Zinc in PDB 5fch: Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn Bound

All present enzymatic activity of Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn Bound:
3.4.13.9;

The structure of Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn Bound, PDB code: 5fch was solved by A.Kumar, V.Are, B.Ghosh, S.Jamdar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.032, 104.080, 112.412, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21.1

The binding sites of Zinc atom in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn Bound (pdb code 5fch). 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 Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn Bound, PDB code: 5fch:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn 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 Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:21.2 occ:1.00 OE2 A:GLU374 2.0 21.4 1.0 OD2 A:ASP262 2.0 21.3 1.0 NE2 A:HIS331 2.1 19.6 1.0 O1 A:PO4403 2.1 18.5 1.0 OE2 A:GLU360 2.3 21.6 1.0 CE1 A:HIS331 2.9 19.0 1.0 P A:PO4403 3.0 27.5 1.0 CD A:GLU374 3.0 21.4 1.0 CG A:ASP262 3.1 22.8 1.0 CD A:GLU360 3.1 21.6 1.0 CD2 A:HIS331 3.2 19.7 1.0 O3 A:PO4403 3.2 23.2 1.0 ZN A:ZN402 3.3 24.8 1.0 OE1 A:GLU360 3.4 21.7 1.0 OE1 A:GLU374 3.4 21.9 1.0 OD1 A:ASP262 3.5 23.9 1.0 O4 A:PO4403 3.6 24.6 1.0 CB A:SER358 3.9 17.3 1.0 OG A:SER358 4.0 17.5 1.0 NE2 A:HIS376 4.1 20.7 1.0 ND1 A:HIS331 4.1 17.8 1.0 CG A:HIS331 4.2 18.5 1.0 CG A:GLU374 4.3 21.9 1.0 O2 A:PO4403 4.3 22.9 1.0 CB A:ASP262 4.4 21.3 1.0 CG A:GLU360 4.4 20.0 1.0 O A:HOH512 4.6 32.4 1.0 NE2 A:HIS338 4.6 25.0 1.0 CE1 A:HIS376 4.6 20.2 1.0 O A:HOH501 4.7 35.4 1.0 CD2 A:HIS338 4.9 26.4 1.0 O A:ASP262 4.9 20.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn 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 Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:24.8 occ:1.00 O1 A:PO4403 1.9 18.5 1.0 OD1 A:ASP251 2.1 19.0 1.0 OD1 A:ASP262 2.1 23.9 1.0 OE1 A:GLU374 2.2 21.9 1.0 OD2 A:ASP251 2.3 16.9 1.0 CG A:ASP251 2.6 18.5 1.0 O A:HOH512 2.9 32.4 1.0 CG A:ASP262 3.0 22.8 1.0 CD A:GLU374 3.1 21.4 1.0 ZN A:ZN401 3.3 21.2 1.0 P A:PO4403 3.3 27.5 1.0 OD2 A:ASP262 3.3 21.3 1.0 OE2 A:GLU374 3.3 21.4 1.0 O2 A:PO4403 3.6 22.9 1.0 OG1 A:THR264 3.6 19.0 1.0 O4 A:PO4403 3.9 24.6 1.0 CB A:ASP251 4.1 18.4 1.0 CZ A:PHE221 4.1 24.3 1.0 CE2 A:PHE221 4.2 24.5 1.0 OE1 A:GLU360 4.3 21.7 1.0 CB A:ASP262 4.3 21.3 1.0 C A:ASP262 4.4 21.1 1.0 CG A:GLU374 4.5 21.9 1.0 N A:ILE263 4.5 19.6 1.0 O3 A:PO4403 4.6 23.2 1.0 O A:ASP262 4.6 20.1 1.0 CA A:ASP262 4.6 21.9 1.0 OE2 A:GLU360 4.8 21.6 1.0 C A:ILE263 4.9 18.8 1.0 NE A:ARG372 4.9 20.0 1.0 NH2 A:ARG372 4.9 22.5 1.0 CD A:GLU360 4.9 21.6 1.0 CA A:ASP251 4.9 20.0 1.0 O A:ILE263 5.0 17.7 1.0 CB A:GLU374 5.0 21.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn Bound


