Zinc in PDB 2y7e: Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Tetragonal Form)

The structure of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Tetragonal Form), PDB code: 2y7e was solved by M.Bellinzoni, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.76 / 1.28
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.188, 102.188, 101.070, 90.00, 90.00, 90.00
R / Rfree (%)	14.333 / 17.02

The structure of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Tetragonal Form) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Tetragonal Form) (pdb code 2y7e). 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 the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Tetragonal Form), PDB code: 2y7e:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Tetragonal Form)


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 the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Tetragonal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.3 occ:0.50 OE2 A:GLU230 2.0 16.4 1.0 O2 A:FMT1275 2.1 15.8 1.0 O A:HOH2296 2.2 16.9 1.0 NE2 A:HIS48 2.2 15.2 1.0 NE2 A:HIS46 2.2 16.4 1.0 O A:HOH2297 2.2 16.4 1.0 CD A:GLU230 3.0 15.0 1.0 C A:FMT1275 3.0 16.7 1.0 CE1 A:HIS46 3.1 17.1 1.0 CD2 A:HIS48 3.1 14.9 1.0 CE1 A:HIS48 3.2 16.2 1.0 CD2 A:HIS46 3.2 14.7 1.0 OE1 A:GLU230 3.4 16.5 1.0 O A:HOH2255 3.8 36.9 1.0 OG A:SER82 4.0 16.6 1.0 NH2 A:ARG226 4.1 22.1 1.0 O1 A:FMT1275 4.2 17.9 1.0 ND1 A:HIS46 4.3 16.9 1.0 NH1 A:ARG226 4.3 20.8 1.0 CB A:SER82 4.3 15.2 1.0 O A:HOH2010 4.3 23.5 1.0 CG A:GLU230 4.3 14.2 1.0 CG A:HIS48 4.3 14.8 1.0 ND1 A:HIS48 4.3 15.7 1.0 CG A:HIS46 4.4 15.4 1.0 O A:HOH2120 4.4 23.3 1.0 CZ A:ARG226 4.6 18.1 1.0 OE1 A:GLU143 4.7 18.6 0.5 OE2 A:GLU143 4.7 17.6 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Tetragonal Form)


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 the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Tetragonal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:13.9 occ:0.50 OE2 B:GLU230 2.0 15.5 1.0 O2 B:FMT1276 2.0 15.8 1.0 O B:HOH2288 2.2 16.9 1.0 O B:HOH2287 2.2 15.9 1.0 NE2 B:HIS48 2.2 13.1 1.0 NE2 B:HIS46 2.2 13.6 1.0 C B:FMT1276 3.0 16.6 1.0 CD B:GLU230 3.0 13.6 1.0 CE1 B:HIS48 3.2 14.5 1.0 CE1 B:HIS46 3.2 14.3 1.0 CD2 B:HIS46 3.2 13.0 1.0 CD2 B:HIS48 3.2 14.1 1.0 OE1 B:GLU230 3.4 15.8 1.0 OG B:SER82 3.9 17.4 1.0 NH2 B:ARG226 4.0 20.4 1.0 O B:HOH2167 4.1 30.9 1.0 O1 B:FMT1276 4.1 18.6 1.0 O B:HOH2006 4.2 23.6 1.0 CB B:SER82 4.2 14.0 1.0 O B:HOH2095 4.3 28.7 1.0 ND1 B:HIS48 4.3 15.0 1.0 ND1 B:HIS46 4.3 13.2 1.0 CG B:HIS46 4.3 11.8 1.0 CG B:HIS48 4.4 13.7 1.0 CG B:GLU230 4.4 14.5 1.0 NH1 B:ARG226 4.4 18.5 1.0 OE1 B:GLU143 4.6 14.8 0.5 OE2 B:GLU143 4.6 16.0 0.5 CZ B:ARG226 4.7 16.7 1.0

M.Bellinzoni, K.Bastard, A.Perret, A.Zaparucha, N.Perchat, C.Vergne, T.Wagner, R.C.De Melo-Minardi, F.Artiguenave, G.N.Cohen, J.Weissenbach, M.Salanoubat, P.M.Alzari. 3-Keto-5-Aminohexanoate Cleavage Enzyme: A Common Fold For An Uncommon Claisen-Type Condensation. J.Biol.Chem. V. 286 27399 2011.
ISSN: ISSN 0021-9258
PubMed: 21632536
DOI: 10.1074/JBC.M111.253260