Zinc in PDB 6zsl: Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution

Enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution:
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 at 1.94 Angstrom Resolution, PDB code: 6zsl was solved by J.A.Newman, Y.Yosaatmadja, A.Douangamath, C.H.Arrowsmith, F.Von Delft, A.Edwards, C.Bountra, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.56 / 1.94
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.151, 70.120, 84.558, 102.47, 95.65, 112.79
R / Rfree (%) 20.9 / 25.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution (pdb code 6zsl). 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 at 1.94 Angstrom Resolution, PDB code: 6zsl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6zsl

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Zinc binding site 1 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution


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 at 1.94 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:47.2
occ:1.00
ND1 B:HIS39 2.1 44.5 1.0
NE2 B:HIS33 2.2 44.5 1.0
SG B:CYS16 2.2 48.5 1.0
SG B:CYS19 2.4 43.9 1.0
CG B:HIS39 3.0 48.2 1.0
CE1 B:HIS39 3.1 49.6 1.0
CD2 B:HIS33 3.1 38.6 1.0
CE1 B:HIS33 3.2 45.7 1.0
CB B:CYS16 3.3 55.1 1.0
CB B:HIS39 3.3 44.8 1.0
CB B:CYS19 3.4 35.6 1.0
N B:CYS19 3.4 46.8 1.0
CA B:CYS19 3.8 45.8 1.0
NE2 B:HIS39 4.2 47.7 1.0
CD2 B:HIS39 4.2 47.7 1.0
CG B:HIS33 4.3 43.3 1.0
ND1 B:HIS33 4.3 39.9 1.0
C B:ALA18 4.3 47.2 1.0
CB B:ALA110 4.5 44.4 1.0
CB B:ALA18 4.6 45.0 1.0
CA B:CYS16 4.7 56.7 1.0
CA B:HIS39 4.8 37.8 1.0
N B:ALA18 4.8 49.4 1.0
CA B:ALA18 4.8 52.3 1.0
CE2 B:PHE106 4.8 37.1 1.0
C B:CYS16 4.9 50.1 1.0
CZ B:PHE106 5.0 43.8 1.0

Zinc binding site 2 out of 6 in 6zsl

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Zinc binding site 2 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution


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 at 1.94 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:66.8
occ:1.00
SG B:CYS26 2.4 77.2 1.0
SG B:CYS8 2.4 79.9 1.0
SG B:CYS5 2.5 69.1 1.0
SG B:CYS29 2.6 67.5 1.0
CB B:CYS8 3.0 68.9 1.0
CB B:CYS29 3.0 53.1 1.0
CB B:CYS26 3.3 56.0 1.0
CB B:CYS5 3.6 73.1 1.0
N B:CYS8 3.7 76.6 1.0
N B:CYS26 3.9 61.3 1.0
CA B:CYS8 4.0 77.4 1.0
N B:CYS29 4.0 62.4 1.0
CA B:CYS26 4.1 65.9 1.0
CA B:CYS29 4.1 54.9 1.0
N B:GLY99 4.2 75.3 1.0
CA B:GLY99 4.2 74.5 1.0
CB B:LEU7 4.5 68.7 1.0
C B:LEU7 4.5 66.7 1.0
OG B:SER100 4.7 64.5 1.0
C B:CYS26 4.7 61.4 1.0
C B:GLY99 4.7 75.6 1.0
O B:CYS26 4.8 55.5 1.0
CA B:LEU7 4.9 67.6 1.0
CA B:CYS5 5.0 76.9 1.0

Zinc binding site 3 out of 6 in 6zsl

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Zinc binding site 3 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution


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 at 1.94 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:69.0
occ:1.00
ND1 B:HIS75 2.0 69.1 1.0
SG B:CYS55 2.3 75.6 1.0
SG B:CYS50 2.4 68.0 1.0
SG B:CYS72 2.5 60.6 1.0
CE1 B:HIS75 2.9 77.1 1.0
CG B:HIS75 3.1 67.7 1.0
CB B:CYS55 3.1 85.4 1.0
CB B:CYS72 3.5 53.5 1.0
CB B:CYS50 3.5 61.6 1.0
CB B:HIS75 3.5 65.8 1.0
CB B:ALA52 3.8 77.6 1.0
N B:CYS72 3.9 54.5 1.0
NE2 B:HIS75 4.0 76.2 1.0
CD2 B:HIS75 4.1 68.7 1.0
CA B:CYS72 4.3 52.7 1.0
N B:HIS75 4.5 61.3 1.0
CG2 B:VAL57 4.5 64.5 1.0
CA B:CYS55 4.6 86.8 1.0
CA B:HIS75 4.6 67.3 1.0
CB B:VAL57 4.7 61.4 1.0
CA B:CYS50 4.9 67.5 1.0
C B:CYS72 5.0 60.2 1.0

