Zinc in PDB 4b6z: Crystal Structure of Metallo-Carboxypeptidase From Burkholderia Cenocepacia

The structure of Crystal Structure of Metallo-Carboxypeptidase From Burkholderia Cenocepacia, PDB code: 4b6z was solved by V.Rimsa, T.C.Eadsforth, R.P.Joosten, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.897, 85.947, 289.016, 90.00, 90.00, 90.00
R / Rfree (%)	16.439 / 20.455

The structure of Crystal Structure of Metallo-Carboxypeptidase From Burkholderia Cenocepacia also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Metallo-Carboxypeptidase From Burkholderia Cenocepacia (pdb code 4b6z). 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 Metallo-Carboxypeptidase From Burkholderia Cenocepacia, PDB code: 4b6z:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Metallo-Carboxypeptidase From Burkholderia Cenocepacia


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 Metallo-Carboxypeptidase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn385 b:32.4 occ:1.00 ND1 A:HIS171 2.1 10.1 1.0 ND1 A:HIS268 2.2 12.6 1.0 OE1 A:GLU174 2.2 10.8 1.0 O A:HOH2181 2.3 19.1 1.0 OE2 A:GLU174 2.6 12.6 1.0 CD A:GLU174 2.7 10.9 1.0 CE1 A:HIS171 3.0 10.6 1.0 CG A:HIS268 3.1 12.2 1.0 CG A:HIS171 3.2 9.8 1.0 CE1 A:HIS268 3.2 12.3 1.0 CB A:HIS268 3.3 11.6 1.0 CB A:HIS171 3.6 9.2 1.0 O A:HOH2178 3.6 13.1 1.0 O A:GLY269 3.9 13.4 1.0 O A:HOH2183 4.0 33.4 1.0 CA A:HIS268 4.2 10.4 1.0 NE2 A:HIS171 4.2 10.6 1.0 CG A:GLU174 4.2 10.3 1.0 CD2 A:HIS171 4.3 10.1 1.0 CD2 A:HIS268 4.3 12.3 1.0 N A:GLY269 4.3 11.0 1.0 NE2 A:HIS268 4.3 13.5 1.0 O A:HOH2182 4.4 21.5 1.0 NH1 A:ARG226 4.7 25.5 1.0 C A:HIS268 4.8 10.7 1.0 CA A:HIS171 4.8 8.9 1.0 CB A:GLU174 4.9 9.4 1.0 N A:HIS171 4.9 8.9 1.0 C A:GLY269 4.9 12.2 1.0 C A:ACT1387 5.0 23.3 1.0 OE1 A:GLU344 5.0 22.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Metallo-Carboxypeptidase From Burkholderia Cenocepacia


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 Metallo-Carboxypeptidase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn385 b:40.5 occ:1.00 ND1 B:HIS171 2.1 11.8 1.0 OE1 B:GLU174 2.2 9.0 1.0 ND1 B:HIS268 2.2 13.4 1.0 O B:HOH2161 2.3 19.4 1.0 OE2 B:GLU174 2.7 9.8 1.0 CD B:GLU174 2.8 9.2 1.0 CE1 B:HIS171 3.1 12.4 1.0 CG B:HIS268 3.1 11.1 1.0 CE1 B:HIS268 3.2 11.9 1.0 CG B:HIS171 3.2 10.5 1.0 CB B:HIS268 3.4 10.5 1.0 O B:HOH2158 3.5 8.4 1.0 CB B:HIS171 3.5 8.9 1.0 O B:GLY269 3.9 12.2 1.0 CA B:HIS268 4.2 8.7 1.0 NE2 B:HIS171 4.2 12.4 1.0 CG B:GLU174 4.2 8.5 1.0 O B:HOH2163 4.3 27.2 1.0 NE2 B:HIS268 4.3 12.3 1.0 CD2 B:HIS268 4.3 12.2 1.0 CD2 B:HIS171 4.3 11.1 1.0 N B:GLY269 4.3 8.9 1.0 O B:HOH2162 4.5 21.4 1.0 CH3 B:ACT1390 4.7 23.9 1.0 N B:HIS171 4.8 8.2 1.0 CA B:HIS171 4.8 8.2 1.0 O B:HOH2242 4.8 42.9 1.0 C B:HIS268 4.8 8.9 1.0 CB B:GLU174 4.9 7.8 1.0 C B:GLY269 4.9 10.7 1.0 OE1 B:GLU344 4.9 20.9 1.0 C B:ACT1390 5.0 27.4 1.0 NH1 B:ARG226 5.0 28.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Metallo-Carboxypeptidase From Burkholderia Cenocepacia


