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Zinc in PDB 7aud: Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm)

Enzymatic activity of Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm)

All present enzymatic activity of Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm):
3.6.4.12;

Protein crystallography data

The structure of Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm), PDB code: 7aud was solved by X.Chen, A.W.Oliver, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.28 / 2.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 84.916, 111.709, 132.344, 72.64, 80.18, 79.22
R / Rfree (%) 22.9 / 26.9

Other elements in 7aud:

The structure of Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm) also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm) (pdb code 7aud). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm), PDB code: 7aud:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7aud

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Zinc binding site 1 out of 6 in the Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1301

b:70.6
occ:1.00
 SG A:CYS1055 2.2 58.9 1.0
SG A:CYS1063 2.3 66.4 1.0
SG A:CYS1036 2.3 76.5 1.0
SG A:CYS1066 2.3 80.2 1.0
CB A:CYS1055 3.1 70.9 1.0
CB A:CYS1066 3.3 80.0 1.0
CB A:CYS1036 3.4 68.0 1.0
CB A:CYS1063 3.5 70.5 1.0
CA A:CYS1036 3.8 76.4 1.0
N A:CYS1063 3.9 72.1 1.0
N A:ARG1037 3.9 69.8 1.0
CA A:CYS1063 4.2 69.7 1.0
C A:CYS1036 4.2 70.5 1.0
N A:CYS1066 4.3 78.0 1.0
CA A:CYS1066 4.4 79.1 1.0
N A:ARG1038 4.5 66.9 1.0
CG A:ARG1038 4.5 60.9 1.0
CA A:CYS1055 4.5 80.5 1.0
OG A:SER1062 4.6 77.9 1.0
CD A:ARG1038 4.7 67.7 1.0
C A:CYS1063 4.8 72.1 1.0
O A:CYS1063 4.8 75.7 1.0
CB A:ARG1038 4.8 65.5 1.0
N A:CYS1055 4.9 87.4 1.0
CA A:ARG1037 5.0 71.2 1.0

Zinc binding site 2 out of 6 in 7aud

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Zinc binding site 2 out of 6 in the Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:94.2
occ:1.00
 SG B:CYS1055 2.2 93.5 1.0
SG B:CYS1063 2.3 87.3 1.0
SG B:CYS1066 2.3 1.0 1.0
SG B:CYS1036 2.3 90.5 1.0
CB B:CYS1055 3.1 0.9 1.0
CB B:CYS1036 3.4 91.8 1.0
CB B:CYS1066 3.4 0.7 1.0
CB B:CYS1063 3.4 89.2 1.0
N B:CYS1063 3.8 93.7 1.0
CA B:CYS1036 3.8 92.5 1.0
N B:ARG1037 4.0 84.2 1.0
CA B:CYS1063 4.1 92.3 1.0
N B:CYS1066 4.2 98.8 1.0
C B:CYS1036 4.3 86.6 1.0
CA B:CYS1066 4.4 99.4 1.0
CA B:CYS1055 4.6 0.0 1.0
OG B:SER1062 4.6 0.9 1.0
N B:ARG1038 4.7 77.1 1.0
C B:CYS1063 4.7 92.9 1.0
CG B:ARG1038 4.7 77.5 1.0
O B:CYS1063 4.7 95.6 1.0
CD B:ARG1038 4.9 83.6 1.0
C B:SER1062 4.9 95.3 1.0

Zinc binding site 3 out of 6 in 7aud

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Zinc binding site 3 out of 6 in the Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1301

b:95.9
occ:1.00
 SG C:CYS1063 2.3 98.7 1.0
SG C:CYS1066 2.3 0.5 1.0
SG C:CYS1036 2.3 94.7 1.0
SG C:CYS1055 2.3 0.3 1.0
CB C:CYS1055 3.3 0.7 1.0
CB C:CYS1036 3.3 96.0 1.0
CB C:CYS1063 3.4 97.1 1.0
CB C:CYS1066 3.5 0.4 1.0
CA C:CYS1036 3.7 91.3 1.0
N C:ARG1037 3.8 84.9 1.0
N C:CYS1063 3.9 0.8 1.0
C C:CYS1036 4.1 88.5 1.0
CA C:CYS1063 4.2 0.8 1.0
N C:CYS1066 4.4 95.4 1.0
N C:ARG1038 4.5 70.8 1.0
CA C:CYS1066 4.5 99.9 1.0
CG C:ARG1038 4.6 76.5 1.0
CA C:CYS1055 4.7 0.5 1.0
CD C:ARG1038 4.8 87.7 1.0
C C:CYS1063 4.9 99.2 1.0
CA C:ARG1037 4.9 81.5 1.0
CB C:ARG1038 5.0 82.3 1.0

