Calcium in PDB 1v7w: Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac

The structure of Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac, PDB code: 1v7w was solved by M.Hidaka, Y.Honda, S.Nirasawa, M.Kitaoka, K.Hayashi, T.Wakagi, H.Shoun, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.87 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.064, 70.729, 80.410, 90.00, 98.41, 90.00
R / Rfree (%)	15.7 / 17.9

The structure of Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac (pdb code 1v7w). 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 Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac, PDB code: 1v7w:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac


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 Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:22.6 occ:1.00 OD1 A:ASP186 2.4 13.6 1.0 O A:LEU187 2.6 9.5 1.0 O A:ASN190 2.7 15.5 1.0 O A:GLY196 2.8 11.1 1.0 O A:HOH1441 3.0 29.8 1.0 CE1 A:PHE197 3.1 22.9 1.0 C A:LEU187 3.4 8.2 1.0 O A:HOH1558 3.4 40.4 1.0 CD1 A:PHE197 3.5 19.4 1.0 C A:GLY196 3.6 10.2 1.0 CG A:ASP186 3.6 12.3 1.0 CZ A:PHE197 3.7 20.7 1.0 N A:LEU187 3.7 5.9 1.0 C A:ASN190 3.8 13.3 1.0 CA A:GLY196 3.8 8.8 1.0 CA A:LEU187 4.1 6.6 1.0 N A:TYR188 4.2 8.2 1.0 OD2 A:ASP186 4.3 14.5 1.0 CA A:TYR188 4.4 9.2 1.0 C A:ASP186 4.4 7.9 1.0 CG A:PHE197 4.4 16.2 1.0 CB A:ASN190 4.4 10.3 1.0 N A:ASN190 4.5 9.7 1.0 CB A:LEU187 4.5 7.6 1.0 CA A:ASN190 4.5 11.4 1.0 CE2 A:PHE197 4.5 20.2 1.0 O A:HOH1255 4.5 18.5 1.0 O A:ASP192 4.6 14.2 1.0 CA A:ASP186 4.6 7.8 1.0 O A:HOH1717 4.6 29.0 1.0 C A:TYR188 4.6 8.8 1.0 CB A:ASP186 4.7 10.6 1.0 O A:HOH1628 4.7 37.4 1.0 N A:PHE197 4.7 9.8 1.0 O A:TYR188 4.7 10.6 1.0 CD2 A:PHE197 4.8 17.2 1.0 N A:THR191 4.9 16.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac


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 Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:22.4 occ:1.00 O A:HOH1011 2.2 9.4 1.0 O A:HOH1007 2.3 31.9 1.0 O A:HOH1210 2.4 17.5 1.0 O A:HOH1258 2.4 23.3 1.0 OD2 A:ASP793 2.5 17.5 1.0 O A:GLY791 2.5 19.2 1.0 CG A:ASP793 3.2 16.9 1.0 C A:GLY791 3.4 19.0 1.0 O A:HOH1797 3.4 33.4 1.0 OD1 A:ASP793 3.4 22.5 1.0 CA A:GLY791 4.0 17.2 1.0 O A:SER792 4.1 15.2 1.0 C A:SER792 4.2 15.0 1.0 OG1 A:THR756 4.3 17.6 1.0 N A:SER792 4.4 15.2 1.0 O A:HOH1314 4.5 27.3 1.0 CB A:ASP793 4.5 13.0 1.0 N A:ASP793 4.5 11.4 1.0 CA A:SER792 4.6 13.5 1.0 CA A:ASP793 4.8 12.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac


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 Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:23.4 occ:1.00 O A:THR140 2.2 15.3 1.0 O A:HOH1372 2.3 24.6 1.0 O A:HOH1321 2.3 24.8 1.0 O A:HOH1350 2.5 24.6 1.0 O A:HOH1222 2.7 22.8 1.0 C A:THR140 3.2 14.5 1.0 CA A:THR140 3.9 13.7 1.0 O A:SER141 4.2 16.1 1.0 N A:SER141 4.2 14.8 1.0 CB A:THR140 4.3 13.4 1.0 C A:SER141 4.4 16.6 1.0 O A:HOH1862 4.5 38.9 1.0 CA A:SER141 4.5 15.2 1.0 O A:HOH1819 4.6 39.3 1.0 O A:HOH1607 4.7 28.6 1.0 O A:HOH1416 4.8 33.1 1.0

M.Hidaka, Y.Honda, M.Kitaoka, S.Nirasawa, K.Hayashi, T.Wakagi, H.Shoun, S.Fushinobu. Chitobiose Phosphorylase From Vibrio Proteolyticus, A Member of Glycosyl Transferase Family 36, Has A Clan Gh-L-Like (Alpha/Alpha)(6) Barrel Fold. Structure V. 12 937 2004.
ISSN: ISSN 0969-2126
PubMed: 15274915
DOI: 10.1016/J.STR.2004.03.027