Calcium in PDB 5d3k: Crystal Structure of the Thioesterase Domain of Deoxyerythronolide B Synthase

All present enzymatic activity of Crystal Structure of the Thioesterase Domain of Deoxyerythronolide B Synthase:
2.3.1.94;

The structure of Crystal Structure of the Thioesterase Domain of Deoxyerythronolide B Synthase, PDB code: 5d3k was solved by F.Bergeret, P.Argyropoulos, C.N.Boddy, T.M.Schmeing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.96 / 1.70
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.920, 112.920, 42.970, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 18.7

The binding sites of Calcium atom in the Crystal Structure of the Thioesterase Domain of Deoxyerythronolide B Synthase (pdb code 5d3k). 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 the Thioesterase Domain of Deoxyerythronolide B Synthase, PDB code: 5d3k:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Thioesterase Domain of Deoxyerythronolide B Synthase


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 Thioesterase Domain of Deoxyerythronolide B Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:24.0 occ:1.00 OD2 A:ASP49 2.3 27.3 1.0 O A:HOH568 2.3 25.4 1.0 O A:HOH411 2.4 22.2 1.0 CG A:ASP49 3.0 23.3 1.0 OD1 A:ASP49 3.2 26.2 1.0 OD2 A:ASP52 3.9 27.8 1.0 OG A:SER51 4.1 34.0 1.0 CB A:ASP52 4.2 36.0 1.0 CB A:ASP49 4.4 18.1 1.0 CG A:ASP52 4.5 36.4 1.0 O A:SER51 4.9 41.1 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Thioesterase Domain of Deoxyerythronolide B Synthase


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 Thioesterase Domain of Deoxyerythronolide B Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:26.6 occ:1.00 OE2 A:GLU108 2.1 33.7 1.0 OD2 A:ASP199 2.3 18.6 1.0 O A:HOH500 2.4 33.7 1.0 CD A:GLU108 3.2 31.7 1.0 CG A:ASP199 3.4 13.2 1.0 CG A:GLU108 3.7 27.1 1.0 OG1 A:THR201 3.9 12.8 1.0 CB A:ASP199 4.0 10.8 1.0 OD1 A:ASP199 4.2 12.9 1.0 OE1 A:GLU108 4.2 34.7 1.0 O A:HOH464 4.3 12.4 1.0 CB A:THR201 4.4 10.1 1.0 O A:HOH473 4.7 20.6 1.0 O A:HOH604 4.8 27.3 1.0 N A:THR201 5.0 9.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Thioesterase Domain of Deoxyerythronolide B Synthase


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 the Thioesterase Domain of Deoxyerythronolide B Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:11.9 occ:1.00 O A:HOH459 2.3 18.6 1.0 O A:HOH469 2.3 13.1 1.0 OD1 A:ASP275 2.4 14.1 1.0 O A:HOH446 2.4 16.3 1.0 CG A:ASP275 3.4 13.6 1.0 OD2 A:ASP275 3.7 16.4 1.0 O A:HOH608 4.0 50.8 1.0 O A:ASP275 4.6 11.1 1.0 CA A:GLY280 4.7 22.7 1.0 CG2 A:ILE95 4.7 14.3 1.0 O A:HOH433 4.7 17.4 1.0 CB A:ASP275 4.7 11.7 1.0 O A:ILE95 4.9 12.7 1.0 O A:HOH447 4.9 12.7 1.0 N A:GLY280 5.0 20.9 1.0

P.Argyropoulos, F.Bergeret, C.Pardin, J.M.Reimer, A.Pinto, C.N.Boddy, T.M.Schmeing. Towards A Characterization of the Structural Determinants of Specificity in the Macrocyclizing Thioesterase For Deoxyerythronolide B Biosynthesis. Biochim.Biophys.Acta V.1860 486 2015.
ISSN: ISSN 0006-3002
PubMed: 26592346
DOI: 10.1016/J.BBAGEN.2015.11.007