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Zinc in PDB 2nyr: Crystal Structure of Human Sirtuin Homolog 5 in Complex with Suramin

Protein crystallography data

The structure of Crystal Structure of Human Sirtuin Homolog 5 in Complex with Suramin, PDB code: 2nyr was solved by J.R.Min, T.Antoshenko, A.Allali-Hassani, A.Dong, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, A.N.Plotnikov, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.12 / 2.06
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.200, 116.205, 55.993, 90.00, 90.46, 90.00
R / Rfree (%) 19.9 / 26.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Sirtuin Homolog 5 in Complex with Suramin (pdb code 2nyr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Sirtuin Homolog 5 in Complex with Suramin, PDB code: 2nyr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2nyr

Go back to Zinc Binding Sites List in 2nyr
Zinc binding site 1 out of 2 in the Crystal Structure of Human Sirtuin Homolog 5 in Complex with Suramin


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 Human Sirtuin Homolog 5 in Complex with Suramin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:24.8
occ:1.00
SG A:CYS169 2.2 19.3 1.0
SG A:CYS212 2.3 19.7 1.0
SG A:CYS166 2.4 20.0 1.0
SG A:CYS207 2.4 18.0 1.0
CB A:CYS207 3.0 18.6 1.0
CB A:CYS166 3.2 19.1 1.0
CB A:CYS169 3.2 19.2 1.0
CB A:CYS212 3.3 19.3 1.0
N A:CYS169 3.8 19.4 1.0
CA A:CYS169 4.0 19.3 1.0
CA A:CYS207 4.5 18.4 1.0
CG A:GLU209 4.5 18.7 1.0
N A:GLY214 4.5 17.0 1.0
CB A:GLU209 4.6 18.5 1.0
CA A:CYS166 4.6 19.1 1.0
CA A:CYS212 4.7 19.6 1.0
CB A:SER168 4.7 19.7 1.0
O A:HOH538 4.7 21.5 1.0
CA A:GLY214 4.8 15.9 1.0
C A:CYS169 4.8 19.1 1.0
N A:GLY170 4.9 18.9 1.0
N A:GLY213 4.9 19.1 1.0
C A:SER168 4.9 19.6 1.0

Zinc binding site 2 out of 2 in 2nyr

Go back to Zinc Binding Sites List in 2nyr
Zinc binding site 2 out of 2 in the Crystal Structure of Human Sirtuin Homolog 5 in Complex with Suramin


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 Human Sirtuin Homolog 5 in Complex with Suramin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:29.5
occ:1.00
SG B:CYS169 2.1 17.6 1.0
SG B:CYS207 2.3 21.0 1.0
SG B:CYS166 2.3 16.2 1.0
SG B:CYS212 2.3 20.1 1.0
CB B:CYS207 3.0 21.6 1.0
CB B:CYS166 3.1 16.7 1.0
CB B:CYS169 3.2 17.4 1.0
CB B:CYS212 3.2 19.7 1.0
N B:CYS169 3.7 17.8 1.0
CA B:CYS169 4.0 17.6 1.0
CA B:CYS207 4.5 21.9 1.0
CB B:GLU209 4.5 22.3 1.0
N B:GLY214 4.5 17.9 1.0
CA B:CYS166 4.6 16.6 1.0
CB B:SER168 4.6 17.9 1.0
CA B:CYS212 4.7 20.0 1.0
CG B:GLU209 4.7 23.1 1.0
CA B:GLY214 4.8 16.5 1.0
C B:CYS169 4.8 17.5 1.0
C B:SER168 4.9 17.9 1.0
N B:GLY170 5.0 17.5 1.0
O B:HOH525 5.0 19.7 1.0

Reference:

A.Schuetz, J.Min, T.Antoshenko, C.L.Wang, A.Allali-Hassani, A.Dong, P.Loppnau, M.Vedadi, A.Bochkarev, R.Sternglanz, A.N.Plotnikov. Structural Basis of Inhibition of the Human Nad+-Dependent Deacetylase SIRT5 By Suramin. Structure V. 15 377 2007.
ISSN: ISSN 0969-2126
PubMed: 17355872
DOI: 10.1016/J.STR.2007.02.002
Page generated: Wed Dec 16 03:44:54 2020

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