Zinc in PDB 5cde: R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris

The structure of R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris, PDB code: 5cde was solved by A.Kumar, V.Are, B.Ghosh, S.Jamdar, R.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.92 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.088, 101.947, 111.509, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.4

The binding sites of Zinc atom in the R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris (pdb code 5cde). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris, PDB code: 5cde:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:28.0 occ:0.81 OD1 A:ASP262 1.9 21.5 1.0 O A:HOH664 1.9 22.0 1.0 OE1 A:GLU374 2.1 26.0 1.0 OD1 A:ASP251 2.1 26.1 1.0 OD2 A:ASP251 2.5 25.9 1.0 CG A:ASP251 2.6 26.1 1.0 CG A:ASP262 2.8 22.1 1.0 CD A:GLU374 3.0 25.6 1.0 ZN A:ZN403 3.1 26.1 0.8 OD2 A:ASP262 3.1 24.2 1.0 OE2 A:GLU374 3.2 22.1 1.0 OG1 A:THR264 3.5 24.2 1.0 O A:HOH655 3.9 33.1 1.0 CZ A:PHE221 3.9 26.0 1.0 OE1 A:GLU360 3.9 27.2 1.0 CB A:ASP251 4.2 25.7 1.0 O A:HOH571 4.2 30.1 1.0 CB A:ASP262 4.2 18.9 1.0 CE2 A:PHE221 4.2 26.2 1.0 C A:ASP262 4.3 23.8 1.0 CG A:GLU374 4.4 23.8 1.0 N A:ILE263 4.4 25.0 1.0 CA A:ASP262 4.5 21.6 1.0 O A:ASP262 4.5 24.9 1.0 OE2 A:GLU360 4.6 24.6 1.0 CD A:GLU360 4.6 26.3 1.0 C A:ILE263 4.7 24.8 1.0 O A:ILE263 4.7 28.1 1.0 CB A:GLU374 4.8 26.1 1.0 CA A:ASP251 4.9 24.4 1.0 CB A:THR264 4.9 24.9 1.0 N A:THR264 5.0 24.5 1.0 NE2 A:HIS331 5.0 23.9 1.0 CE1 A:PHE221 5.0 26.3 1.0

Zinc binding site 2 out of 7 in the R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:26.1 occ:0.80 O A:HOH664 2.0 22.0 1.0 NE2 A:HIS331 2.1 23.9 1.0 OE2 A:GLU374 2.1 22.1 1.0 OD2 A:ASP262 2.1 24.2 1.0 OE2 A:GLU360 2.2 24.6 1.0 CD A:GLU374 3.0 25.6 1.0 CD2 A:HIS331 3.0 20.2 1.0 CD A:GLU360 3.0 26.3 1.0 CE1 A:HIS331 3.1 25.0 1.0 ZN A:ZN402 3.1 28.0 0.8 CG A:ASP262 3.1 22.1 1.0 OE1 A:GLU360 3.2 27.2 1.0 OE1 A:GLU374 3.3 26.0 1.0 OD1 A:ASP262 3.5 21.5 1.0 O1 A:SO4401 3.6 40.8 1.0 O A:HOH655 3.7 33.1 1.0 CB A:SER358 3.9 21.5 1.0 OG A:SER358 3.9 22.8 1.0 NE2 A:HIS376 4.0 21.1 1.0 CG A:HIS331 4.1 23.0 1.0 ND1 A:HIS331 4.1 23.4 1.0 CG A:GLU374 4.2 23.8 1.0 CB A:ASP262 4.4 18.9 1.0 CG A:GLU360 4.4 25.2 1.0 CE1 A:HIS376 4.6 22.4 1.0 NE2 A:HIS338 4.7 27.5 1.0 S A:SO4401 4.8 39.4 1.0 O A:ASP262 5.0 24.9 1.0 CD2 A:HIS338 5.0 26.7 1.0

Zinc binding site 3 out of 7 in the R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:33.5 occ:0.43 ND1 A:HIS234 2.1 39.1 1.0 OE2 B:GLU92 2.1 30.8 1.0 CD B:GLU92 2.9 28.1 1.0 CG A:HIS234 3.0 39.5 1.0 CE1 A:HIS234 3.1 38.2 1.0 OE1 B:GLU92 3.1 27.5 1.0 CB A:HIS234 3.3 39.1 1.0 O B:HOH553 3.9 31.6 1.0 CD2 A:HIS234 4.1 39.5 1.0 NE2 A:HIS234 4.1 38.8 1.0 CG B:GLU92 4.3 25.7 1.0 CA A:HIS234 4.8 37.9 1.0 CE3 B:TRP67 4.9 27.4 1.0 O B:HOH678 4.9 43.1 1.0 CZ3 B:TRP67 5.0 27.4 1.0 CD2 B:TRP67 5.0 28.1 1.0

