Zinc in PDB 4keq: Crystal Structure of 4-Pyridoxolactonase, 5-Pyridoxolactone Bound

All present enzymatic activity of Crystal Structure of 4-Pyridoxolactonase, 5-Pyridoxolactone Bound:
3.1.1.27;

The structure of Crystal Structure of 4-Pyridoxolactonase, 5-Pyridoxolactone Bound, PDB code: 4keq was solved by J.Kobayashi, Y.Yoshikane, S.Baba, K.Mizutani, N.Takahashi, B.Mikami, T.Yagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.18 / 2.28
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.426, 39.576, 84.660, 90.00, 117.73, 90.00
R / Rfree (%)	18.8 / 24.6

The binding sites of Zinc atom in the Crystal Structure of 4-Pyridoxolactonase, 5-Pyridoxolactone Bound (pdb code 4keq). 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 4-Pyridoxolactonase, 5-Pyridoxolactone Bound, PDB code: 4keq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of 4-Pyridoxolactonase, 5-Pyridoxolactone Bound


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 4-Pyridoxolactonase, 5-Pyridoxolactone Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:20.2 occ:1.00 NE2 A:HIS101 2.1 16.3 1.0 NE2 A:HIS252 2.1 16.6 1.0 OD1 A:ASP207 2.4 13.1 1.0 OD2 A:ASP207 2.4 17.5 1.0 CG A:ASP207 2.7 14.7 1.0 OD2 A:ASP100 2.8 25.1 1.0 CD2 A:HIS101 2.9 13.3 1.0 O A:HOH401 2.9 18.4 1.0 CE1 A:HIS252 3.0 16.6 1.0 CD2 A:HIS252 3.1 19.1 1.0 CE1 A:HIS101 3.2 15.3 1.0 CG A:ASP100 3.6 18.9 1.0 OD1 A:ASP100 3.7 19.8 1.0 ZN A:ZN302 3.9 19.4 0.9 CG A:HIS101 4.1 16.7 1.0 ND1 A:HIS252 4.2 19.9 1.0 ND1 A:HIS101 4.2 12.7 1.0 CB A:ASP207 4.2 14.7 1.0 OAC A:5PN303 4.2 20.4 0.8 CG A:HIS252 4.2 19.7 1.0 OH A:TYR210 4.3 23.7 1.0 CZ A:TYR210 4.6 20.3 1.0 CE1 A:TYR210 4.7 18.2 1.0 CE1 A:HIS96 4.7 12.1 1.0 NE2 A:HIS96 4.7 11.8 1.0 CB A:ASP100 4.9 17.1 1.0 OG A:SER251 5.0 16.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of 4-Pyridoxolactonase, 5-Pyridoxolactone Bound


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 4-Pyridoxolactonase, 5-Pyridoxolactone Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:19.4 occ:0.93 O A:HOH401 2.1 18.4 1.0 OD2 A:ASP207 2.1 17.5 1.0 NE2 A:HIS185 2.1 13.5 1.0 ND1 A:HIS98 2.2 16.4 1.0 NE2 A:HIS96 2.2 11.8 1.0 CD2 A:HIS185 3.1 12.3 1.0 CG A:HIS98 3.1 15.4 1.0 CD2 A:HIS96 3.1 13.1 1.0 CE1 A:HIS98 3.1 15.3 1.0 CE1 A:HIS185 3.2 13.7 1.0 CG A:ASP207 3.2 14.7 1.0 CE1 A:HIS96 3.3 12.1 1.0 CB A:HIS98 3.4 14.2 1.0 CB A:ASP207 3.7 14.7 1.0 ZN A:ZN301 3.9 20.2 1.0 OAC A:5PN303 4.0 20.4 0.8 CD2 A:HIS98 4.2 14.9 1.0 NE2 A:HIS98 4.2 12.9 1.0 CG A:HIS185 4.2 14.6 1.0 ND1 A:HIS185 4.2 13.7 1.0 CG A:HIS96 4.3 14.7 1.0 OD1 A:ASP207 4.3 13.1 1.0 CD2 A:HIS101 4.3 13.3 1.0 OH A:TYR210 4.3 23.7 1.0 ND1 A:HIS96 4.3 11.4 1.0 CAE A:5PN303 4.4 17.7 0.8 OD1 A:ASP100 4.6 19.8 1.0 NE2 A:HIS101 4.6 16.3 1.0 CA A:HIS98 4.8 13.8 1.0

J.Kobayashi, Y.Yoshikane, T.Yagi, S.Baba, K.Mizutani, N.Takahashi, B.Mikami. Structure of 4-Pyridoxolactonase From Mesorhizobium Loti Acta Crystallogr.,Sect.F V. 70 424 2014.
ISSN: ESSN 1744-3091
DOI: 10.1107/S2053230X14003926