Zinc in PDB 2y7d: Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Orthorombic Form)

The structure of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Orthorombic Form), PDB code: 2y7d 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)	19.45 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.870, 100.820, 147.430, 90.00, 90.00, 90.00
R / Rfree (%)	15.77 / 17.4

The binding sites of Zinc atom in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Orthorombic Form) (pdb code 2y7d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Orthorombic Form), PDB code: 2y7d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Orthorombic 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 (Orthorombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.4 occ:0.75 OE2 A:GLU230 2.0 20.9 1.0 NE2 A:HIS46 2.0 19.7 1.0 NE2 A:HIS48 2.1 20.4 1.0 O A:HOH2248 2.1 27.7 1.0 O A:HOH2247 2.4 24.3 1.0 CD A:GLU230 2.8 23.8 1.0 OE1 A:GLU230 3.0 19.6 1.0 CD2 A:HIS46 3.0 19.2 1.0 CD2 A:HIS48 3.0 20.4 1.0 CE1 A:HIS46 3.1 19.3 1.0 CE1 A:HIS48 3.1 20.7 1.0 CG A:HIS46 4.2 17.2 1.0 CG A:HIS48 4.2 19.1 1.0 O A:HOH2010 4.2 30.7 1.0 NH2 A:ARG226 4.2 24.5 1.0 O A:HOH2151 4.2 33.5 1.0 ND1 A:HIS46 4.2 20.0 1.0 ND1 A:HIS48 4.2 21.5 1.0 CG A:GLU230 4.2 20.4 1.0 CB A:SER82 4.3 25.5 1.0 OG A:SER82 4.3 30.9 1.0 OE2 A:GLU143 4.4 24.3 1.0 NH1 A:ARG226 4.5 17.0 1.0 CZ A:ARG226 4.7 23.2 1.0 OE1 A:GLU143 4.8 23.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Orthorombic 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 (Orthorombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:16.0 occ:0.88 OE2 B:GLU230 2.0 17.3 1.0 NE2 B:HIS46 2.0 17.9 1.0 NE2 B:HIS48 2.0 17.7 1.0 O B:HOH2236 2.1 20.9 1.0 O B:HOH2237 2.4 27.1 1.0 CD B:GLU230 2.8 18.3 1.0 OE1 B:GLU230 2.9 17.6 1.0 CD2 B:HIS46 3.0 17.5 1.0 CD2 B:HIS48 3.0 18.7 1.0 CE1 B:HIS48 3.1 17.8 1.0 CE1 B:HIS46 3.1 17.6 1.0 O B:HOH2008 4.1 25.7 1.0 OG B:SER82 4.1 24.2 1.0 CG B:HIS46 4.1 16.2 1.0 NH2 B:ARG226 4.1 20.8 1.0 CG B:HIS48 4.1 17.4 1.0 O B:HOH2140 4.2 34.7 1.0 ND1 B:HIS48 4.2 18.7 1.0 CB B:SER82 4.2 18.3 1.0 ND1 B:HIS46 4.2 18.3 1.0 CG B:GLU230 4.2 16.7 1.0 OE2 B:GLU143 4.3 21.4 1.0 NH1 B:ARG226 4.4 16.5 1.0 OE1 B:GLU143 4.5 21.9 1.0 CZ B:ARG226 4.6 25.3 1.0 O B:HOH2141 4.6 39.6 1.0 CD B:GLU143 4.8 25.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Orthorombic Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Orthorombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:17.9 occ:0.72 OE2 C:GLU230 2.0 20.8 1.0 NE2 C:HIS46 2.0 20.6 1.0 O C:HOH2252 2.0 27.1 1.0 NE2 C:HIS48 2.1 18.7 1.0 O C:HOH2253 2.5 23.1 1.0 CD C:GLU230 2.8 24.8 1.0 OE1 C:GLU230 3.0 21.2 1.0 CD2 C:HIS46 3.0 20.3 1.0 CD2 C:HIS48 3.0 19.0 1.0 CE1 C:HIS46 3.1 20.5 1.0 CE1 C:HIS48 3.1 19.4 1.0 CG C:HIS46 4.2 19.4 1.0 CG C:HIS48 4.2 18.7 1.0 NH2 C:ARG226 4.2 24.7 1.0 ND1 C:HIS46 4.2 21.7 1.0 ND1 C:HIS48 4.2 20.5 1.0 CB C:SER82 4.2 25.0 1.0 CG C:GLU230 4.2 19.2 1.0 O C:HOH2118 4.2 42.8 1.0 O C:HOH2014 4.3 27.1 1.0 OE2 C:GLU143 4.4 24.3 1.0 OG C:SER82 4.4 33.2 1.0 NH1 C:ARG226 4.5 18.7 1.0 CZ C:ARG226 4.7 24.0 1.0 O C:HOH2148 4.7 42.6 1.0 OE1 C:GLU143 4.9 24.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Orthorombic Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) From Candidatus Cloacamonas Acidaminovorans (Orthorombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:16.5 occ:0.89 OE2 D:GLU230 2.0 17.1 1.0 NE2 D:HIS46 2.0 18.2 1.0 NE2 D:HIS48 2.1 15.2 1.0 O D:HOH2236 2.1 21.0 1.0 O D:HOH2235 2.4 23.7 1.0 CD D:GLU230 2.8 21.6 1.0 OE1 D:GLU230 2.9 17.3 1.0 CD2 D:HIS46 3.0 17.4 1.0 CD2 D:HIS48 3.0 15.8 1.0 CE1 D:HIS46 3.1 16.9 1.0 CE1 D:HIS48 3.1 16.4 1.0 NH2 D:ARG226 4.1 21.8 1.0 OG D:SER82 4.1 27.4 1.0 O D:HOH2011 4.1 25.7 1.0 CG D:HIS46 4.1 16.7 1.0 CG D:HIS48 4.2 16.8 1.0 ND1 D:HIS46 4.2 17.0 1.0 CG D:GLU230 4.2 16.7 1.0 ND1 D:HIS48 4.2 18.3 1.0 O D:HOH2133 4.2 27.4 1.0 OE2 D:GLU143 4.2 20.9 1.0 CB D:SER82 4.2 21.2 1.0 NH1 D:ARG226 4.4 15.8 1.0 OE1 D:GLU143 4.5 21.5 1.0 O D:HOH2134 4.5 53.7 1.0 CZ D:ARG226 4.6 24.5 1.0 CD D:GLU143 4.8 25.0 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