Zinc in PDB 6eo0: Zebrafish SIRT5 in Complex with Stalled Peptidylimidate and Bicyclic Intermediate of Inhibitory Compound 29

The structure of Zebrafish SIRT5 in Complex with Stalled Peptidylimidate and Bicyclic Intermediate of Inhibitory Compound 29, PDB code: 6eo0 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)	48.41 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.930, 113.590, 72.310, 90.00, 103.24, 90.00
R / Rfree (%)	25.3 / 30.5

The binding sites of Zinc atom in the Zebrafish SIRT5 in Complex with Stalled Peptidylimidate and Bicyclic Intermediate of Inhibitory Compound 29 (pdb code 6eo0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Zebrafish SIRT5 in Complex with Stalled Peptidylimidate and Bicyclic Intermediate of Inhibitory Compound 29, PDB code: 6eo0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Zebrafish SIRT5 in Complex with Stalled Peptidylimidate and Bicyclic 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 Zebrafish SIRT5 in Complex with Stalled Peptidylimidate and Bicyclic Intermediate of Inhibitory Compound 29 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:50.4 occ:1.00 SG A:CYS165 2.3 54.4 1.0 SG A:CYS203 2.3 43.4 1.0 SG A:CYS162 2.3 66.1 1.0 SG A:CYS208 2.4 58.2 1.0 CB A:CYS203 3.1 46.8 1.0 CB A:CYS165 3.2 56.8 1.0 CB A:CYS208 3.3 57.9 1.0 CB A:CYS162 3.3 64.0 1.0 N A:CYS165 3.8 60.0 1.0 CA A:CYS165 4.1 58.3 1.0 N A:GLY210 4.5 52.5 1.0 CB A:ARG205 4.6 56.6 1.0 CB A:SER164 4.6 61.4 1.0 CA A:CYS203 4.6 47.1 1.0 CA A:CYS208 4.7 57.4 1.0 CA A:CYS162 4.8 59.0 1.0 C A:CYS165 4.8 57.5 1.0 CA A:GLY210 4.8 51.2 1.0 N A:GLY166 4.9 56.3 1.0 C A:SER164 4.9 61.4 1.0 C A:CYS208 5.0 54.1 1.0

Zinc binding site 2 out of 4 in the Zebrafish SIRT5 in Complex with Stalled Peptidylimidate and Bicyclic 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 Zebrafish SIRT5 in Complex with Stalled Peptidylimidate and Bicyclic Intermediate of Inhibitory Compound 29 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:50.7 occ:1.00 SG B:CYS165 2.3 57.5 1.0 SG B:CYS203 2.3 47.5 1.0 SG B:CYS162 2.4 54.5 1.0 SG B:CYS208 2.4 63.2 1.0 CB B:CYS203 3.1 50.8 1.0 CB B:CYS165 3.3 56.9 1.0 CB B:CYS208 3.3 64.2 1.0 CB B:CYS162 3.3 54.0 1.0 N B:CYS165 3.8 55.8 1.0 CA B:CYS165 4.1 55.4 1.0 N B:GLY210 4.5 55.7 1.0 CB B:ARG205 4.5 62.2 1.0 CA B:CYS203 4.6 49.0 1.0 NH1 B:ARG205 4.6 70.1 1.0 CA B:CYS208 4.7 64.4 1.0 CB B:SER164 4.7 55.9 1.0 CA B:CYS162 4.8 54.4 1.0 C B:CYS165 4.8 53.8 1.0 CA B:GLY210 4.9 52.2 1.0 N B:GLY166 4.9 52.7 1.0 C B:CYS208 4.9 59.6 1.0 C B:SER164 5.0 56.6 1.0

Zinc binding site 3 out of 4 in the Zebrafish SIRT5 in Complex with Stalled Peptidylimidate and Bicyclic 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 Zebrafish SIRT5 in Complex with Stalled Peptidylimidate and Bicyclic Intermediate of Inhibitory Compound 29 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:57.6 occ:1.00 SG C:CYS203 2.3 51.0 1.0 SG C:CYS208 2.3 63.5 1.0 SG C:CYS165 2.3 62.2 1.0 SG C:CYS162 2.3 57.9 1.0 CB C:CYS203 3.1 54.9 1.0 CB C:CYS208 3.3 62.0 1.0 CB C:CYS162 3.3 55.3 1.0 CB C:CYS165 3.4 60.5 1.0 N C:CYS165 3.9 59.6 1.0 CA C:CYS165 4.2 57.8 1.0 CA C:CYS203 4.5 55.5 1.0 N C:GLY210 4.6 46.6 1.0 CD C:ARG205 4.6 70.0 1.0 CA C:CYS208 4.7 59.5 1.0 CA C:CYS162 4.8 52.8 1.0 CB C:SER164 4.8 59.2 1.0 CB C:ARG205 4.8 62.9 1.0 C C:CYS165 4.9 53.9 1.0 N C:GLY166 4.9 56.7 1.0 CA C:GLY210 5.0 43.8 1.0 C C:CYS208 5.0 55.2 1.0

Zinc binding site 4 out of 4 in the Zebrafish SIRT5 in Complex with Stalled Peptidylimidate and Bicyclic 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 Zebrafish SIRT5 in Complex with Stalled Peptidylimidate and Bicyclic Intermediate of Inhibitory Compound 29 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:48.0 occ:1.00 SG D:CYS165 2.3 58.9 1.0 SG D:CYS203 2.3 48.6 1.0 SG D:CYS208 2.3 50.9 1.0 SG D:CYS162 2.3 71.0 1.0 CB D:CYS203 3.1 51.2 1.0 CB D:CYS208 3.3 52.7 1.0 CB D:CYS162 3.3 64.0 1.0 CB D:CYS165 3.4 58.2 1.0 N D:CYS165 3.9 57.6 1.0 CA D:CYS165 4.2 57.7 1.0 N D:GLY210 4.5 52.9 1.0 CA D:CYS203 4.6 50.8 1.0 CD D:ARG205 4.6 48.8 1.0 CA D:CYS208 4.7 50.6 1.0 CB D:SER164 4.7 57.0 1.0 CB D:ARG205 4.8 47.8 1.0 CA D:CYS162 4.8 58.1 1.0 CA D:GLY210 4.9 52.2 1.0 C D:CYS165 4.9 56.0 1.0 N D:GLY166 5.0 54.5 1.0 C D:CYS208 5.0 50.6 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