Zinc binding site 4 out of 6 in 7aud

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Zinc binding site 4 out of 6 in the Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1301

b:0.3
occ:1.00
 SG D:CYS1063 2.3 0.3 1.0
SG D:CYS1055 2.3 0.1 1.0
SG D:CYS1036 2.3 93.1 1.0
SG D:CYS1066 2.3 0.3 1.0
CB D:CYS1055 3.1 0.9 1.0
CB D:CYS1036 3.2 0.7 1.0
CB D:CYS1063 3.3 0.1 1.0
CA D:CYS1036 3.6 0.3 1.0
CB D:CYS1066 3.7 0.4 1.0
N D:ARG1037 3.8 91.9 1.0
N D:CYS1063 4.0 0.2 1.0
C D:CYS1036 4.1 100.0 1.0
CA D:CYS1063 4.3 0.4 1.0
N D:CYS1066 4.5 0.0 1.0
CA D:CYS1055 4.5 0.6 1.0
N D:ARG1038 4.6 95.6 1.0
CA D:CYS1066 4.7 0.5 1.0
CG D:ARG1038 4.9 92.5 1.0
N D:CYS1036 4.9 0.8 1.0
CA D:ARG1037 4.9 88.6 1.0
C D:CYS1063 5.0 0.7 1.0

Zinc binding site 5 out of 6 in 7aud

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Zinc binding site 5 out of 6 in the Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1301

b:0.1
occ:1.00
 SG E:CYS1055 2.3 0.4 1.0
SG E:CYS1036 2.3 0.2 1.0
SG E:CYS1066 2.3 0.8 1.0
SG E:CYS1063 2.3 0.1 1.0
CB E:CYS1055 3.3 0.9 1.0
CB E:CYS1063 3.3 0.6 1.0
CB E:CYS1036 3.5 0.8 1.0
CB E:CYS1066 3.6 0.5 1.0
N E:CYS1063 3.8 0.1 1.0
N E:ARG1037 4.0 0.0 1.0
CA E:CYS1036 4.0 0.5 1.0
CA E:CYS1063 4.2 0.9 1.0
CG E:ARG1038 4.3 0.8 1.0
N E:ARG1038 4.3 0.2 1.0
C E:CYS1036 4.4 0.9 1.0
CD E:ARG1038 4.4 0.9 1.0
N E:CYS1066 4.6 0.6 1.0
CB E:ARG1038 4.6 0.5 1.0
CA E:CYS1066 4.7 0.5 1.0
CA E:CYS1055 4.7 1.0 1.0
NE E:ARG1038 4.8 0.0 1.0
C E:CYS1063 4.9 0.5 1.0
OG E:SER1062 4.9 0.3 1.0
C E:SER1062 5.0 0.3 1.0
N E:CYS1055 5.0 0.7 1.0
O E:CYS1063 5.0 0.7 1.0

Zinc binding site 6 out of 6 in 7aud

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Zinc binding site 6 out of 6 in the Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of An Engineered Helicase Domain Construct For Human Bloom Syndrome Protein (Blm) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1301

b:0.1
occ:1.00
 SG F:CYS1055 2.3 0.9 1.0
SG F:CYS1066 2.3 0.7 1.0
SG F:CYS1063 2.3 0.2 1.0
SG F:CYS1036 2.3 0.8 1.0
CB F:CYS1055 3.1 0.4 1.0
CB F:CYS1066 3.2 0.4 1.0
CB F:CYS1036 3.4 0.2 1.0
CB F:CYS1063 3.5 98.0 1.0
CA F:CYS1036 3.8 0.8 1.0
N F:ARG1037 3.9 84.1 1.0
N F:CYS1063 3.9 0.8 1.0
N F:CYS1066 4.2 97.5 1.0
C F:CYS1036 4.2 99.1 1.0
CA F:CYS1063 4.2 0.0 1.0
CA F:CYS1066 4.3 99.0 1.0
CA F:CYS1055 4.5 0.1 1.0
N F:ARG1038 4.6 87.5 1.0
OG F:SER1062 4.7 0.6 1.0
C F:CYS1063 4.8 0.5 1.0
O F:CYS1063 4.8 0.2 1.0
CG F:ARG1038 4.9 79.9 1.0
CA F:ARG1037 5.0 84.0 1.0

Reference:

X.Chen, Y.Ali, C.E.L.Fisher, R.Arribas-Bosacoma, M.B.Rajasekaran, G.Williams, S.Walker, S.M.Roe, L.H.Pearl, S.E.Ward, F.M.G.Pearl, A.W.Oliver. Uncovering An Allosteric Mode of Action For A Selective Inhibitor of Human Bloom Syndrome Protein Biorxiv 2020.
DOI: 10.1101/2020.11.30.403493
Page generated: Tue Oct 29 17:12:10 2024

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