Calcium in PDB 1w5d: Crystal Structure of PBP4A From Bacillus Subtilis

All present enzymatic activity of Crystal Structure of PBP4A From Bacillus Subtilis:
3.4.16.4;

The structure of Crystal Structure of PBP4A From Bacillus Subtilis, PDB code: 1w5d was solved by E.Sauvage, R.Herman, S.Petrella, C.Duez, J.M.Frere, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.87 / 2.1
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	67.411, 67.411, 228.464, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 26.8

The binding sites of Calcium atom in the Crystal Structure of PBP4A From Bacillus Subtilis (pdb code 1w5d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of PBP4A From Bacillus Subtilis, PDB code: 1w5d:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of PBP4A From Bacillus Subtilis


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 PBP4A From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1463 b:35.8 occ:0.50 NE2 A:HIS218 2.1 26.6 1.0 OE1 A:GLU146 2.1 30.5 1.0 CD A:GLU146 2.9 24.5 1.0 CE1 A:HIS218 3.0 23.2 1.0 OE2 A:GLU146 3.1 21.6 1.0 CD2 A:HIS218 3.1 21.9 1.0 CB A:TRP143 4.2 30.9 1.0 ND1 A:HIS218 4.2 21.9 1.0 CG A:HIS218 4.2 26.1 1.0 CG A:GLU146 4.4 28.6 1.0 CA A:TRP143 4.7 30.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of PBP4A From Bacillus Subtilis


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 PBP4A From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1464 b:75.5 occ:1.00 OD1 A:ASP164 3.2 28.6 1.0 OD1 A:ASP166 3.3 30.2 1.0 CE2 A:TRP239 4.1 38.0 1.0 CG A:ASP166 4.1 27.3 1.0 CG A:ASP164 4.2 27.9 1.0 CD2 A:TRP239 4.2 36.1 1.0 OD2 A:ASP166 4.3 26.1 1.0 O A:HOH2089 4.3 44.9 1.0 CB A:ASP164 4.4 27.3 1.0 O A:HOH2148 4.4 34.2 1.0 NE1 A:TRP239 4.4 36.0 1.0 CZ2 A:TRP239 4.4 38.0 1.0 O A:HOH2143 4.5 43.1 1.0 CG A:TRP239 4.5 35.8 1.0 CE3 A:TRP239 4.6 36.3 1.0 CD1 A:TRP239 4.6 36.2 1.0 CH2 A:TRP239 4.8 38.8 1.0 O A:HOH2127 4.8 52.6 1.0 CZ3 A:TRP239 4.9 39.4 1.0 CE1 A:TYR149 5.0 31.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of PBP4A From Bacillus Subtilis


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 PBP4A From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1465 b:18.3 occ:1.00 ND1 A:HIS283 2.1 29.8 1.0 CE1 A:HIS283 3.0 29.2 1.0 CG A:HIS283 3.1 30.4 1.0 CB A:HIS283 3.5 29.8 1.0 CA A:HIS283 4.1 29.1 1.0 NE2 A:HIS283 4.1 29.9 1.0 O A:HOH2251 4.1 38.9 1.0 CD2 A:HIS283 4.2 29.8 1.0 CE A:LYS108 4.5 50.9 1.0 CD A:LYS108 4.9 48.3 1.0 CG A:LYS108 4.9 44.5 1.0 N A:ARG284 5.0 28.8 1.0

E.Sauvage, C.Duez, R.Herman, F.Kerff, S.Petrella, J.W.Anderson, S.A.Adediran, R.F.Pratt, J.M.Frere, P.Charlier. Crystal Structure of the Bacillus Subtilis Penicillin-Binding Protein 4A, and Its Complex with A Peptidoglycan Mimetic Peptide. J.Mol.Biol. V. 371 528 2007.
ISSN: ISSN 0022-2836
PubMed: 17582436
DOI: 10.1016/J.JMB.2007.05.071