Sites List in 7nio
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

Go back to Zinc Binding Sites List in 7nio
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

Last articles

Zn in 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy