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Zinc in PDB 3riy: SIRT5 Is An Nad-Dependent Protein Lysine Demalonylase and Desuccinylase

Protein crystallography data

The structure of SIRT5 Is An Nad-Dependent Protein Lysine Demalonylase and Desuccinylase, PDB code: 3riy was solved by Y.Zhou, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.691, 69.417, 156.321, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 19.1

Zinc Binding Sites:

The binding sites of Zinc atom in the SIRT5 Is An Nad-Dependent Protein Lysine Demalonylase and Desuccinylase (pdb code 3riy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the SIRT5 Is An Nad-Dependent Protein Lysine Demalonylase and Desuccinylase, PDB code: 3riy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3riy

Go back to Zinc Binding Sites List in 3riy
Zinc binding site 1 out of 2 in the SIRT5 Is An Nad-Dependent Protein Lysine Demalonylase and Desuccinylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SIRT5 Is An Nad-Dependent Protein Lysine Demalonylase and Desuccinylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:19.3
occ:1.00
SG A:CYS169 2.3 19.6 1.0
SG A:CYS212 2.4 23.9 1.0
SG A:CYS166 2.4 17.6 1.0
SG A:CYS207 2.4 18.5 1.0
CB A:CYS207 3.0 16.0 1.0
CB A:CYS166 3.1 16.3 1.0
CB A:CYS212 3.2 27.3 1.0
CB A:CYS169 3.4 19.6 1.0
N A:CYS169 3.6 19.3 1.0
CA A:CYS169 4.1 20.3 1.0
CG1 A:VAL171 4.4 22.9 1.0
N A:GLY214 4.5 19.7 1.0
CA A:CYS207 4.5 15.1 1.0
CA A:CYS166 4.5 16.0 1.0
CB A:SER168 4.6 19.4 1.0
CA A:CYS212 4.7 27.6 1.0
C A:SER168 4.7 20.9 1.0
CA A:GLY214 4.8 17.6 1.0
C A:CYS169 4.8 19.8 1.0
N A:GLY170 4.9 20.7 1.0
O A:HOH414 5.0 19.5 1.0
CA A:SER168 5.0 19.9 1.0

Zinc binding site 2 out of 2 in 3riy

Go back to Zinc Binding Sites List in 3riy
Zinc binding site 2 out of 2 in the SIRT5 Is An Nad-Dependent Protein Lysine Demalonylase and Desuccinylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SIRT5 Is An Nad-Dependent Protein Lysine Demalonylase and Desuccinylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:16.6
occ:1.00
SG B:CYS169 2.2 18.6 1.0
SG B:CYS212 2.3 19.0 1.0
SG B:CYS207 2.3 14.1 1.0
SG B:CYS166 2.4 15.4 1.0
CB B:CYS207 3.0 14.4 1.0
CB B:CYS166 3.1 14.6 1.0
CB B:CYS212 3.2 17.9 1.0
CB B:CYS169 3.3 19.1 1.0
N B:CYS169 3.7 19.9 1.0
CA B:CYS169 4.0 19.6 1.0
CA B:CYS207 4.5 14.5 1.0
N B:GLY214 4.5 14.8 1.0
O B:HOH689 4.5 30.9 1.0
CB B:GLU209 4.5 20.0 1.0
CA B:CYS166 4.6 12.9 1.0
CG B:GLU209 4.6 22.9 1.0
CB B:SER168 4.6 19.1 0.5
CB B:SER168 4.7 19.3 0.5
CA B:CYS212 4.7 19.4 1.0
O B:HOH636 4.7 33.9 1.0
C B:CYS169 4.8 18.7 1.0
C B:SER168 4.8 19.6 1.0
CA B:GLY214 4.9 14.7 1.0
N B:GLY213 4.9 17.9 1.0
N B:GLY170 4.9 20.1 1.0
O B:HOH462 5.0 17.0 1.0

Reference:

J.Du, Y.Zhou, X.Su, J.J.Yu, S.Khan, H.Jiang, J.Kim, J.Woo, J.H.Kim, B.H.Choi, B.He, W.Chen, S.Zhang, R.A.Cerione, J.Auwerx, Q.Hao, H.Lin. SIRT5 Is A Nad-Dependent Protein Lysine Demalonylase and Desuccinylase Science V. 334 806 2011.
ISSN: ISSN 0036-8075
PubMed: 22076378
DOI: 10.1126/SCIENCE.1207861
Page generated: Wed Dec 16 04:47:34 2020

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