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

Protein crystallography data

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

Other elements in 6fky:

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

Zinc Binding Sites:

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 6fky

Go back to Zinc Binding Sites List in 6fky
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 6fky

Go back to Zinc Binding Sites List in 6fky
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

Reference:

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
Page generated: Mon Oct 28 21:08:40 2024

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