Calcium in PDB 5tzb: Burkholderia Sp. Beta-Aminopeptidase

The structure of Burkholderia Sp. Beta-Aminopeptidase, PDB code: 5tzb was solved by S.Mcgowan, N.Drinkwater, M.John, G.Dumsday, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.71 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.451, 133.260, 117.068, 90.00, 91.61, 90.00
R / Rfree (%)	19.8 / 23.8

The binding sites of Calcium atom in the Burkholderia Sp. Beta-Aminopeptidase (pdb code 5tzb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Burkholderia Sp. Beta-Aminopeptidase, PDB code: 5tzb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Burkholderia Sp. Beta-Aminopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Burkholderia Sp. Beta-Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:18.9 occ:1.00 ND1 A:HIS253 3.1 14.7 1.0 ND1 C:HIS253 3.1 12.2 1.0 N C:HIS253 3.3 11.9 1.0 N A:HIS253 3.4 9.5 1.0 CB C:HIS253 3.7 11.5 1.0 CD C:PRO252 3.7 12.9 1.0 CB A:HIS253 3.7 12.9 1.0 CD A:PRO252 3.7 12.0 1.0 CB C:LEU251 3.8 13.1 1.0 CG C:HIS253 3.8 12.5 1.0 CG A:HIS253 3.8 14.6 1.0 N C:PRO252 3.9 13.9 1.0 CB A:LEU251 3.9 12.7 1.0 N A:PRO252 3.9 12.4 1.0 CB C:PRO252 4.0 13.8 1.0 CB A:PRO252 4.0 12.4 1.0 CA C:HIS253 4.1 11.8 1.0 CA A:HIS253 4.2 11.3 1.0 CG C:PRO252 4.2 13.1 1.0 CG A:PRO252 4.2 12.4 1.0 CE1 A:HIS253 4.2 14.6 1.0 CE1 C:HIS253 4.2 13.5 1.0 C C:PRO252 4.2 12.1 1.0 CA C:PRO252 4.3 13.5 1.0 C A:PRO252 4.3 11.4 1.0 CA A:PRO252 4.3 11.7 1.0 C C:LEU251 4.4 14.7 1.0 C A:LEU251 4.5 12.4 1.0 CD1 C:LEU251 4.5 14.3 1.0 CD1 A:LEU251 4.6 12.6 1.0 CA C:LEU251 4.7 13.9 1.0 CG C:LEU251 4.7 13.6 1.0 CA A:LEU251 4.8 12.6 1.0 CG A:LEU251 4.8 13.1 1.0

Calcium binding site 2 out of 4 in the Burkholderia Sp. Beta-Aminopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Burkholderia Sp. Beta-Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:18.7 occ:1.00 ND1 D:HIS253 3.0 15.4 1.0 ND1 B:HIS253 3.2 13.9 1.0 N D:HIS253 3.3 12.7 1.0 N B:HIS253 3.4 11.6 1.0 CB D:HIS253 3.7 13.3 1.0 CD B:PRO252 3.7 12.3 1.0 CG D:HIS253 3.7 15.2 1.0 CB B:HIS253 3.8 13.1 1.0 CB D:LEU251 3.8 14.1 1.0 CD D:PRO252 3.8 13.0 1.0 CG B:HIS253 3.9 13.2 1.0 N D:PRO252 3.9 13.4 1.0 N B:PRO252 3.9 12.2 1.0 CB B:LEU251 3.9 16.8 1.0 CB B:PRO252 4.0 11.9 1.0 CE1 D:HIS253 4.0 16.9 1.0 CB D:PRO252 4.1 13.4 1.0 CA D:HIS253 4.1 12.7 1.0 CG B:PRO252 4.2 18.0 1.0 CA B:HIS253 4.2 13.8 1.0 CE1 B:HIS253 4.2 14.3 1.0 C D:PRO252 4.3 13.4 1.0 CA B:PRO252 4.3 14.9 1.0 C B:PRO252 4.3 15.3 1.0 CA D:PRO252 4.3 13.5 1.0 CG D:PRO252 4.3 13.3 1.0 C D:LEU251 4.4 12.5 1.0 C B:LEU251 4.5 17.2 1.0 CD1 B:LEU251 4.5 15.7 1.0 CD1 D:LEU251 4.5 13.7 1.0 CA D:LEU251 4.7 13.5 1.0 CG D:LEU251 4.8 14.0 1.0 O D:HOH613 4.8 35.3 1.0 CA B:LEU251 4.8 17.4 1.0 CG B:LEU251 4.8 17.0 1.0 CD2 D:HIS253 5.0 16.7 1.0

