Zinc in PDB 6eqs: Human SIRT5 in Complex with Stalled Peptidylimidate Intermediate of Inhibitory Compound 29

The structure of Human SIRT5 in Complex with Stalled Peptidylimidate Intermediate of Inhibitory Compound 29, PDB code: 6eqs was solved by M.Pannek, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.77 / 1.32
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.326, 55.969, 123.034, 97.39, 99.29, 90.52
R / Rfree (%)	16 / 20.9

The binding sites of Zinc atom in the Human SIRT5 in Complex with Stalled Peptidylimidate Intermediate of Inhibitory Compound 29 (pdb code 6eqs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human SIRT5 in Complex with Stalled Peptidylimidate Intermediate of Inhibitory Compound 29, PDB code: 6eqs:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human SIRT5 in Complex with Stalled Peptidylimidate Intermediate of Inhibitory Compound 29


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT5 in Complex with Stalled Peptidylimidate Intermediate of Inhibitory Compound 29 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:15.1 occ:1.00 SG A:CYS207 2.3 14.4 1.0 SG A:CYS212 2.3 16.4 1.0 SG A:CYS169 2.3 16.6 1.0 SG A:CYS166 2.3 13.8 1.0 CB A:CYS207 3.1 16.7 1.0 CB A:CYS166 3.2 12.0 1.0 CB A:CYS169 3.3 16.4 1.0 CB A:CYS212 3.3 18.2 1.0 N A:CYS169 3.7 16.2 1.0 CA A:CYS169 3.9 15.5 1.0 CG1 A:VAL171 4.4 24.7 1.0 N A:GLY214 4.5 16.2 1.0 CA A:CYS207 4.6 14.4 1.0 CA A:CYS166 4.6 12.1 1.0 CA A:CYS212 4.6 17.5 1.0 CB A:GLU209 4.7 18.9 1.0 C A:SER168 4.8 15.6 1.0 C A:CYS169 4.8 18.5 1.0 CB A:SER168 4.8 18.9 1.0 CG A:GLU209 4.8 21.4 1.0 CA A:GLY214 4.8 13.9 1.0 O A:HOH774 4.9 17.6 1.0 N A:GLY213 4.9 21.3 1.0

Zinc binding site 2 out of 4 in the Human SIRT5 in Complex with Stalled Peptidylimidate Intermediate of Inhibitory Compound 29


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT5 in Complex with Stalled Peptidylimidate Intermediate of Inhibitory Compound 29 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:16.0 occ:1.00 SG B:CYS169 2.3 16.4 1.0 SG B:CYS212 2.3 16.5 1.0 SG B:CYS207 2.4 16.3 1.0 SG B:CYS166 2.4 15.0 1.0 CB B:CYS207 3.0 15.5 1.0 CB B:CYS166 3.2 14.9 1.0 CB B:CYS169 3.3 16.7 1.0 CB B:CYS212 3.3 17.4 1.0 N B:CYS169 3.8 14.9 1.0 CA B:CYS169 4.1 15.1 1.0 O B:HOH759 4.2 31.4 1.0 CG1 B:VAL171 4.5 11.1 0.5 N B:GLY214 4.5 16.2 1.0 CA B:CYS207 4.5 13.7 1.0 CA B:CYS166 4.6 10.8 1.0 CB B:SER168 4.7 12.3 0.3 CA B:CYS212 4.7 16.5 1.0 CB B:GLU209 4.7 20.3 1.0 CG B:GLU209 4.8 25.8 1.0 CB B:SER168 4.8 15.4 0.7 C B:SER168 4.8 15.7 1.0 C B:CYS169 4.9 17.3 1.0 CA B:GLY214 4.9 15.5 1.0 N B:GLY213 4.9 20.1 1.0 O B:HOH767 4.9 17.9 1.0 N B:GLY170 5.0 17.3 1.0

Zinc binding site 3 out of 4 in the Human SIRT5 in Complex with Stalled Peptidylimidate Intermediate of Inhibitory Compound 29


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human SIRT5 in Complex with Stalled Peptidylimidate Intermediate of Inhibitory Compound 29 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:19.1 occ:1.00 SG C:CYS212 2.3 18.8 1.0 SG C:CYS169 2.3 20.2 1.0 SG C:CYS207 2.4 20.2 1.0 SG C:CYS166 2.4 16.8 1.0 CB C:CYS207 3.1 17.7 1.0 CB C:CYS166 3.2 16.9 1.0 CB C:CYS169 3.3 17.7 1.0 CB C:CYS212 3.3 21.1 1.0 N C:CYS169 3.8 21.8 1.0 CA C:CYS169 4.1 21.0 1.0 CG1 C:VAL171 4.4 18.2 0.5 CA C:CYS207 4.6 18.3 1.0 N C:GLY214 4.6 16.1 1.0 CA C:CYS166 4.6 15.1 1.0 CA C:CYS212 4.6 25.0 1.0 CB C:GLU209 4.7 22.0 1.0 CB C:SER168 4.8 23.6 1.0 CG C:GLU209 4.8 26.7 1.0 C C:CYS169 4.8 18.0 1.0 C C:SER168 4.8 19.6 1.0 CA C:GLY214 4.9 17.1 1.0 N C:GLY170 5.0 16.7 1.0 O C:HOH740 5.0 22.6 1.0

Zinc binding site 4 out of 4 in the Human SIRT5 in Complex with Stalled Peptidylimidate Intermediate of Inhibitory Compound 29


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human SIRT5 in Complex with Stalled Peptidylimidate Intermediate of Inhibitory Compound 29 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:17.7 occ:1.00 SG D:CYS207 2.3 16.7 1.0 SG D:CYS169 2.3 18.9 1.0 SG D:CYS212 2.3 19.5 1.0 SG D:CYS166 2.4 16.4 1.0 CB D:CYS207 3.0 18.2 1.0 CB D:CYS166 3.1 14.3 1.0 CB D:CYS169 3.3 19.6 1.0 CB D:CYS212 3.3 22.1 1.0 N D:CYS169 3.7 18.1 1.0 CA D:CYS169 4.1 18.2 1.0 O D:HOH741 4.4 44.6 1.0 CG1 D:VAL171 4.4 30.1 1.0 N D:GLY214 4.5 17.5 1.0 CA D:CYS207 4.5 18.0 1.0 CA D:CYS166 4.5 12.8 1.0 CA D:CYS212 4.7 19.7 1.0 CB D:GLU209 4.7 19.6 1.0 CG D:GLU209 4.8 25.2 1.0 C D:SER168 4.8 18.5 1.0 C D:CYS169 4.8 20.5 1.0 CA D:GLY214 4.8 18.5 1.0 N D:GLY213 4.9 24.2 1.0 CB D:SER168 4.9 25.8 1.0 O D:HOH740 4.9 19.4 1.0 N D:GLY170 5.0 16.3 1.0

N.Rajabi, M.Auth, K.R.Troelsen, M.Pannek, D.P.Bhatt, M.Fontenas, M.D.Hirschey, C.Steegborn, A.S.Madsen, C.A.Olsen. Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight. Angew. Chem. Int. Ed. Engl. V. 56 14836 2017.
ISSN: ESSN 1521-3773
PubMed: 29044784
DOI: 10.1002/ANIE.201709050