Zinc in PDB 6fky: Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-CPS1 Peptide

The structure of Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-CPS1 Peptide, PDB code: 6fky 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)	48.51 / 2.98
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.134, 87.134, 316.677, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 27.5

The structure of Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-CPS1 Peptide also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-CPS1 Peptide (pdb code 6fky). 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 Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-CPS1 Peptide, PDB code: 6fky:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-CPS1 Peptide


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 Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-CPS1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:51.1 occ:1.00 SG A:CYS203 2.3 54.8 1.0 SG A:CYS165 2.3 65.6 1.0 SG A:CYS162 2.3 50.5 1.0 SG A:CYS208 2.4 65.5 1.0 CB A:CYS203 3.1 56.6 1.0 CB A:CYS162 3.2 48.4 1.0 CB A:CYS208 3.3 68.8 1.0 CB A:CYS165 3.3 63.8 1.0 N A:CYS165 3.7 58.1 1.0 CA A:CYS165 4.0 60.8 1.0 NH1 A:ARG205 4.3 0.3 1.0 N A:GLY210 4.4 54.4 1.0 CD A:ARG205 4.5 98.7 1.0 CA A:CYS203 4.6 57.3 1.0 CA A:GLY210 4.6 55.7 1.0 CA A:CYS162 4.7 48.0 1.0 CB A:SER164 4.7 57.6 1.0 C A:CYS165 4.7 58.3 1.0 CA A:CYS208 4.8 72.6 1.0 C A:SER164 4.8 55.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-CPS1 Peptide


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 Zebrafish Sirtuin 5 in Complex with 3- (Benzylthio)Succinyl-CPS1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:0.7 occ:1.00 SG B:CYS165 2.3 96.3 1.0 SG B:CYS203 2.3 0.4 1.0 SG B:CYS208 2.3 0.6 1.0 SG B:CYS162 2.4 1.0 1.0 CB B:CYS203 3.2 0.8 1.0 CB B:CYS162 3.2 0.1 1.0 CB B:CYS165 3.3 96.5 1.0 CB B:CYS208 3.3 0.1 1.0 N B:CYS165 3.6 92.8 1.0 CA B:CYS165 3.9 94.1 1.0 N B:GLY210 4.4 0.9 1.0 CA B:GLY210 4.6 0.2 1.0 CD B:ARG205 4.6 0.5 1.0 CA B:CYS203 4.6 0.1 1.0 C B:CYS165 4.7 95.9 1.0 CB B:SER164 4.7 0.8 1.0 CA B:CYS162 4.7 96.8 1.0 CA B:CYS208 4.7 0.7 1.0 C B:SER164 4.8 94.2 1.0 N B:GLY166 5.0 92.9 1.0

D.Kalbas, S.Liebscher, T.Nowak, M.Meleshin, M.Pannek, C.Popp, Z.Alhalabi, F.Bordusa, W.Sippl, C.Steegborn, M.Schutkowski. Potent and Selective Inhibitors of Human Sirtuin 5. J. Med. Chem. V. 61 2460 2018.
ISSN: ISSN 1520-4804
PubMed: 29494161
DOI: 10.1021/ACS.JMEDCHEM.7B01648