Zinc in PDB 7nng: Crystal Structure of the Sars-Cov-2 Helicase in Complex with Z2327226104

Enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase in Complex with Z2327226104

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase in Complex with Z2327226104:
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 in Complex with Z2327226104, PDB code: 7nng 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) 81.35 / 2.38
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.205, 70.353, 85.499, 103.16, 96.1, 112.04
R / Rfree (%) 24.5 / 29.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Z2327226104 (pdb code 7nng). 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 in Complex with Z2327226104, PDB code: 7nng:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7nng

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Zinc binding site 1 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Z2327226104


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 in Complex with Z2327226104 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:56.1
occ:1.00
ND1 B:HIS39 2.0 50.3 1.0
NE2 B:HIS33 2.1 65.0 1.0
SG B:CYS16 2.3 47.2 1.0
SG B:CYS19 2.3 56.5 1.0
CE1 B:HIS39 3.0 54.1 1.0
CG B:HIS39 3.0 61.6 1.0
CD2 B:HIS33 3.0 66.5 1.0
CE1 B:HIS33 3.1 57.9 1.0
CB B:HIS39 3.3 63.3 1.0
CB B:CYS16 3.3 53.5 1.0
CB B:CYS19 3.6 55.3 1.0
N B:CYS19 3.8 69.1 1.0
NE2 B:HIS39 4.1 49.4 1.0
CD2 B:HIS39 4.1 55.2 1.0
ND1 B:HIS33 4.2 64.0 1.0
CG B:HIS33 4.2 70.3 1.0
CA B:CYS19 4.2 65.1 1.0
C B:ALA18 4.5 71.0 1.0
CB B:ALA18 4.6 61.7 1.0
CA B:CYS16 4.7 54.3 1.0
CB B:ALA110 4.8 41.4 1.0
CA B:HIS39 4.8 54.6 1.0
CA B:ALA18 5.0 63.7 1.0
N B:ALA18 5.0 57.3 1.0

Zinc binding site 2 out of 6 in 7nng

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Zinc binding site 2 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Z2327226104


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 in Complex with Z2327226104 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:90.9
occ:1.00
SG B:CYS26 2.3 100.7 1.0
SG B:CYS5 2.3 101.4 1.0
SG B:CYS29 2.3 84.1 1.0
CB B:CYS29 2.8 84.6 1.0
CB B:CYS8 3.4 107.3 1.0
CB B:CYS5 3.4 96.4 1.0
CB B:CYS26 3.5 85.5 1.0
N B:CYS8 3.5 99.2 1.0
SG B:CYS8 3.7 103.1 1.0
N B:CYS26 3.8 97.4 1.0
CB B:LEU7 4.0 85.1 1.0
CA B:CYS29 4.0 92.4 1.0
CA B:CYS8 4.0 111.5 1.0
N B:CYS29 4.1 97.5 1.0
CA B:CYS26 4.2 93.5 1.0
C B:LEU7 4.3 83.9 1.0
O B:CYS26 4.4 93.8 1.0
CA B:LEU7 4.5 83.2 1.0
N B:LEU7 4.5 80.2 1.0
C B:CYS26 4.7 93.1 1.0
C B:CYS8 4.7 95.4 1.0
CA B:CYS5 4.8 85.8 1.0
C B:LEU25 4.9 91.9 1.0
N B:ASN9 4.9 99.4 1.0

Zinc binding site 3 out of 6 in 7nng

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Zinc binding site 3 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Z2327226104


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 in Complex with Z2327226104 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:102.1
occ:1.00
ND1 B:HIS75 2.1 107.4 1.0
SG B:CYS55 2.3 77.7 1.0
SG B:CYS72 2.3 101.0 1.0
SG B:CYS50 2.3 80.6 1.0
CG B:HIS75 2.9 96.4 1.0
CE1 B:HIS75 2.9 97.6 1.0
CB B:CYS55 3.1 89.6 1.0
CB B:CYS72 3.3 76.9 1.0
CB B:HIS75 3.3 94.1 1.0
CB B:CYS50 3.5 90.8 1.0
NE2 B:HIS75 3.8 87.1 1.0
CD2 B:HIS75 3.8 88.0 1.0
N B:CYS72 3.8 78.1 1.0
CA B:CYS72 4.1 75.3 1.0
N B:HIS75 4.3 79.0 1.0
CB B:ALA52 4.3 92.1 1.0
CG2 B:VAL57 4.4 86.8 1.0
CA B:HIS75 4.4 90.2 1.0
CA B:CYS55 4.6 90.5 1.0
CB B:VAL57 4.7 85.4 1.0
C B:CYS72 4.8 80.8 1.0
CA B:CYS50 4.9 91.1 1.0
C B:TYR71 4.9 79.7 1.0

