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

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

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.538, 67.876, 156.749, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 25.6

The binding sites of Zinc atom in the SIRT5 Is An Nad-Dependent Protein Lysine Demalonylase and Desuccinylase (pdb code 3rig). 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: 3rig:
Jump to Zinc binding site number: 1; 2;

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:46.5 occ:1.00 SG A:CYS207 1.9 35.3 1.0 SG A:CYS166 2.2 37.7 1.0 SG A:CYS212 2.4 51.8 1.0 SG A:CYS169 2.7 50.1 1.0 CB A:CYS207 2.9 41.5 1.0 CB A:CYS166 3.1 34.3 1.0 CB A:CYS169 3.5 49.3 1.0 CB A:CYS212 3.6 56.5 1.0 N A:CYS169 3.7 45.8 1.0 CA A:CYS169 4.2 47.5 1.0 CB A:SER168 4.3 46.4 1.0 N A:GLY214 4.4 43.8 1.0 CA A:CYS207 4.5 41.9 1.0 CA A:CYS166 4.6 32.0 1.0 C A:SER168 4.7 46.2 1.0 CB A:GLU209 4.8 59.5 1.0 CA A:GLY214 4.8 38.8 1.0 CG1 A:VAL171 4.8 41.0 1.0 C A:CYS169 4.8 45.4 1.0 N A:GLY170 4.9 42.1 1.0 CA A:SER168 4.9 45.2 1.0 CG A:GLU209 4.9 58.4 1.0 CA A:CYS212 5.0 58.0 1.0 N A:SER168 5.0 41.8 1.0

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:61.2 occ:1.00 SG B:CYS169 2.1 48.2 1.0 SG B:CYS207 2.3 52.0 1.0 SG B:CYS212 2.4 57.5 1.0 SG B:CYS166 2.4 51.5 1.0 CB B:CYS207 2.9 49.9 1.0 CB B:CYS166 3.2 44.0 1.0 CB B:CYS212 3.3 61.2 1.0 CB B:CYS169 3.6 56.4 1.0 N B:CYS169 4.1 54.2 1.0 N B:GLY214 4.1 49.5 1.0 CA B:GLY214 4.4 45.5 1.0 CA B:CYS207 4.4 49.8 1.0 CA B:CYS169 4.5 54.8 1.0 CB B:SER168 4.5 54.2 1.0 CA B:CYS166 4.6 41.4 1.0 CA B:CYS212 4.7 63.3 1.0 N B:GLY213 4.8 57.1 1.0 C B:CYS212 5.0 60.7 1.0

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