Zinc in PDB 4uua: Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3S- Z-Amino-Succinylated CPS1-Peptide

The structure of Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3S- Z-Amino-Succinylated CPS1-Peptide, PDB code: 4uua was solved by M.Pannek, M.Gertz, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.87 / 2.80
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.190, 87.190, 313.870, 90.00, 90.00, 120.00
R / Rfree (%)	20.803 / 26.138

The structure of Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3S- Z-Amino-Succinylated 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 3S- Z-Amino-Succinylated CPS1-Peptide (pdb code 4uua). 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 3S- Z-Amino-Succinylated CPS1-Peptide, PDB code: 4uua:
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 3S- Z-Amino-Succinylated 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 3S- Z-Amino-Succinylated CPS1-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1299 b:51.6 occ:1.00 SG A:CYS203 2.3 61.2 1.0 SG A:CYS162 2.3 52.2 1.0 SG A:CYS208 2.3 65.7 1.0 SG A:CYS165 2.4 61.5 1.0 CB A:CYS203 3.1 62.1 1.0 CB A:CYS162 3.3 48.6 1.0 CB A:CYS208 3.4 68.1 1.0 CB A:CYS165 3.4 62.9 1.0 N A:CYS165 3.7 60.9 1.0 CA A:CYS165 4.1 60.1 1.0 NH1 A:ARG205 4.2 93.7 1.0 N A:GLY210 4.3 55.8 1.0 CA A:GLY210 4.5 54.1 1.0 CA A:CYS203 4.6 60.0 1.0 CB A:SER164 4.6 62.6 1.0 CA A:CYS162 4.7 45.6 1.0 C A:SER164 4.8 60.4 1.0 CA A:CYS208 4.8 69.1 1.0 C A:CYS165 4.9 57.1 1.0 CD A:ARG205 4.9 81.5 1.0 N A:GLY166 5.0 57.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3S- Z-Amino-Succinylated 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 3S- Z-Amino-Succinylated CPS1-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1299 b:0.1 occ:1.00 SG B:CYS165 2.3 0.3 1.0 SG B:CYS208 2.3 0.6 1.0 SG B:CYS203 2.3 0.6 1.0 SG B:CYS162 2.4 0.9 1.0 CB B:CYS203 3.2 0.1 1.0 CB B:CYS162 3.3 0.8 1.0 CB B:CYS208 3.3 1.0 1.0 CB B:CYS165 3.4 0.8 1.0 N B:CYS165 3.7 0.4 1.0 CA B:CYS165 4.1 0.9 1.0 N B:GLY210 4.3 0.2 1.0 CB B:SER164 4.4 0.2 1.0 CA B:GLY210 4.6 0.0 1.0 CA B:CYS203 4.7 0.7 1.0 CA B:CYS162 4.7 96.0 1.0 CA B:CYS208 4.7 0.4 1.0 C B:SER164 4.8 0.6 1.0 C B:CYS165 4.8 0.4 1.0 CD B:ARG205 4.9 0.1 1.0 N B:GLY166 4.9 0.5 1.0 C B:CYS208 5.0 0.5 1.0 N B:ASN209 5.0 0.5 1.0

C.Roessler, T.Nowak, M.Pannek, M.Gertz, G.T.Nguyen, M.Scharfe, I.Born, W.Sippl, C.Steegborn, M.Schutkowski. Chemical Probing of the Human Sirtuin 5 Active Site Reveals Its Substrate Acyl Specificity and Peptide-Based Inhibitors. Angew.Chem.Int.Ed.Engl. V. 53 10728 2014.
ISSN: ISSN 1433-7851
PubMed: 25111069
DOI: 10.1002/ANIE.201402679