Zinc in PDB 4kep: Crystal Structure of 4-Pyridoxolactonase, Wild-Type

All present enzymatic activity of Crystal Structure of 4-Pyridoxolactonase, Wild-Type:
3.1.1.27;

The structure of Crystal Structure of 4-Pyridoxolactonase, Wild-Type, PDB code: 4kep 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)	36.14 / 1.83
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.751, 39.198, 84.200, 90.00, 117.68, 90.00
R / Rfree (%)	17.4 / 20.9

The structure of Crystal Structure of 4-Pyridoxolactonase, Wild-Type also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

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

Zinc binding site 1 out of 2 in the Crystal Structure of 4-Pyridoxolactonase, Wild-Type


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, Wild-Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:21.6 occ:0.59 OXT A:ACT303 2.1 33.2 0.8 OD2 A:ASP207 2.1 21.6 1.0 OD2 A:ASP100 2.1 27.9 1.0 NE2 A:HIS101 2.2 21.6 1.0 O A:ACT303 2.3 25.7 0.8 NE2 A:HIS252 2.4 29.5 1.0 C A:ACT303 2.5 32.1 0.8 CG A:ASP207 2.9 23.7 1.0 OD1 A:ASP207 3.0 25.4 1.0 CD2 A:HIS101 3.0 20.4 1.0 CG A:ASP100 3.1 26.4 1.0 CE1 A:HIS101 3.2 25.3 1.0 CE1 A:HIS252 3.3 25.7 1.0 CD2 A:HIS252 3.4 28.4 1.0 ZN A:ZN302 3.5 20.8 0.6 OD1 A:ASP100 3.5 24.3 1.0 CH3 A:ACT303 3.9 25.1 0.8 CG A:HIS101 4.2 23.4 1.0 ND1 A:HIS101 4.3 23.6 1.0 CB A:ASP207 4.4 17.8 1.0 CB A:ASP100 4.4 19.8 1.0 ND1 A:HIS252 4.5 25.2 1.0 CG A:HIS252 4.5 27.4 1.0 CE1 A:HIS96 4.5 21.5 1.0 NE2 A:HIS96 4.5 19.9 1.0 OH A:TYR210 4.6 32.6 1.0 CZ A:TYR210 4.8 29.4 1.0 O1 A:EDO307 4.9 27.5 0.5 CE1 A:TYR210 4.9 28.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of 4-Pyridoxolactonase, Wild-Type


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, Wild-Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:20.8 occ:0.62 O A:ACT303 2.0 25.7 0.8 NE2 A:HIS185 2.1 19.7 1.0 NE2 A:HIS96 2.2 19.9 1.0 ND1 A:HIS98 2.3 24.1 1.0 OD2 A:ASP207 2.3 21.6 1.0 CH3 A:ACT303 2.4 25.1 0.8 C A:ACT303 2.4 32.1 0.8 CE1 A:HIS185 3.1 21.4 1.0 CD2 A:HIS185 3.1 18.2 1.0 CE1 A:HIS98 3.2 25.2 1.0 CD2 A:HIS96 3.2 19.4 1.0 CE1 A:HIS96 3.2 21.5 1.0 CG A:HIS98 3.2 22.6 1.0 CG A:ASP207 3.3 23.7 1.0 OXT A:ACT303 3.4 33.2 0.8 ZN A:ZN301 3.5 21.6 0.6 CB A:HIS98 3.6 22.1 1.0 CB A:ASP207 3.7 17.8 1.0 NE2 A:HIS101 4.2 21.6 1.0 ND1 A:HIS185 4.2 22.9 1.0 CD2 A:HIS101 4.3 20.4 1.0 CG A:HIS185 4.3 21.1 1.0 NE2 A:HIS98 4.3 23.7 1.0 CD2 A:HIS98 4.3 20.1 1.0 ND1 A:HIS96 4.3 18.7 1.0 CG A:HIS96 4.4 19.2 1.0 OH A:TYR210 4.4 32.6 1.0 OD1 A:ASP207 4.5 25.4 1.0 OD1 A:ASP100 4.5 24.3 1.0 O2 A:EDO307 4.8 32.5 0.5 OD2 A:ASP100 4.8 27.9 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