Zinc in PDB 4utv: Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3-Phenyl- Succinylated CPS1-Peptide

The structure of Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3-Phenyl- Succinylated CPS1-Peptide, PDB code: 4utv 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)	47.85 / 2.40
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	88.910, 88.910, 305.330, 90.00, 90.00, 120.00
R / Rfree (%)	19.696 / 22.699

The structure of Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3-Phenyl- 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 3-Phenyl- Succinylated CPS1-Peptide (pdb code 4utv). 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-Phenyl- Succinylated CPS1-Peptide, PDB code: 4utv:
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-Phenyl- 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 3-Phenyl- Succinylated CPS1-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1299 b:30.6 occ:1.00 SG A:CYS162 2.3 28.9 1.0 SG A:CYS208 2.3 34.1 1.0 SG A:CYS165 2.3 34.2 1.0 SG A:CYS203 2.3 30.2 1.0 CB A:CYS203 3.1 32.4 1.0 CB A:CYS162 3.2 29.2 1.0 CB A:CYS208 3.3 36.3 1.0 CB A:CYS165 3.3 31.7 1.0 N A:CYS165 3.8 31.6 1.0 NH1 A:ARG205 3.9 52.4 1.0 CA A:CYS165 4.1 30.7 1.0 N A:GLY210 4.4 33.5 1.0 CA A:CYS203 4.6 31.8 1.0 CB A:SER164 4.6 30.1 1.0 CA A:CYS162 4.7 28.5 1.0 CD A:ARG205 4.7 47.3 1.0 O A:HOH2063 4.7 28.5 1.0 CA A:CYS208 4.7 37.2 1.0 CA A:GLY210 4.8 32.2 1.0 C A:CYS165 4.8 32.3 1.0 C A:SER164 4.8 29.8 1.0 N A:ASN209 4.9 34.6 1.0 N A:GLY166 4.9 32.6 1.0 CZ A:ARG205 4.9 49.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Zebrafish Sirtuin 5 in Complex with 3-Phenyl- 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 3-Phenyl- Succinylated CPS1-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1299 b:45.8 occ:1.00 SG B:CYS165 2.3 49.1 1.0 SG B:CYS162 2.3 49.5 1.0 SG B:CYS203 2.3 49.1 1.0 SG B:CYS208 2.3 55.4 1.0 CB B:CYS203 3.1 46.5 1.0 CB B:CYS162 3.1 50.1 1.0 CB B:CYS208 3.3 59.8 1.0 CB B:CYS165 3.3 49.3 1.0 N B:CYS165 3.7 47.9 1.0 CA B:CYS165 4.0 48.4 1.0 N B:GLY210 4.4 51.7 1.0 CA B:CYS203 4.6 48.5 1.0 CA B:CYS162 4.6 48.5 1.0 CA B:CYS208 4.7 61.4 1.0 NH1 B:ARG205 4.7 64.3 1.0 C B:CYS165 4.7 44.4 1.0 CD B:ARG205 4.8 59.6 1.0 C B:SER164 4.8 51.0 1.0 CA B:GLY210 4.8 48.8 1.0 CB B:SER164 4.8 54.7 1.0 N B:GLY166 4.9 44.3 1.0 N B:ASN209 4.9 61.1 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