Calcium binding site 3 out of 4 in the Burkholderia Sp. Beta-Aminopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Burkholderia Sp. Beta-Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca401 b:29.9 occ:1.00 ND1 G:HIS253 3.1 21.3 1.0 ND1 H:HIS253 3.1 28.9 1.0 N H:HIS253 3.3 21.6 1.0 N G:HIS253 3.4 22.4 1.0 CD G:PRO252 3.7 21.8 1.0 CB H:HIS253 3.7 21.0 1.0 CD H:PRO252 3.7 22.7 1.0 CB G:HIS253 3.8 20.4 1.0 CB G:LEU251 3.8 22.2 1.0 N G:PRO252 3.8 21.3 1.0 N H:PRO252 3.8 22.6 1.0 CG H:HIS253 3.8 28.8 1.0 CB H:LEU251 3.9 25.7 1.0 CG G:HIS253 3.9 20.8 1.0 CB H:PRO252 3.9 21.8 1.0 CB G:PRO252 4.0 20.9 1.0 CA H:HIS253 4.1 21.2 1.0 CE1 G:HIS253 4.2 23.0 1.0 CG H:PRO252 4.2 22.2 1.0 CE1 H:HIS253 4.2 22.3 1.0 C H:PRO252 4.2 28.1 1.0 CA G:HIS253 4.2 21.5 1.0 CA H:PRO252 4.2 22.1 1.0 CG G:PRO252 4.2 23.5 1.0 CA G:PRO252 4.3 20.7 1.0 C G:PRO252 4.3 20.3 1.0 C G:LEU251 4.4 21.4 1.0 C H:LEU251 4.4 23.0 1.0 CD1 H:LEU251 4.4 24.6 1.0 CD1 G:LEU251 4.6 25.6 1.0 CA G:LEU251 4.7 22.0 1.0 CA H:LEU251 4.8 26.1 1.0 CG G:LEU251 4.8 25.4 1.0 CG H:LEU251 4.8 25.7 1.0

Calcium binding site 4 out of 4 in the Burkholderia Sp. Beta-Aminopeptidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Burkholderia Sp. Beta-Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca401 b:22.7 occ:1.00 ND1 F:HIS253 3.1 21.2 1.0 ND1 E:HIS253 3.1 17.1 1.0 N F:HIS253 3.3 14.8 1.0 N E:HIS253 3.4 17.6 1.0 CB F:HIS253 3.7 18.0 1.0 CB E:HIS253 3.7 13.5 1.0 CD E:PRO252 3.8 13.8 1.0 CD F:PRO252 3.8 16.0 1.0 CG F:HIS253 3.8 20.4 1.0 CG E:HIS253 3.8 16.2 1.0 CB E:LEU251 3.9 14.6 1.0 CB F:LEU251 3.9 17.3 1.0 N F:PRO252 3.9 17.1 1.0 N E:PRO252 3.9 15.1 1.0 CB F:PRO252 4.0 15.1 1.0 CB E:PRO252 4.0 16.1 1.0 CA F:HIS253 4.1 17.0 1.0 CA E:HIS253 4.1 17.5 1.0 CE1 F:HIS253 4.2 21.6 1.0 CE1 E:HIS253 4.2 17.9 1.0 C F:PRO252 4.2 15.0 1.0 CG F:PRO252 4.3 15.5 1.0 CG E:PRO252 4.3 14.2 1.0 CA F:PRO252 4.3 15.7 1.0 C E:PRO252 4.3 17.0 1.0 CA E:PRO252 4.3 16.2 1.0 C F:LEU251 4.4 16.7 1.0 C E:LEU251 4.5 13.3 1.0 CD1 F:LEU251 4.5 16.2 1.0 CD1 E:LEU251 4.6 14.1 1.0 CA F:LEU251 4.7 16.7 1.0 CA E:LEU251 4.7 14.4 1.0 CG F:LEU251 4.8 17.2 1.0 CG E:LEU251 4.8 13.9 1.0

M.John-White, G.J.Dumsday, P.Johanesen, D.Lyras, N.Drinkwater, S.Mcgowan. Crystal Structure of A Beta-Aminopeptidase From An Australian Burkholderia Sp. Acta Crystallogr F Struct V. 73 386 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 28695846
DOI: 10.1107/S2053230X17007737