Zinc binding site 4 out of 6 in 7nng

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Zinc binding site 4 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Z2327226104


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 in Complex with Z2327226104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:71.8
occ:1.00
ND1 A:HIS75 2.3 88.2 1.0
SG A:CYS72 2.3 63.0 1.0
SG A:CYS55 2.3 67.9 1.0
SG A:CYS50 2.3 69.7 1.0
CE1 A:HIS75 2.9 82.7 1.0
CB A:CYS55 3.1 58.3 1.0
CB A:CYS72 3.2 70.3 1.0
CG A:HIS75 3.4 67.5 1.0
CB A:CYS50 3.4 66.3 1.0
N A:CYS72 3.9 66.4 1.0
CB A:HIS75 4.0 64.0 1.0
NE2 A:HIS75 4.0 69.8 1.0
CB A:ALA52 4.1 64.9 1.0
CA A:CYS72 4.1 69.5 1.0
CD2 A:HIS75 4.3 69.9 1.0
CA A:CYS55 4.5 59.6 1.0
N A:HIS75 4.6 77.5 1.0
C A:CYS72 4.8 78.8 1.0
CA A:CYS50 4.8 68.1 1.0
CA A:HIS75 5.0 68.9 1.0

Zinc binding site 5 out of 6 in 7nng

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Zinc binding site 5 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Z2327226104


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 in Complex with Z2327226104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:68.8
occ:1.00
NE2 A:HIS33 2.0 49.8 1.0
ND1 A:HIS39 2.0 77.0 1.0
SG A:CYS19 2.3 62.1 1.0
SG A:CYS16 2.3 93.3 1.0
CE1 A:HIS39 2.8 78.2 1.0
CD2 A:HIS33 2.9 60.8 1.0
CG A:HIS39 3.0 81.7 1.0
CE1 A:HIS33 3.1 62.4 1.0
CB A:CYS16 3.3 70.0 1.0
CB A:HIS39 3.5 72.3 1.0
CB A:CYS19 3.6 47.0 1.0
N A:CYS19 3.7 79.5 1.0
NE2 A:HIS39 3.8 68.5 1.0
CD2 A:HIS39 3.9 76.9 1.0
CA A:CYS19 4.1 68.2 1.0
CG A:HIS33 4.1 60.6 1.0
ND1 A:HIS33 4.1 64.3 1.0
CB A:ALA18 4.6 79.8 1.0
C A:ALA18 4.6 78.9 1.0
CB A:ALA110 4.7 66.2 1.0
CA A:CYS16 4.7 77.6 1.0
CZ A:PHE106 4.9 62.5 1.0
CA A:HIS39 4.9 68.3 1.0
CA A:ALA18 5.0 78.2 1.0

Zinc binding site 6 out of 6 in 7nng

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Zinc binding site 6 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Z2327226104


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 in Complex with Z2327226104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:102.9
occ:1.00
SG A:CYS26 2.3 147.8 1.0
SG A:CYS8 2.3 113.5 1.0
SG A:CYS29 2.3 95.5 1.0
SG A:CYS5 2.3 93.3 1.0
CB A:CYS26 3.2 106.1 1.0
CB A:CYS29 3.4 103.6 1.0
CB A:CYS5 3.4 95.9 1.0
CB A:CYS8 3.8 91.0 1.0
N A:CYS26 4.0 106.8 1.0
N A:CYS8 4.1 104.0 1.0
CA A:CYS26 4.1 103.1 1.0
N A:CYS29 4.1 113.3 1.0
CA A:CYS29 4.4 101.9 1.0
CA A:CYS8 4.5 100.4 1.0
CB A:LEU7 4.5 81.5 1.0
O A:CYS26 4.5 107.5 1.0
C A:CYS26 4.6 104.4 1.0
CB A:SER10 4.9 98.6 1.0
CA A:CYS5 4.9 99.0 1.0
CB A:LYS28 4.9 106.3 1.0
C A:LEU7 4.9 92.8 1.0
OG A:SER10 4.9 86.3 1.0

Reference:

J.A.Newman, Y.Yosaatmadja, A.Douangamath, C.Bountra, O.Gileadi. Crystal Structure of the Sars-Cov-2 Helicase in Complex with Z2327226104 To Be Published.
Page generated: Sat Apr 17 17:49:12 2021

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