Calcium in PDB 3by9: Crystal Structure of the V. Cholerae Histidine Kinase Dctb Sensor Domain

All present enzymatic activity of Crystal Structure of the V. Cholerae Histidine Kinase Dctb Sensor Domain:
2.7.13.3;

The structure of Crystal Structure of the V. Cholerae Histidine Kinase Dctb Sensor Domain, PDB code: 3by9 was solved by J.Cheung, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.78 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.311, 90.982, 114.196, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.9

The binding sites of Calcium atom in the Crystal Structure of the V. Cholerae Histidine Kinase Dctb Sensor Domain (pdb code 3by9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the V. Cholerae Histidine Kinase Dctb Sensor Domain, PDB code: 3by9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the V. Cholerae Histidine Kinase Dctb Sensor Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the V. Cholerae Histidine Kinase Dctb Sensor Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:7.6 occ:1.00 OD1 A:ASP66 2.3 8.6 1.0 O A:LEU62 2.4 8.6 1.0 O A:HOH427 2.5 7.6 1.0 O A:HOH428 2.5 8.0 1.0 CG A:ASP66 3.5 7.6 1.0 C A:LEU62 3.6 6.6 1.0 O A:HOH293 4.0 11.3 1.0 N A:ASP66 4.2 7.2 1.0 CA A:ILE63 4.2 6.7 1.0 OD2 A:ASP66 4.2 11.0 1.0 N A:ILE63 4.3 7.9 1.0 C A:ILE63 4.4 8.3 1.0 N A:LYS65 4.5 6.6 1.0 CA A:ASP66 4.6 5.5 1.0 CA A:LEU62 4.6 8.1 1.0 O A:HIS61 4.6 8.3 1.0 C A:LYS65 4.6 8.6 1.0 CB A:ASP66 4.7 6.7 1.0 O A:ILE63 4.7 8.8 1.0 N A:SER64 4.8 7.4 1.0 CB A:LYS65 4.8 8.1 1.0 CD1 A:LEU62 4.8 17.2 1.0 CA A:LYS65 4.9 5.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the V. Cholerae Histidine Kinase Dctb Sensor Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the V. Cholerae Histidine Kinase Dctb Sensor Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:21.8 occ:1.00 O A:HOH425 2.4 25.4 1.0 O A:HOH435 2.4 24.7 1.0 O A:LYS284 2.4 20.7 1.0 OD1 A:ASP263 2.5 21.1 1.0 O A:HOH436 2.5 29.9 1.0 O A:HOH337 2.7 22.7 1.0 CG A:ASP263 3.5 25.7 1.0 C A:LYS284 3.7 23.1 1.0 O A:HOH617 3.9 57.9 1.0 OD2 A:ASP263 3.9 29.2 1.0 O A:GLN261 4.1 28.4 1.0 O A:ASP263 4.4 14.2 1.0 CB A:LYS284 4.4 19.0 1.0 CA A:LYS284 4.5 16.0 1.0 CB A:ILE285 4.5 44.9 1.0 N A:ASP263 4.5 19.8 1.0 O A:ILE285 4.5 57.0 1.0 N A:LYS284 4.6 15.9 1.0 N A:ILE285 4.7 29.6 1.0 CB A:ASP263 4.8 17.1 1.0 CA A:ILE285 4.9 42.9 1.0 O A:HOH437 4.9 29.9 1.0 C A:ILE285 5.0 49.2 1.0

J.Cheung, W.A.Hendrickson. Crystal Structures of C4-Dicarboxylate Ligand Complexes with Sensor Domains of Histidine Kinases Dcus and Dctb. J.Biol.Chem. V. 283 30256 2008.
ISSN: ISSN 0021-9258
PubMed: 18701447
DOI: 10.1074/JBC.M805253200