Zinc binding site 4 out of 6 in 6zsl

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Zinc binding site 4 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution


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 at 1.94 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:56.0
occ:1.00
ND1 A:HIS75 2.1 56.6 1.0
SG A:CYS55 2.2 61.1 1.0
SG A:CYS50 2.3 48.4 1.0
SG A:CYS72 2.5 57.4 1.0
CE1 A:HIS75 3.0 56.5 1.0
CB A:CYS55 3.1 53.8 1.0
CB A:CYS50 3.2 53.7 1.0
CG A:HIS75 3.2 53.9 1.0
CB A:CYS72 3.4 57.6 1.0
CB A:HIS75 3.7 53.8 1.0
N A:CYS72 3.8 47.1 1.0
NE2 A:HIS75 4.2 46.3 1.0
CA A:CYS72 4.2 53.4 1.0
CD2 A:HIS75 4.3 52.6 1.0
CB A:ALA52 4.3 53.9 1.0
CG2 A:VAL57 4.4 53.1 1.0
CA A:CYS55 4.6 54.9 1.0
CB A:VAL57 4.6 55.7 1.0
N A:HIS75 4.6 56.4 1.0
CA A:CYS50 4.6 49.9 1.0
CA A:HIS75 4.8 51.3 1.0
C A:CYS72 4.9 64.1 1.0
C A:TYR71 5.0 50.2 1.0

Zinc binding site 5 out of 6 in 6zsl

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Zinc binding site 5 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution


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 at 1.94 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:45.7
occ:1.00
NE2 A:HIS33 2.0 28.4 1.0
ND1 A:HIS39 2.0 40.5 1.0
SG A:CYS16 2.3 47.9 1.0
SG A:CYS19 2.4 48.0 1.0
CE1 A:HIS39 2.9 50.4 1.0
CD2 A:HIS33 2.9 51.7 1.0
CE1 A:HIS33 3.0 47.8 1.0
CG A:HIS39 3.0 56.1 1.0
N A:CYS19 3.3 50.3 1.0
CB A:CYS16 3.4 46.3 1.0
CB A:HIS39 3.4 50.5 1.0
CB A:CYS19 3.4 36.5 1.0
CA A:CYS19 3.7 45.1 1.0
NE2 A:HIS39 4.0 50.3 1.0
ND1 A:HIS33 4.1 49.9 1.0
CD2 A:HIS39 4.1 50.3 1.0
CG A:HIS33 4.1 44.4 1.0
C A:ALA18 4.1 49.0 1.0
CB A:ALA18 4.2 52.9 1.0
CB A:ALA110 4.5 47.7 1.0
CA A:ALA18 4.6 54.2 1.0
N A:ALA18 4.6 52.0 1.0
CA A:CYS16 4.7 51.1 1.0
CA A:HIS39 4.8 51.5 1.0
C A:CYS16 5.0 50.6 1.0
CE2 A:PHE106 5.0 50.4 1.0
O A:ALA18 5.0 61.1 1.0

Zinc binding site 6 out of 6 in 6zsl

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Zinc binding site 6 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution


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 at 1.94 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:70.1
occ:1.00
SG A:CYS5 2.3 69.7 1.0
SG A:CYS26 2.4 70.3 1.0
SG A:CYS29 2.4 73.5 1.0
SG A:CYS8 2.5 84.8 1.0
CB A:CYS29 3.0 69.0 1.0
CB A:CYS26 3.2 68.9 1.0
CB A:CYS5 3.3 70.5 1.0
CB A:CYS8 3.4 75.7 1.0
N A:CYS26 3.6 59.0 1.0
N A:CYS8 3.7 76.2 1.0
CA A:CYS26 4.0 68.7 1.0
CA A:CYS8 4.1 79.8 1.0
CB A:LEU7 4.2 67.2 1.0
CA A:CYS29 4.2 65.5 1.0
N A:CYS29 4.2 69.0 1.0
C A:LEU7 4.5 72.1 1.0
C A:CYS26 4.7 69.3 1.0
CA A:LEU7 4.8 69.2 1.0
CA A:CYS5 4.8 73.3 1.0
C A:CYS8 4.8 77.9 1.0
C A:LEU25 4.8 64.4 1.0
N A:LEU7 4.8 67.4 1.0
O A:CYS26 4.8 70.4 1.0

Reference:

J.A.Newman, Y.Yosaatmadja, A.Douangamath, C.H.Arrowsmith, F.Von Delft, A.Edwards, C.Bountra, O.Gileadi. Crystal Structure of the Sars-Cov-2 Helicase at 1.94 Angstrom Resolution To Be Published.
Page generated: Wed Dec 16 13:30:38 2020

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