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 Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:17.3 occ:1.00 O4 B:PO4403 2.0 16.3 1.0 OE2 B:GLU374 2.0 17.0 1.0 NE2 B:HIS331 2.1 14.7 1.0 OD2 B:ASP262 2.1 17.2 1.0 OE2 B:GLU360 2.3 17.0 1.0 P B:PO4403 2.9 22.2 1.0 CD B:GLU374 3.0 16.5 1.0 CE1 B:HIS331 3.0 14.8 1.0 O3 B:PO4403 3.1 19.7 1.0 CG B:ASP262 3.1 17.8 1.0 CD2 B:HIS331 3.1 15.9 1.0 ZN B:ZN402 3.2 21.6 1.0 CD B:GLU360 3.3 17.3 1.0 OD1 B:ASP262 3.3 16.4 1.0 OE1 B:GLU374 3.4 16.2 1.0 OE1 B:GLU360 3.6 17.1 1.0 O1 B:PO4403 3.7 20.2 1.0 CB B:SER358 4.0 13.8 1.0 OG B:SER358 4.0 13.5 1.0 NE2 B:HIS376 4.1 15.5 1.0 ND1 B:HIS331 4.2 15.4 1.0 O2 B:PO4403 4.2 20.1 1.0 CG B:HIS331 4.2 15.9 1.0 CG B:GLU374 4.3 15.5 1.0 CB B:ASP262 4.4 16.8 1.0 O B:HOH511 4.5 33.3 1.0 CG B:GLU360 4.6 16.1 1.0 CE1 B:HIS376 4.6 16.2 1.0 NE2 B:HIS338 4.6 24.7 1.0 O B:HOH503 4.7 21.1 1.0 O B:ASP262 4.8 15.1 1.0 CD2 B:HIS338 5.0 23.1 1.0 CG2 B:ILE337 5.0 19.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn Bound


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 Xaa-Pro Dipeptidase From Xanthomonas Campestris, Phosphate and Zn Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:21.6 occ:1.00 O4 B:PO4403 2.1 16.3 1.0 OD1 B:ASP262 2.1 16.4 1.0 OE1 B:GLU374 2.1 16.2 1.0 OD1 B:ASP251 2.2 17.3 1.0 OD2 B:ASP251 2.3 18.6 1.0 O B:HOH511 2.5 33.3 1.0 CG B:ASP251 2.6 17.3 1.0 CD B:GLU374 3.0 16.5 1.0 CG B:ASP262 3.1 17.8 1.0 OE2 B:GLU374 3.2 17.0 1.0 ZN B:ZN401 3.2 17.3 1.0 P B:PO4403 3.3 22.2 1.0 OD2 B:ASP262 3.4 17.2 1.0 O2 B:PO4403 3.5 20.1 1.0 OG1 B:THR264 3.6 17.3 1.0 O1 B:PO4403 3.9 20.2 1.0 CB B:ASP251 4.1 17.4 1.0 CZ B:PHE221 4.1 20.3 1.0 CE2 B:PHE221 4.2 22.7 1.0 C B:ASP262 4.3 15.9 1.0 CB B:ASP262 4.4 16.8 1.0 CG B:GLU374 4.4 15.5 1.0 OE1 B:GLU360 4.5 17.1 1.0 N B:ILE263 4.5 16.2 1.0 O3 B:PO4403 4.5 19.7 1.0 O B:ASP262 4.5 15.1 1.0 CA B:ASP262 4.6 16.1 1.0 OE2 B:GLU360 4.8 17.0 1.0 C B:ILE263 4.8 16.7 1.0 NE B:ARG372 4.9 19.5 1.0 CB B:GLU374 4.9 16.0 1.0 O B:ILE263 4.9 15.4 1.0 CA B:ASP251 4.9 17.9 1.0 CD B:GLU360 4.9 17.3 1.0 CB B:THR264 5.0 17.2 1.0 NH2 B:ARG372 5.0 21.4 1.0

V.N.Are, A.Kumar, S.Kumar, V.D.Goyal, B.Ghosh, D.Bhatnagar, S.N.Jamdar, R.D.Makde. Crystal Structure and Biochemical Investigations Reveal Novel Mode of Substrate Selectivity and Illuminate Substrate Inhibition and Allostericity in A Subfamily of Xaa-Pro Dipeptidases Biochim. Biophys. Acta V.1865 153 2017.
ISSN: ISSN 0006-3002
PubMed: 27816563
DOI: 10.1016/J.BBAPAP.2016.10.016