Calcium in PDB 7vev: Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes

The structure of Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes, PDB code: 7vev was solved by K.Anamizu, R.Takase, M.Hio, D.Watanebe, B.Mikami, W.Hashimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.13 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.06, 54.21, 57.012, 75.86, 66.9, 87.95
R / Rfree (%)	16.7 / 18.8

The binding sites of Calcium atom in the Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes (pdb code 7vev). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes, PDB code: 7vev:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes


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 Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:12.9 occ:1.00 OE1 A:GLU10 2.3 25.2 1.0 CD A:GLU10 3.3 24.1 1.0 CG A:GLU10 3.8 21.9 1.0 O A:HOH850 4.1 24.1 1.0 OE2 A:GLU10 4.4 25.6 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes


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 Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:21.4 occ:1.00 O A:HOH832 2.3 23.9 1.0 O A:HOH1056 2.4 18.8 1.0 O A:HOH1089 2.4 38.3 1.0 OE1 A:GLU90 2.4 21.3 1.0 O A:HOH1244 2.5 25.6 1.0 CD A:GLU90 3.4 19.4 1.0 OD2 A:ASP87 3.9 16.4 1.0 CG A:GLU90 4.1 15.1 1.0 OE2 A:GLU90 4.2 20.8 1.0 O A:HOH1023 4.3 25.4 1.0 OE2 A:GLU153 4.4 28.7 1.0 OD1 A:ASP87 4.7 12.2 1.0 CG A:ASP87 4.7 14.0 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:32.8 occ:1.00 O A:HOH1232 2.4 39.3 1.0 O A:HOH1225 2.5 26.2 1.0 OD1 A:ASP349 2.5 14.3 1.0 OD2 A:ASP349 2.6 17.8 1.0 O A:HOH1288 2.6 37.7 1.0 CG A:ASP349 2.9 13.6 1.0 O A:HOH1223 3.2 26.3 1.0 O A:HOH1198 3.8 26.0 1.0 CB A:ASP349 4.4 10.2 1.0 ND1 A:HIS348 4.5 9.2 1.0 OE1 A:GLN352 4.5 11.2 1.0 O A:HOH1200 4.6 30.1 1.0 CE1 A:HIS348 4.8 10.5 1.0 O A:HOH997 4.9 14.2 1.0 O A:HOH1279 4.9 24.3 1.0 O A:HOH1147 5.0 11.4 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:25.2 occ:1.00 O A:GLN72 2.4 14.0 1.0 O A:HOH1235 2.4 31.8 1.0 O A:HOH1217 2.7 26.4 1.0 C A:GLN72 3.5 12.6 1.0 CA A:GLN72 4.2 12.1 1.0 O A:HOH923 4.3 20.6 1.0 OE2 A:GLU163 4.4 15.6 1.0 N A:THR73 4.6 9.6 1.0 CB A:GLN72 4.8 11.4 1.0 CA A:THR73 4.8 8.2 1.0 CG2 A:THR73 4.8 12.5 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:22.6 occ:1.00 NZ A:LYS381 3.7 15.8 1.0 CE A:LYS381 3.7 11.3 1.0 CD A:LYS381 4.0 11.6 1.0 CG A:LYS381 4.6 9.8 1.0 CE2 A:TYR386 4.8 8.3 1.0 CD2 A:TYR386 4.8 7.9 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Bacterial Chemotaxis-Dependent Pectin-Binding Protein SPH1118 in Complex with Mes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:13.3 occ:1.00 O A:HOH1176 2.4 18.3 1.0 O A:LEU159 2.4 8.4 1.0 O A:HOH1210 2.4 17.2 1.0 O A:HOH1136 2.4 13.2 1.0 OE2 A:GLU163 2.4 15.6 1.0 O A:HOH1191 2.5 17.3 1.0 OE1 A:GLU163 2.5 12.2 1.0 CD A:GLU163 2.8 13.8 1.0 C A:LEU159 3.5 8.3 1.0 CA A:SER160 4.0 9.5 1.0 N A:SER160 4.2 9.2 1.0 O A:HOH1241 4.4 31.7 1.0 CG A:GLU163 4.4 11.9 1.0 O A:HOH1076 4.5 13.9 1.0 CA A:LEU159 4.5 7.2 1.0 CB A:LEU159 4.5 9.1 1.0 CD A:PRO162 4.6 8.0 1.0 C A:SER160 4.7 8.6 1.0 NE2 A:GLN546 4.8 23.8 0.5 CG A:PRO162 4.9 7.0 1.0

K.Anamizu, R.Takase, M.Hio, D.Watanabe, B.Mikami, W.Hashimoto. Substrate Size-Dependent Conformational Changes of Bacterial Pectin-Binding Protein Crucial For Chemotaxis and Assimilation. Sci Rep V. 12 12653 2022.
ISSN: ESSN 2045-2322
PubMed: 35879323
DOI: 10.1038/S41598-022-16540-5