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Zinc in PDB 7nn0: Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp

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

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp:
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 Amp-Pnp, PDB code: 7nn0 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) 81.03 / 3.04
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 324.886, 59.5, 132.379, 90, 93.89, 90
R / Rfree (%) 24.4 / 28.4

Other elements in 7nn0:

The structure of Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp (pdb code 7nn0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp, PDB code: 7nn0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 7nn0

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Zinc binding site 1 out of 12 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp


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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 Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:58.3
occ:1.00
ND1 A:HIS39 2.0 40.8 1.0
NE2 A:HIS33 2.1 49.1 1.0
SG A:CYS16 2.3 34.9 1.0
SG A:CYS19 2.3 60.7 1.0
CG A:HIS39 2.9 48.9 1.0
CD2 A:HIS33 2.9 47.6 1.0
CE1 A:HIS39 3.1 45.6 1.0
CB A:HIS39 3.1 50.0 1.0
CE1 A:HIS33 3.2 47.1 1.0
CB A:CYS19 3.4 43.2 1.0
N A:CYS19 3.4 50.2 1.0
CB A:CYS16 3.5 35.0 1.0
CA A:CYS19 3.8 46.8 1.0
CD2 A:HIS39 4.1 44.6 1.0
CG A:HIS33 4.1 49.2 1.0
NE2 A:HIS39 4.2 42.3 1.0
ND1 A:HIS33 4.2 44.9 1.0
C A:ALA18 4.3 49.6 1.0
CB A:ALA18 4.5 48.2 1.0
CA A:HIS39 4.6 51.4 1.0
CB A:ALA110 4.7 43.8 1.0
CA A:ALA18 4.8 40.4 1.0
CA A:CYS16 4.8 37.5 1.0
N A:ALA18 4.9 37.1 1.0

Zinc binding site 2 out of 12 in 7nn0

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Zinc binding site 2 out of 12 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp


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 Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:61.0
occ:1.00
SG A:CYS26 2.3 84.4 1.0
SG A:CYS29 2.3 57.8 1.0
SG A:CYS8 2.3 96.6 1.0
SG A:CYS5 2.3 59.8 1.0
CB A:CYS29 3.1 69.6 1.0
CB A:CYS26 3.2 78.1 1.0
CB A:CYS8 3.3 78.3 1.0
CB A:CYS5 3.7 64.8 1.0
N A:CYS8 3.8 64.7 1.0
N A:CYS26 3.9 74.3 1.0
CB A:LEU7 4.1 59.1 1.0
CA A:CYS26 4.1 72.4 1.0
CA A:CYS8 4.2 68.7 1.0
N A:CYS29 4.2 69.3 1.0
CA A:CYS29 4.2 68.9 1.0
C A:LEU7 4.3 64.6 1.0
CA A:LEU7 4.6 61.9 1.0
N A:LEU7 4.7 57.7 1.0
C A:CYS26 4.8 75.0 1.0
N A:GLY99 4.9 98.3 1.0
N A:SER100 4.9 87.2 1.0
O A:CYS26 5.0 73.4 1.0

Zinc binding site 3 out of 12 in 7nn0

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Zinc binding site 3 out of 12 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp


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 Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:74.3
occ:1.00
ND1 A:HIS75 2.1 71.7 1.0
SG A:CYS72 2.3 53.4 1.0
SG A:CYS55 2.3 63.6 1.0
SG A:CYS50 2.3 70.7 1.0
CE1 A:HIS75 3.0 69.6 1.0
CB A:CYS72 3.1 59.8 1.0
CG A:HIS75 3.1 60.7 1.0
CB A:CYS55 3.2 77.2 1.0
CB A:CYS50 3.5 73.6 1.0
CB A:HIS75 3.5 63.5 1.0
CB A:ALA52 3.7 73.0 1.0
N A:CYS72 3.8 70.3 1.0
CA A:CYS72 4.0 64.9 1.0
NE2 A:HIS75 4.1 70.1 1.0
CD2 A:HIS75 4.2 61.1 1.0
N A:HIS75 4.3 63.4 1.0
CA A:HIS75 4.5 61.1 1.0
CG2 A:VAL57 4.5 77.7 1.0
CA A:CYS55 4.6 88.0 1.0
C A:CYS72 4.7 74.9 1.0
CB A:VAL57 4.9 69.5 1.0
CA A:CYS50 4.9 68.7 1.0
CA A:ALA52 5.0 73.5 1.0

Zinc binding site 4 out of 12 in 7nn0

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Zinc binding site 4 out of 12 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp


