Zinc in PDB 2y7f: Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce)

The structure of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce), PDB code: 2y7f 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)	33.50 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.500, 98.480, 103.180, 90.00, 90.00, 90.00
R / Rfree (%)	14.97 / 17.36

The structure of Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce) 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) (pdb code 2y7f). 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), PDB code: 2y7f:
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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.9 occ:0.57 OF1 A:KMH1276 2.0 14.3 1.0 OE2 A:GLU230 2.1 16.1 1.0 O A:HOH2236 2.2 18.7 1.0 O A:KMH1276 2.2 19.0 1.0 NE2 A:HIS48 2.2 13.2 1.0 NE2 A:HIS46 2.3 15.5 1.0 CE A:KMH1276 3.0 21.6 1.0 C A:KMH1276 3.0 76.4 1.0 CD A:GLU230 3.1 17.0 1.0 CD2 A:HIS48 3.2 14.7 1.0 CE1 A:HIS48 3.2 12.8 1.0 CE1 A:HIS46 3.2 15.8 1.0 C2 A:KMH1276 3.3 36.9 1.0 CD2 A:HIS46 3.3 15.5 1.0 OE1 A:GLU230 3.4 16.2 1.0 OG A:SER82 3.9 17.6 1.0 O A:HOH2237 3.9 40.8 1.0 O A:HOH2007 4.1 17.2 1.0 NH2 A:ARG226 4.1 24.4 1.0 OF2 A:KMH1276 4.1 17.6 1.0 CB A:SER82 4.2 14.9 1.0 CG A:HIS48 4.3 13.0 1.0 NH1 A:ARG226 4.3 22.5 1.0 ND1 A:HIS48 4.3 14.1 1.0 ND1 A:HIS46 4.4 16.3 1.0 CG A:GLU230 4.4 15.5 1.0 CG A:HIS46 4.4 14.2 1.0 CA A:KMH1276 4.4 48.6 1.0 CZ A:ARG226 4.6 28.4 1.0 N A:KMH1276 4.9 27.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce)


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) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:15.3 occ:0.52 OE2 B:GLU230 2.1 17.0 1.0 OF2 B:KMH1276 2.1 16.1 1.0 O B:HOH2228 2.1 15.9 1.0 NE2 B:HIS48 2.2 14.9 1.0 O B:KMH1276 2.2 18.8 1.0 NE2 B:HIS46 2.3 14.9 1.0 CD B:GLU230 3.0 16.6 1.0 C B:KMH1276 3.1 38.8 1.0 CE B:KMH1276 3.1 30.5 1.0 CD2 B:HIS48 3.1 15.4 1.0 CE1 B:HIS46 3.2 15.2 1.0 CE1 B:HIS48 3.2 14.4 1.0 CD2 B:HIS46 3.3 15.2 1.0 OE1 B:GLU230 3.3 15.8 1.0 C2 B:KMH1276 3.4 33.4 1.0 OG B:SER82 3.9 16.1 1.0 NH2 B:ARG226 4.1 20.4 1.0 O B:HOH2011 4.1 16.1 1.0 CB B:SER82 4.2 16.4 1.0 OF1 B:KMH1276 4.2 17.9 1.0 CG B:HIS48 4.3 14.1 1.0 ND1 B:HIS48 4.3 15.5 1.0 NH1 B:ARG226 4.3 18.3 1.0 ND1 B:HIS46 4.4 15.7 1.0 CG B:GLU230 4.4 16.0 1.0 CG B:HIS46 4.4 13.8 1.0 CA B:KMH1276 4.5 33.0 1.0 CZ B:ARG226 4.7 27.0 1.0 N B:KMH1276 5.0 21.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce)


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) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:14.8 occ:0.52 OF1 C:KMH1276 2.1 18.0 1.0 OE2 C:GLU230 2.1 14.3 1.0 O C:HOH2198 2.1 15.7 1.0 O C:KMH1276 2.2 19.9 1.0 NE2 C:HIS46 2.2 16.2 1.0 NE2 C:HIS48 2.2 16.4 1.0 C C:KMH1276 3.0 0.1 1.0 CE C:KMH1276 3.0 25.5 1.0 CD C:GLU230 3.0 21.1 1.0 CE1 C:HIS46 3.2 16.5 1.0 CD2 C:HIS48 3.2 17.4 1.0 CE1 C:HIS48 3.3 16.5 1.0 C2 C:KMH1276 3.3 55.9 1.0 CD2 C:HIS46 3.3 16.9 1.0 OE1 C:GLU230 3.4 15.8 1.0 OG C:SER82 3.9 18.5 1.0 NH2 C:ARG226 4.0 22.8 1.0 OF2 C:KMH1276 4.2 18.4 1.0 CB C:SER82 4.2 17.1 1.0 O C:HOH2007 4.2 19.6 1.0 NH1 C:ARG226 4.3 18.7 1.0 ND1 C:HIS46 4.3 17.6 1.0 CG C:HIS48 4.3 16.3 1.0 CA C:KMH1276 4.4 32.3 1.0 CG C:HIS46 4.4 15.7 1.0 ND1 C:HIS48 4.4 17.4 1.0 CG C:GLU230 4.4 14.2 1.0 CZ C:ARG226 4.6 26.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the 3-Keto-5-Aminohexanoate Cleavage Enzyme (Kce)


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) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:17.6 occ:0.56 OE2 D:GLU230 2.0 16.9 1.0 OF2 D:KMH1276 2.0 16.2 1.0 NE2 D:HIS48 2.1 14.8 1.0 O D:KMH1276 2.2 18.3 1.0 O D:HOH2209 2.2 16.5 1.0 NE2 D:HIS46 2.3 14.8 1.0 CE D:KMH1276 3.0 19.4 1.0 C D:KMH1276 3.0 52.1 1.0 CD D:GLU230 3.0 17.3 1.0 CD2 D:HIS48 3.1 15.9 1.0 CE1 D:HIS48 3.2 15.3 1.0 CE1 D:HIS46 3.2 14.9 1.0 C2 D:KMH1276 3.2 39.3 1.0 CD2 D:HIS46 3.3 15.3 1.0 OE1 D:GLU230 3.3 13.1 1.0 OG D:SER82 3.9 16.1 1.0 O D:HOH2008 4.1 15.6 1.0 NH2 D:ARG226 4.1 20.1 1.0 OF1 D:KMH1276 4.1 18.2 1.0 CB D:SER82 4.2 17.1 1.0 CG D:HIS48 4.3 15.8 1.0 ND1 D:HIS48 4.3 16.7 1.0 NH1 D:ARG226 4.3 16.7 1.0 CG D:GLU230 4.4 16.9 1.0 ND1 D:HIS46 4.4 15.6 1.0 CA D:KMH1276 4.4 38.1 1.0 CG D:HIS46 4.4 13.6 1.0 CZ D:ARG226 4.7 26.4 1.0 N D:KMH1276 5.0 26.2 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