Zinc in PDB 6jyt: Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis

Enzymatic activity of Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis

All present enzymatic activity of Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis:
3.6.4.12; 3.6.4.13;

Protein crystallography data

The structure of Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis, PDB code: 6jyt was solved by L.Yan, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.83 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 191.990, 189.150, 57.330, 90.00, 102.89, 90.00
R / Rfree (%) 23.8 / 29.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis (pdb code 6jyt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis, PDB code: 6jyt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6jyt

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Zinc binding site 1 out of 6 in the Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:54.3
occ:1.00
 SG A:CYS29 2.2 0.1 1.0
SG A:CYS5 2.4 38.8 1.0
SG A:CYS8 2.5 49.1 1.0
SG A:CYS26 2.5 47.0 1.0
CB A:CYS29 3.0 60.6 1.0
CB A:CYS8 3.3 47.6 1.0
CB A:CYS5 3.3 42.9 1.0
CB A:CYS26 3.5 43.8 1.0
N A:CYS8 3.9 46.7 1.0
N A:CYS26 3.9 41.0 1.0
N A:CYS29 4.1 46.9 1.0
CA A:CYS8 4.2 46.3 1.0
CA A:CYS29 4.2 45.0 1.0
N A:GLY99 4.2 51.1 1.0
CA A:CYS26 4.2 46.5 1.0
CA A:GLY99 4.2 43.6 1.0
CB A:LEU7 4.5 47.3 1.0
OG A:SER10 4.6 49.5 1.0
C A:GLY99 4.7 48.4 1.0
C A:LEU7 4.7 48.8 1.0
CA A:CYS5 4.8 40.2 1.0
C A:CYS26 4.8 44.1 1.0
C A:CYS8 4.9 46.6 1.0
N A:ASN9 4.9 45.1 1.0
O A:CYS26 4.9 42.3 1.0
CA A:LEU7 5.0 42.9 1.0
N A:LEU7 5.0 42.8 1.0

Zinc binding site 2 out of 6 in 6jyt

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Zinc binding site 2 out of 6 in the Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:77.5
occ:1.00
 SG A:CYS72 1.9 57.4 1.0
SG A:CYS55 2.1 54.3 1.0
SG A:CYS50 2.2 51.9 1.0
ND1 A:HIS75 2.5 63.4 1.0
CB A:CYS55 3.0 55.2 1.0
CB A:CYS50 3.2 52.5 1.0
CE1 A:HIS75 3.2 63.1 1.0
CG A:HIS75 3.2 57.4 1.0
CB A:CYS72 3.5 50.6 1.0
CB A:HIS75 3.6 58.4 1.0
CB A:ALA52 3.8 63.5 1.0
N A:CYS72 3.8 48.4 1.0
NE2 A:HIS75 4.1 65.6 1.0
CD2 A:HIS75 4.2 60.4 1.0
CA A:CYS72 4.3 51.7 1.0
CA A:CYS55 4.4 53.4 1.0
N A:HIS75 4.5 62.1 1.0
CA A:CYS50 4.6 49.7 1.0
CG2 A:VAL57 4.6 40.5 1.0
CA A:HIS75 4.7 55.3 1.0
CB A:VAL57 4.9 49.2 1.0
C A:TYR71 4.9 52.5 1.0
CA A:ALA52 5.0 59.5 1.0
N A:ALA52 5.0 57.0 1.0

Zinc binding site 3 out of 6 in 6jyt

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Zinc binding site 3 out of 6 in the Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:30.1
occ:1.00
 ND1 A:HIS39 2.1 31.6 1.0
NE2 A:HIS33 2.1 35.4 1.0
SG A:CYS19 2.3 31.8 1.0
SG A:CYS16 2.5 26.3 1.0
CE1 A:HIS39 2.9 32.6 1.0
CE1 A:HIS33 2.9 34.2 1.0
CD2 A:HIS33 3.2 33.8 1.0
CG A:HIS39 3.2 35.0 1.0
CB A:CYS19 3.4 37.2 1.0
CB A:CYS16 3.4 31.9 1.0
CB A:HIS39 3.6 34.4 1.0
N A:CYS19 3.8 34.4 1.0
CA A:CYS19 3.9 36.6 1.0
NE2 A:HIS39 4.1 32.9 1.0
ND1 A:HIS33 4.1 35.3 1.0
CD2 A:HIS39 4.2 30.9 1.0
CG A:HIS33 4.2 32.4 1.0
CB A:ALA18 4.4 31.2 1.0
CB A:ALA110 4.5 32.8 1.0
C A:ALA18 4.6 31.8 1.0
CA A:CYS16 4.8 36.4 1.0
CA A:ALA18 4.9 32.6 1.0
CE2 A:PHE106 5.0 33.5 1.0