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 Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:39.9
occ:1.00
ND1 B:HIS39 2.0 38.9 1.0
NE2 B:HIS33 2.0 35.4 1.0
SG B:CYS19 2.3 34.7 1.0
SG B:CYS16 2.3 23.3 1.0
CG B:HIS39 3.0 43.5 1.0
CD2 B:HIS33 3.0 30.1 1.0
CE1 B:HIS39 3.0 41.1 1.0
CE1 B:HIS33 3.1 38.6 1.0
CB B:HIS39 3.3 37.1 1.0
CB B:CYS19 3.4 34.0 1.0
CB B:CYS16 3.4 30.2 1.0
N B:CYS19 3.5 36.8 1.0
CA B:CYS19 3.9 32.8 1.0
NE2 B:HIS39 4.1 43.4 1.0
CD2 B:HIS39 4.1 41.9 1.0
CG B:HIS33 4.1 35.9 1.0
ND1 B:HIS33 4.1 38.4 1.0
C B:ALA18 4.4 37.5 1.0
CB B:ALA18 4.6 30.9 1.0
CB B:ALA110 4.7 34.2 1.0
CA B:CYS16 4.8 29.5 1.0
CA B:HIS39 4.8 33.9 1.0
CA B:ALA18 4.9 29.9 1.0
N B:ALA18 5.0 28.1 1.0

Zinc binding site 5 out of 12 in 7nn0

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Zinc binding site 5 out of 12 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp


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 Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:39.7
occ:1.00
SG B:CYS26 2.3 49.1 1.0
SG B:CYS29 2.3 33.9 1.0
SG B:CYS8 2.3 59.2 1.0
SG B:CYS5 2.3 35.0 1.0
CB B:CYS29 3.1 42.5 1.0
CB B:CYS26 3.2 45.0 1.0
CB B:CYS8 3.2 48.0 1.0
CB B:CYS5 3.5 40.7 1.0
N B:CYS8 3.8 45.6 1.0
N B:CYS26 3.8 47.0 1.0
CA B:CYS26 4.1 48.4 1.0
CA B:CYS8 4.1 42.3 1.0
N B:CYS29 4.2 47.5 1.0
CA B:CYS29 4.2 46.1 1.0
CB B:LEU7 4.3 38.6 1.0
C B:LEU7 4.4 43.7 1.0
N B:GLY99 4.5 43.3 1.0
CA B:GLY99 4.5 47.7 1.0
CA B:LEU7 4.7 38.9 1.0
C B:CYS26 4.8 46.7 1.0
N B:LEU7 4.8 37.7 1.0
N B:SER100 4.8 36.4 1.0
CB B:SER10 4.9 39.5 1.0
CA B:CYS5 4.9 34.6 1.0
O B:CYS26 5.0 45.8 1.0

Zinc binding site 6 out of 12 in 7nn0

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Zinc binding site 6 out of 12 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp


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 Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:37.9
occ:1.00
ND1 B:HIS75 2.1 41.3 1.0
SG B:CYS72 2.3 28.8 1.0
SG B:CYS50 2.3 43.6 1.0
SG B:CYS55 2.3 40.0 1.0
CE1 B:HIS75 3.0 46.5 1.0
CG B:HIS75 3.1 37.9 1.0
CB B:CYS72 3.2 40.2 1.0
CB B:CYS50 3.3 33.5 1.0
CB B:CYS55 3.3 39.5 1.0
CB B:HIS75 3.4 42.3 1.0
N B:CYS72 3.9 36.5 1.0
CB B:ALA52 4.1 41.5 1.0
NE2 B:HIS75 4.1 39.0 1.0
CA B:CYS72 4.1 44.0 1.0
CD2 B:HIS75 4.1 37.6 1.0
N B:HIS75 4.3 39.1 1.0
CG2 B:VAL57 4.5 56.1 1.0
CA B:HIS75 4.5 42.9 1.0
CA B:CYS55 4.8 50.6 1.0
CA B:CYS50 4.8 34.1 1.0
C B:CYS72 4.8 42.8 1.0
CB B:VAL57 4.8 46.9 1.0
N B:ALA52 5.0 38.2 1.0

Zinc binding site 7 out of 12 in 7nn0

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Zinc binding site 7 out of 12 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:76.9
occ:1.00
ND1 C:HIS39 2.0 72.7 1.0
NE2 C:HIS33 2.1 75.4 1.0
SG C:CYS16 2.3 50.4 1.0
SG C:CYS19 2.3 80.9 1.0
CG C:HIS39 3.0 78.3 1.0
CE1 C:HIS39 3.0 69.3 1.0
CD2 C:HIS33 3.0 75.7 1.0
CE1 C:HIS33 3.1 74.7 1.0
CB C:HIS39 3.3 70.9 1.0
CB C:CYS19 3.5 69.7 1.0
CB C:CYS16 3.5 60.2 1.0
N C:CYS19 3.6 68.8 1.0
CA C:CYS19 4.0 68.2 1.0
NE2 C:HIS39 4.1 69.0 1.0
CD2 C:HIS39 4.1 78.4 1.0
CG C:HIS33 4.2 81.1 1.0
ND1 C:HIS33 4.2 78.4 1.0
CB C:ALA110 4.3 69.5 1.0
C C:ALA18 4.5 77.5 1.0
CB C:ALA18 4.7 67.1 1.0
CA C:HIS39 4.8 71.3 1.0
CA C:CYS16 4.9 60.9 1.0
CE2 C:PHE106 5.0 74.7 1.0
CA C:ALA18 5.0 69.2 1.0

