Zinc in PDB 3aj3: Crystal Structure of Selenomethionine Substituted 4-Pyridoxolactonase From Mesorhizobium Loti

All present enzymatic activity of Crystal Structure of Selenomethionine Substituted 4-Pyridoxolactonase From Mesorhizobium Loti:
3.1.1.27;

The structure of Crystal Structure of Selenomethionine Substituted 4-Pyridoxolactonase From Mesorhizobium Loti, PDB code: 3aj3 was solved by J.Kobayashi, Y.Yoshikane, S.Baba, B.Mikami, T.Yagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.99 / 1.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.777, 39.214, 84.191, 90.00, 117.92, 90.00
R / Rfree (%)	16.3 / 19

The binding sites of Zinc atom in the Crystal Structure of Selenomethionine Substituted 4-Pyridoxolactonase From Mesorhizobium Loti (pdb code 3aj3). 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 Selenomethionine Substituted 4-Pyridoxolactonase From Mesorhizobium Loti, PDB code: 3aj3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Selenomethionine Substituted 4-Pyridoxolactonase From Mesorhizobium Loti


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 Selenomethionine Substituted 4-Pyridoxolactonase From Mesorhizobium Loti within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn275 b:14.3 occ:0.90 OD2 A:ASP207 2.0 13.6 1.0 O A:HOH384 2.1 15.2 1.0 OD2 A:ASP100 2.2 13.9 1.0 O A:HOH502 2.2 12.4 1.0 NE2 A:HIS252 2.2 13.0 1.0 NE2 A:HIS101 2.3 12.4 1.0 CG A:ASP207 2.9 11.9 1.0 CD2 A:HIS101 3.1 11.6 1.0 CG A:ASP100 3.1 12.6 1.0 CD2 A:HIS252 3.2 12.4 1.0 OD1 A:ASP207 3.2 12.6 1.0 CE1 A:HIS252 3.2 12.8 1.0 CE1 A:HIS101 3.3 11.6 1.0 OD1 A:ASP100 3.4 11.0 1.0 ZN A:ZN276 3.5 30.2 0.2 O A:HOH537 4.0 28.0 1.0 O A:HOH290 4.2 22.4 1.0 OH A:TYR210 4.3 14.1 1.0 CG A:HIS101 4.3 10.7 1.0 ND1 A:HIS252 4.3 10.6 1.0 CB A:ASP207 4.3 8.5 1.0 CG A:HIS252 4.4 10.5 1.0 ND1 A:HIS101 4.4 10.3 1.0 NE2 A:HIS96 4.4 12.6 1.0 CB A:ASP100 4.5 9.7 1.0 CE1 A:HIS96 4.5 11.4 1.0 O A:HOH420 4.6 20.0 1.0 CZ A:TYR210 4.6 11.1 1.0 NE2 A:HIS185 4.8 12.3 1.0 CE1 A:TYR210 4.9 13.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Selenomethionine Substituted 4-Pyridoxolactonase From Mesorhizobium Loti


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 Selenomethionine Substituted 4-Pyridoxolactonase From Mesorhizobium Loti within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn276 b:30.2 occ:0.23 NE2 A:HIS185 1.9 12.3 1.0 O A:HOH502 1.9 12.4 1.0 NE2 A:HIS96 2.2 12.6 1.0 ND1 A:HIS98 2.4 13.4 1.0 OD2 A:ASP207 2.7 13.6 1.0 CE1 A:HIS185 2.7 11.9 1.0 CD2 A:HIS185 3.0 11.3 1.0 O A:HOH420 3.0 20.0 1.0 CD2 A:HIS96 3.1 12.3 1.0 CE1 A:HIS96 3.2 11.4 1.0 CG A:HIS98 3.2 10.0 1.0 CE1 A:HIS98 3.4 14.3 1.0 CB A:HIS98 3.4 8.8 1.0 ZN A:ZN275 3.5 14.3 0.9 CG A:ASP207 3.7 11.9 1.0 O A:HOH384 3.9 15.2 1.0 ND1 A:HIS185 3.9 15.7 1.0 CB A:ASP207 4.0 8.5 1.0 CG A:HIS185 4.1 8.6 1.0 NE2 A:HIS101 4.2 12.4 1.0 CD2 A:HIS101 4.2 11.6 1.0 OH A:TYR210 4.2 14.1 1.0 CG A:HIS96 4.3 10.3 1.0 ND1 A:HIS96 4.3 10.1 1.0 CD2 A:HIS98 4.3 11.0 1.0 OD1 A:ASP100 4.3 11.0 1.0 NE2 A:HIS98 4.3 12.7 1.0 OD1 A:ASP207 4.8 12.6 1.0 O A:HOH290 4.8 22.4 1.0 OD2 A:ASP100 4.9 13.9 1.0 CA A:HIS98 4.9 8.5 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 2053-230X
PubMed: 24699732
DOI: 10.1107/S2053230X14003926