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 Metallo-Carboxypeptidase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn385 b:39.3 occ:1.00 ND1 C:HIS171 2.1 12.9 1.0 O C:HOH2185 2.1 19.2 1.0 OE1 C:GLU174 2.1 9.8 1.0 ND1 C:HIS268 2.2 13.8 1.0 OE2 C:GLU174 2.6 9.8 1.0 CD C:GLU174 2.7 9.8 1.0 CE1 C:HIS171 2.9 13.1 1.0 CE1 C:HIS268 3.1 14.2 1.0 CG C:HIS171 3.1 11.7 1.0 CG C:HIS268 3.2 12.6 1.0 CB C:HIS268 3.5 11.6 1.0 CB C:HIS171 3.6 10.4 1.0 O C:HOH2182 3.6 11.7 1.0 O C:HOH2225 3.8 41.2 1.0 O C:GLY269 4.0 11.6 1.0 NE2 C:HIS171 4.1 13.0 1.0 CG C:GLU174 4.2 9.0 1.0 CD2 C:HIS171 4.2 12.7 1.0 NE2 C:HIS268 4.3 14.4 1.0 CA C:HIS268 4.3 10.1 1.0 CD2 C:HIS268 4.3 12.6 1.0 N C:GLY269 4.3 10.4 1.0 O C:HOH2186 4.5 21.6 1.0 NH1 C:ARG226 4.7 26.3 1.0 O C:HOH2227 4.8 32.9 1.0 CA C:HIS171 4.8 9.5 1.0 N C:HIS171 4.8 9.5 1.0 CH3 C:ACT1390 4.8 28.6 1.0 CB C:GLU174 4.9 8.3 1.0 C C:HIS268 4.9 10.4 1.0 OE1 C:GLU344 4.9 25.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Metallo-Carboxypeptidase From Burkholderia Cenocepacia


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 Metallo-Carboxypeptidase From Burkholderia Cenocepacia within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn385 b:40.5 occ:1.00 ND1 D:HIS268 2.1 11.8 1.0 ND1 D:HIS171 2.1 9.8 1.0 OE1 D:GLU174 2.2 9.2 1.0 O D:HOH2154 2.2 17.8 1.0 OE2 D:GLU174 2.6 10.9 1.0 CD D:GLU174 2.7 9.7 1.0 CE1 D:HIS171 3.0 10.4 1.0 CG D:HIS268 3.1 10.6 1.0 CE1 D:HIS268 3.1 12.1 1.0 CG D:HIS171 3.2 9.5 1.0 CB D:HIS268 3.4 9.6 1.0 O D:HOH2150 3.5 10.7 1.0 CB D:HIS171 3.6 8.7 1.0 O D:GLY269 3.9 11.0 1.0 CA D:HIS268 4.2 8.8 1.0 CG D:GLU174 4.2 8.8 1.0 O D:HOH2155 4.2 26.4 1.0 NE2 D:HIS171 4.2 10.6 1.0 NE2 D:HIS268 4.2 11.8 1.0 CD2 D:HIS268 4.2 11.3 1.0 N D:GLY269 4.3 9.1 1.0 CD2 D:HIS171 4.3 9.9 1.0 O D:HOH2156 4.6 17.4 1.0 CH3 D:ACT1391 4.8 24.5 1.0 N D:HIS171 4.8 8.0 1.0 C D:HIS268 4.8 9.0 1.0 CA D:HIS171 4.8 8.2 1.0 CB D:GLU174 4.9 8.0 1.0 C D:GLY269 4.9 10.4 1.0 OE1 D:GLU344 4.9 34.8 1.0 NH1 D:ARG226 4.9 32.9 1.0 C D:ACT1391 5.0 29.1 1.0

V.Rimsa, T.C.Eadsforth, R.P.Joosten, W.N.Hunter. High-Resolution Structure of the M14-Type Cytosolic Carboxypeptidase From Burkholderia Cenocepacia Refined Exploiting PDB_REDO Strategies. Acta Crystallogr.,Sect.D V. 70 279 2014.
ISSN: ISSN 0907-4449
PubMed: 24531462
DOI: 10.1107/S1399004713026801