Zinc binding site 8 out of 12 in 7nn0

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Zinc binding site 8 out of 12 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn702

b:95.2
occ:1.00
SG C:CYS26 2.3 104.0 1.0
SG C:CYS29 2.3 82.4 1.0
SG C:CYS8 2.3 105.6 1.0
SG C:CYS5 2.3 83.3 1.0
CB C:CYS29 3.0 95.9 1.0
CB C:CYS8 3.2 90.6 1.0
CB C:CYS26 3.3 92.8 1.0
CB C:CYS5 3.7 78.3 1.0
N C:CYS8 3.8 91.0 1.0
N C:CYS29 4.0 94.9 1.0
N C:CYS26 4.0 92.0 1.0
CA C:CYS8 4.1 93.5 1.0
CA C:CYS29 4.1 96.9 1.0
CA C:CYS26 4.2 93.6 1.0
CB C:LEU7 4.4 86.3 1.0
C C:LEU7 4.4 83.2 1.0
N C:GLY99 4.5 93.5 1.0
CA C:GLY99 4.5 97.6 1.0
N C:SER100 4.7 100.0 1.0
CA C:LEU7 4.7 85.4 1.0
N C:LEU7 4.8 80.1 1.0
C C:CYS26 4.8 89.7 1.0
CB C:SER10 4.9 99.5 1.0
C C:GLY99 5.0 100.5 1.0

Zinc binding site 9 out of 12 in 7nn0

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Zinc binding site 9 out of 12 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn703

b:73.5
occ:1.00
ND1 C:HIS75 2.1 82.5 1.0
SG C:CYS55 2.3 81.6 1.0
SG C:CYS72 2.3 70.0 1.0
SG C:CYS50 2.3 69.8 1.0
CE1 C:HIS75 3.0 82.8 1.0
CG C:HIS75 3.1 72.1 1.0
CB C:CYS72 3.2 84.6 1.0
CB C:CYS55 3.3 76.5 1.0
CB C:CYS50 3.3 78.3 1.0
CB C:HIS75 3.6 71.4 1.0
N C:CYS72 3.9 81.1 1.0
NE2 C:HIS75 4.1 78.0 1.0
CA C:CYS72 4.1 83.2 1.0
CB C:ALA52 4.2 67.0 1.0
CD2 C:HIS75 4.2 69.7 1.0
N C:HIS75 4.3 76.2 1.0
CA C:HIS75 4.6 73.1 1.0
CA C:CYS55 4.7 70.3 1.0
CG2 C:VAL57 4.7 88.1 1.0
CA C:CYS50 4.8 81.9 1.0
C C:CYS72 4.8 81.7 1.0
CB C:VAL57 4.9 85.4 1.0

Zinc binding site 10 out of 12 in 7nn0

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Zinc binding site 10 out of 12 in the Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Sars-Cov-2 Helicase in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn701

b:60.6
occ:1.00
ND1 D:HIS39 2.0 59.7 1.0
NE2 D:HIS33 2.1 59.8 1.0
SG D:CYS16 2.3 45.6 1.0
SG D:CYS19 2.3 69.6 1.0
CE1 D:HIS39 3.0 64.2 1.0
CD2 D:HIS33 3.0 62.7 1.0
CG D:HIS39 3.1 67.8 1.0
CE1 D:HIS33 3.1 60.1 1.0
CB D:HIS39 3.4 68.3 1.0
CB D:CYS19 3.5 59.8 1.0
CB D:CYS16 3.6 55.4 1.0
N D:CYS19 3.7 59.4 1.0
CA D:CYS19 4.0 57.9 1.0
NE2 D:HIS39 4.1 67.9 1.0
CD2 D:HIS39 4.2 66.9 1.0
ND1 D:HIS33 4.2 64.9 1.0
CG D:HIS33 4.2 65.4 1.0
CB D:ALA110 4.3 63.9 1.0
C D:ALA18 4.5 61.0 1.0
CB D:ALA18 4.6 57.3 1.0
CA D:CYS16 4.9 56.4 1.0
CE2 D:PHE106 4.9 71.6 1.0
CZ D:PHE106 4.9 72.7 1.0
CA D:HIS39 4.9 64.8 1.0
CA D:ALA18 5.0 52.8 1.0
N D:ALA18 5.0 47.4 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 Amp-Pnp To Be Published.
Page generated: Sat Apr 3 18:40:10 2021

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