Zinc binding site 4 out of 6 in 6jyt

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Zinc binding site 4 out of 6 in the Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:50.2
occ:1.00
 SG B:CYS29 2.0 0.6 1.0
SG B:CYS26 2.4 49.5 1.0
SG B:CYS8 2.4 55.3 1.0
SG B:CYS5 2.5 34.4 1.0
CB B:CYS29 2.9 48.1 1.0
CB B:CYS8 3.3 46.1 1.0
CB B:CYS26 3.5 48.8 1.0
CB B:CYS5 3.6 45.7 1.0
CA B:GLY99 3.9 48.1 1.0
N B:CYS29 4.0 46.2 1.0
N B:CYS8 4.0 47.3 1.0
CA B:CYS29 4.0 44.4 1.0
N B:GLY99 4.0 46.3 1.0
N B:CYS26 4.1 42.7 1.0
CA B:CYS8 4.2 46.2 1.0
CA B:CYS26 4.3 46.7 1.0
CB B:LEU7 4.6 43.2 1.0
C B:GLY99 4.6 45.1 1.0
C B:CYS26 4.7 45.8 1.0
O B:CYS26 4.8 44.3 1.0
N B:SER100 4.8 45.1 1.0
C B:LEU7 4.8 44.2 1.0
OG B:SER10 4.8 49.4 1.0
C B:CYS8 5.0 47.0 1.0

Zinc binding site 5 out of 6 in 6jyt

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Zinc binding site 5 out of 6 in the Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:0.5
occ:1.00
 SG B:CYS72 2.0 63.7 1.0
SG B:CYS55 2.0 79.4 1.0
SG B:CYS50 2.1 61.9 1.0
ND1 B:HIS75 2.3 67.9 1.0
CE1 B:HIS75 2.9 66.7 1.0
CB B:CYS55 3.0 55.0 1.0
CB B:CYS50 3.2 57.0 1.0
CB B:CYS72 3.3 58.5 1.0
CG B:HIS75 3.5 63.1 1.0
N B:CYS72 3.8 50.4 1.0
CB B:HIS75 4.0 59.8 1.0
NE2 B:HIS75 4.1 64.3 1.0
CA B:CYS72 4.2 55.6 1.0
CB B:ALA52 4.3 66.2 1.0
CD2 B:HIS75 4.4 62.2 1.0
CA B:CYS55 4.4 51.8 1.0
CG2 B:VAL57 4.4 47.9 1.0
N B:HIS75 4.5 59.2 1.0
CA B:CYS50 4.6 54.1 1.0
CB B:VAL57 4.8 43.4 1.0
CB B:SER74 4.9 60.8 1.0
CA B:HIS75 4.9 57.5 1.0
C B:CYS72 5.0 61.6 1.0
C B:TYR71 5.0 51.7 1.0

Zinc binding site 6 out of 6 in 6jyt

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Zinc binding site 6 out of 6 in the Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:0.5
occ:1.00
 SG B:CYS19 2.0 30.4 1.0
ND1 B:HIS39 2.1 46.4 1.0
CG B:HIS39 2.3 45.4 1.0
SG B:CYS16 2.4 0.3 1.0
CB B:ALA18 2.4 44.3 1.0
CB B:HIS39 2.7 40.3 1.0
N B:CYS19 2.8 42.1 1.0
CE1 B:HIS39 2.9 36.6 1.0
CD2 B:HIS39 3.1 37.0 1.0
CA B:ALA18 3.2 38.5 1.0
C B:ALA18 3.2 35.3 1.0
CB B:CYS19 3.3 45.2 1.0
NE2 B:HIS39 3.4 38.1 1.0
CA B:CYS19 3.4 50.3 1.0
N B:ALA18 3.5 40.3 1.0
NE2 B:HIS33 3.6 35.4 1.0
CB B:CYS16 3.6 42.4 1.0
CA B:HIS39 3.7 38.9 1.0
O B:ALA18 4.1 40.7 1.0
C B:HIS39 4.3 40.4 1.0
O B:HIS39 4.4 38.6 1.0
CE1 B:HIS33 4.5 35.2 1.0
CD2 B:HIS33 4.5 33.8 1.0
C B:GLY17 4.8 40.5 1.0
CA B:CYS16 4.8 47.8 1.0
C B:CYS16 4.9 50.1 1.0
C B:CYS19 4.9 43.6 1.0
N B:HIS39 4.9 35.1 1.0
N B:GLY17 5.0 46.4 1.0

Reference:

Z.Jia, L.Yan, Z.Ren, L.Wu, J.Wang, J.Guo, L.Zheng, Z.Ming, L.Zhang, Z.Lou, Z.Rao. Delicate Structural Coordination of the Severe Acute Respiratory Syndrome Coronavirus NSP13 Upon Atp Hydrolysis. Nucleic Acids Res. V. 47 6538 2019.
ISSN: ESSN 1362-4962
PubMed: 31131400
DOI: 10.1093/NAR/GKZ409
Page generated: Wed Dec 16 12:05:40 2020

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