Zinc binding site 4 out of 7 in the R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:29.1 occ:0.89 OE2 B:GLU374 2.0 22.4 1.0 NE2 B:HIS331 2.1 20.3 1.0 OD2 B:ASP262 2.1 24.1 1.0 O B:HOH644 2.2 23.0 1.0 OE2 B:GLU360 2.2 25.3 1.0 CD B:GLU374 3.0 22.1 1.0 CD2 B:HIS331 3.0 19.4 1.0 CD B:GLU360 3.1 25.3 1.0 CG B:ASP262 3.1 19.6 1.0 CE1 B:HIS331 3.1 19.9 1.0 ZN B:ZN404 3.1 29.0 0.9 OE1 B:GLU360 3.3 26.0 1.0 OE1 B:GLU374 3.4 22.9 1.0 OD1 B:ASP262 3.4 18.1 1.0 O B:HOH627 3.8 37.7 1.0 CB B:SER358 3.9 22.9 1.0 OG B:SER358 3.9 20.1 1.0 O4 B:SO4401 3.9 52.0 1.0 NE2 B:HIS376 4.0 19.6 1.0 ND1 B:HIS331 4.2 18.7 1.0 CG B:HIS331 4.2 19.8 1.0 CG B:GLU374 4.3 20.8 1.0 CB B:ASP262 4.4 19.4 1.0 CG B:GLU360 4.4 24.8 1.0 CE1 B:HIS376 4.6 18.9 1.0 NE2 B:HIS338 4.8 29.8 1.0 O B:ASP262 4.9 26.7 1.0

Zinc binding site 5 out of 7 in the R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:29.0 occ:0.89 O B:HOH644 1.9 23.0 1.0 OD1 B:ASP262 2.0 18.1 1.0 OE1 B:GLU374 2.0 22.9 1.0 OD1 B:ASP251 2.2 25.0 1.0 OD2 B:ASP251 2.5 31.2 1.0 CG B:ASP251 2.7 26.6 1.0 CD B:GLU374 2.9 22.1 1.0 CG B:ASP262 2.9 19.6 1.0 OE2 B:GLU374 3.1 22.4 1.0 ZN B:ZN403 3.1 29.1 0.9 OD2 B:ASP262 3.2 24.1 1.0 OG1 B:THR264 3.5 23.5 1.0 OE1 B:GLU360 3.9 26.0 1.0 O B:HOH627 3.9 37.7 1.0 CZ B:PHE221 3.9 31.6 1.0 CB B:ASP251 4.2 26.3 1.0 CE1 B:PHE221 4.2 31.3 1.0 CB B:ASP262 4.3 19.4 1.0 CG B:GLU374 4.3 20.8 1.0 C B:ASP262 4.3 23.9 1.0 O B:HOH617 4.3 27.8 1.0 N B:ILE263 4.5 27.3 1.0 OE2 B:GLU360 4.5 25.3 1.0 O B:ASP262 4.5 26.7 1.0 CD B:GLU360 4.5 25.3 1.0 CA B:ASP262 4.5 21.1 1.0 C B:ILE263 4.8 28.4 1.0 CB B:GLU374 4.8 21.1 1.0 O B:ILE263 4.8 24.6 1.0 CA B:ASP251 4.9 25.4 1.0 CB B:THR264 4.9 25.9 1.0

Zinc binding site 6 out of 7 in the R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn405 b:39.1 occ:0.40 ND1 B:HIS234 2.2 53.2 1.0 OE2 A:GLU92 2.4 35.0 1.0 CG B:HIS234 2.8 52.3 1.0 CE1 B:HIS234 3.1 53.7 1.0 CB B:HIS234 3.2 50.2 1.0 CD A:GLU92 3.2 34.3 1.0 OE1 A:GLU92 3.4 36.9 1.0 CD2 B:HIS234 3.8 52.2 1.0 NE2 B:HIS234 3.9 52.8 1.0 O A:HOH595 4.1 38.2 1.0 CG A:GLU92 4.7 34.2 1.0 CA B:HIS234 4.7 48.0 1.0

Zinc binding site 7 out of 7 in the R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn406 b:38.4 occ:0.29 ND1 A:HIS338 1.8 29.3 1.0 OE1 B:GLU71 2.0 24.6 1.0 CE1 A:HIS338 2.5 28.6 1.0 CD B:GLU71 2.8 27.0 1.0 CG A:HIS338 2.9 26.3 1.0 OE2 B:GLU71 3.0 27.2 1.0 O B:HOH704 3.0 35.2 1.0 O B:HOH678 3.0 43.1 1.0 CB B:SER70 3.4 28.4 1.0 CB A:HIS338 3.5 24.7 1.0 NE2 A:HIS338 3.7 27.5 1.0 CD2 A:HIS338 3.9 26.7 1.0 OG B:SER70 4.0 26.8 1.0 N B:GLU71 4.1 24.5 1.0 CG B:GLU71 4.3 23.1 1.0 CA B:SER70 4.3 26.3 1.0 NH2 A:ARG328 4.4 21.5 1.0 NH1 B:ARG72 4.6 21.7 1.0 O3 A:SO4401 4.7 40.0 1.0 CB B:GLU71 4.7 24.1 1.0 C B:SER70 4.7 24.8 1.0 CA A:HIS338 5.0 21.4 1.0 CA B:GLU71 5.0 23.2 1.0

A.Kumar, V.Are, B.Ghosh, S.Jamdar, R.Makde. R372A Mutant of Xaa-Pro Dipeptidase From Xanthomonas Campestris at 1.85 Angstrom Resolution To Be Published.