Zinc in PDB 2y7g: Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From C. Cloacamonas Acidaminovorans in Complex with the Product Acetoacetate

The structure of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From C. Cloacamonas Acidaminovorans in Complex with the Product Acetoacetate, PDB code: 2y7g 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)	28.00 / 1.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.100, 102.100, 100.736, 90.00, 90.00, 90.00
R / Rfree (%)	16.66 / 18.63

The structure of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From C. Cloacamonas Acidaminovorans in Complex with the Product Acetoacetate also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From C. Cloacamonas Acidaminovorans in Complex with the Product Acetoacetate (pdb code 2y7g). 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 C. Cloacamonas Acidaminovorans in Complex with the Product Acetoacetate, PDB code: 2y7g:
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 C. Cloacamonas Acidaminovorans in Complex with the Product Acetoacetate


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 C. Cloacamonas Acidaminovorans in Complex with the Product Acetoacetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.4 occ:0.56 OE2 A:GLU230 2.0 16.8 1.0 O1 A:AAE1276 2.0 14.3 1.0 O8 A:AAE1276 2.1 15.9 1.0 NE2 A:HIS48 2.2 14.3 1.0 NE2 A:HIS46 2.2 16.2 1.0 O A:HOH2265 2.3 17.3 1.0 CD A:GLU230 3.0 17.1 1.0 C5 A:AAE1276 3.0 20.1 1.0 C2 A:AAE1276 3.1 16.0 1.0 CE1 A:HIS46 3.1 15.7 1.0 CD2 A:HIS48 3.2 14.0 1.0 CE1 A:HIS48 3.2 15.0 1.0 CD2 A:HIS46 3.3 15.6 1.0 OE1 A:GLU230 3.4 17.6 1.0 C4 A:AAE1276 3.5 17.3 1.0 O A:HOH2228 3.8 36.7 1.0 OG A:SER82 3.9 16.4 1.0 NH2 A:ARG226 4.1 19.1 1.0 O3 A:AAE1276 4.2 15.3 1.0 CB A:SER82 4.2 15.1 1.0 NH1 A:ARG226 4.2 16.7 1.0 O A:HOH2015 4.3 21.1 1.0 CG A:HIS48 4.3 15.3 1.0 ND1 A:HIS46 4.3 16.2 1.0 ND1 A:HIS48 4.3 14.9 1.0 CG A:GLU230 4.3 14.7 1.0 O A:HOH2111 4.4 22.9 1.0 CG A:HIS46 4.4 15.0 1.0 C9 A:AAE1276 4.4 18.1 1.0 CZ A:ARG226 4.6 16.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From C. Cloacamonas Acidaminovorans in Complex with the Product Acetoacetate


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 C. Cloacamonas Acidaminovorans in Complex with the Product Acetoacetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:16.0 occ:0.50 OE2 B:GLU230 2.0 17.1 1.0 O1 B:AAE1276 2.0 16.6 1.0 O8 B:AAE1276 2.1 16.0 1.0 NE2 B:HIS48 2.2 15.5 1.0 O B:HOH2230 2.2 19.5 1.0 NE2 B:HIS46 2.2 15.8 1.0 C5 B:AAE1276 3.0 19.8 1.0 CD B:GLU230 3.0 18.2 1.0 C2 B:AAE1276 3.0 17.8 1.0 CE1 B:HIS46 3.1 15.6 1.0 CE1 B:HIS48 3.2 17.2 1.0 CD2 B:HIS48 3.2 16.9 1.0 CD2 B:HIS46 3.3 16.0 1.0 OE1 B:GLU230 3.4 20.3 1.0 C4 B:AAE1276 3.5 18.7 1.0 OG B:SER82 3.9 17.2 1.0 O B:HOH2189 3.9 43.5 1.0 NH2 B:ARG226 4.1 20.5 1.0 O B:HOH2004 4.2 25.1 1.0 O3 B:AAE1276 4.2 16.7 1.0 CB B:SER82 4.2 15.7 1.0 NH1 B:ARG226 4.3 18.6 1.0 CG B:HIS48 4.3 16.9 1.0 ND1 B:HIS48 4.3 19.0 1.0 ND1 B:HIS46 4.3 16.4 1.0 CG B:GLU230 4.3 18.3 1.0 CG B:HIS46 4.4 14.8 1.0 O B:HOH2062 4.4 25.9 1.0 C9 B:AAE1276 4.4 22.2 1.0 CZ B:ARG226 4.7 19.5 1.0 O B:HOH2121 5.0 30.1 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