Zinc in PDB 1ps7: Crystal Structure of E.Coli Pdxa

All present enzymatic activity of Crystal Structure of E.Coli Pdxa:
1.1.1.262;

The structure of Crystal Structure of E.Coli Pdxa, PDB code: 1ps7 was solved by J.Sivaraman, Y.Li, J.Banks, D.E.Cane, A.Matte, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.050, 76.693, 95.424, 90.00, 109.73, 90.00
R / Rfree (%)	21.3 / 27.2

The binding sites of Zinc atom in the Crystal Structure of E.Coli Pdxa (pdb code 1ps7). 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 E.Coli Pdxa, PDB code: 1ps7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of E.Coli Pdxa


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 E.Coli Pdxa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn331 b:29.5 occ:1.00 NE2 A:HIS166 1.9 22.9 1.0 NE2 B:HIS211 2.1 25.6 1.0 NE2 A:HIS266 2.1 10.6 1.0 O A:HOH484 2.7 19.6 1.0 CE1 B:HIS211 2.9 26.9 1.0 CD2 A:HIS166 2.9 22.1 1.0 CE1 A:HIS166 2.9 23.1 1.0 CD2 A:HIS266 3.1 10.5 1.0 CE1 A:HIS266 3.1 10.0 1.0 O A:HOH611 3.1 32.5 1.0 CD2 B:HIS211 3.3 25.6 1.0 ND1 A:HIS166 4.0 23.1 1.0 CG A:HIS166 4.0 22.0 1.0 ND1 B:HIS211 4.1 26.0 1.0 ND1 A:HIS266 4.1 11.9 1.0 CG A:HIS266 4.2 11.4 1.0 CG B:HIS211 4.3 25.0 1.0 CD1 A:LEU270 4.6 9.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of E.Coli Pdxa


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 E.Coli Pdxa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn330 b:28.6 occ:1.00 NE2 A:HIS211 2.1 23.1 1.0 NE2 B:HIS266 2.4 12.9 1.0 NE2 B:HIS166 2.6 24.3 1.0 CE1 A:HIS211 2.6 23.7 1.0 O B:HOH440 2.9 17.9 1.0 CE1 B:HIS266 3.2 12.6 1.0 CD2 A:HIS211 3.4 23.7 1.0 CD2 B:HIS166 3.4 23.1 1.0 CD2 B:HIS266 3.4 11.9 1.0 CE1 B:HIS166 3.5 23.6 1.0 ND1 A:HIS211 3.9 23.4 1.0 CG A:HIS211 4.3 23.1 1.0 ND1 B:HIS266 4.4 12.6 1.0 CG B:HIS266 4.5 11.1 1.0 CG B:HIS166 4.6 22.9 1.0 CD1 B:LEU270 4.6 4.2 1.0 ND1 B:HIS166 4.6 23.4 1.0 OD2 A:ASP247 4.8 17.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of E.Coli Pdxa


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 E.Coli Pdxa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn333 b:26.0 occ:1.00 NE2 C:HIS166 1.9 19.6 1.0 NE2 C:HIS266 2.2 10.7 1.0 NE2 D:HIS211 2.6 25.4 1.0 CE1 D:HIS211 2.6 25.7 1.0 O C:HOH365 2.8 8.4 1.0 CE1 C:HIS166 2.9 19.9 1.0 CD2 C:HIS166 2.9 18.7 1.0 O C:HOH631 3.0 34.5 1.0 CD2 C:HIS266 3.1 10.3 1.0 CE1 C:HIS266 3.3 10.6 1.0 ND1 D:HIS211 3.8 24.5 1.0 CD2 D:HIS211 3.8 24.4 1.0 ND1 C:HIS166 4.0 19.8 1.0 CG C:HIS166 4.0 18.6 1.0 CG C:HIS266 4.3 10.1 1.0 CG D:HIS211 4.3 23.8 1.0 ND1 C:HIS266 4.3 10.6 1.0 CD1 C:LEU270 5.0 7.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of E.Coli Pdxa


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 E.Coli Pdxa within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn332 b:43.0 occ:1.00 NE2 C:HIS211 2.0 18.0 1.0 NE2 D:HIS266 2.2 12.4 1.0 CE1 C:HIS211 2.3 19.1 1.0 NE2 D:HIS166 2.5 20.6 1.0 O C:HOH560 2.7 17.7 1.0 CD2 D:HIS266 3.2 11.2 1.0 O C:HOH683 3.2 43.3 1.0 CE1 D:HIS266 3.2 10.9 1.0 CE1 D:HIS166 3.3 21.1 1.0 CD2 C:HIS211 3.4 18.4 1.0 ND1 C:HIS211 3.6 19.2 1.0 CD2 D:HIS166 3.6 20.4 1.0 CG C:HIS211 4.1 18.9 1.0 CE D:MSE151 4.3 51.4 1.0 ND1 D:HIS266 4.3 9.9 1.0 CG D:HIS266 4.3 10.1 1.0 CD1 D:LEU270 4.4 4.2 1.0 ND1 D:HIS166 4.5 21.3 1.0 CG D:HIS166 4.7 21.1 1.0 OD2 C:ASP247 4.7 17.1 1.0

J.Sivaraman, Y.Li, J.Banks, D.E.Cane, A.Matte, M.Cygler. Crystal Structure of Escherichia Coli Pdxa, An Enzyme Involved in the Pyridoxal Phosphate Biosynthesis Pathway J.Biol.Chem. V. 278 43682 2003.
ISSN: ISSN 0021-9258
PubMed: 12896974
DOI: 10.1074/JBC.M306344200