Calcium in PDB 5gub: Crystal Structure of Solute-Binding Protein Complexed with Sulfate Group-Free Unsaturated Chondroitin Disaccharide

The structure of Crystal Structure of Solute-Binding Protein Complexed with Sulfate Group-Free Unsaturated Chondroitin Disaccharide, PDB code: 5gub was solved by S.Oiki, B.Mikami, K.Murata, W.Hashimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.57 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.914, 112.213, 166.276, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.8

The binding sites of Calcium atom in the Crystal Structure of Solute-Binding Protein Complexed with Sulfate Group-Free Unsaturated Chondroitin Disaccharide (pdb code 5gub). 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 Solute-Binding Protein Complexed with Sulfate Group-Free Unsaturated Chondroitin Disaccharide, PDB code: 5gub:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Solute-Binding Protein Complexed with Sulfate Group-Free Unsaturated Chondroitin Disaccharide


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 Solute-Binding Protein Complexed with Sulfate Group-Free Unsaturated Chondroitin Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:14.2 occ:1.00 OD1 A:ASN191 2.3 13.2 1.0 OD1 A:ASP189 2.3 13.1 1.0 O A:LYS195 2.3 15.2 1.0 OD1 A:ASP197 2.4 14.9 1.0 OE2 A:GLU198 2.4 10.9 1.0 OD1 A:ASN193 2.5 12.7 1.0 OE1 A:GLU198 2.7 11.4 1.0 CD A:GLU198 2.8 9.3 1.0 CG A:ASN191 3.2 14.2 1.0 CG A:ASN193 3.5 20.2 1.0 CG A:ASP197 3.5 17.1 1.0 CG A:ASP189 3.5 18.2 1.0 C A:LYS195 3.5 14.3 1.0 ND2 A:ASN191 3.5 15.2 1.0 ND2 A:ASN193 3.9 18.6 1.0 N A:LYS195 4.0 18.1 1.0 OD2 A:ASP197 4.0 16.2 1.0 N A:ASP197 4.0 13.8 1.0 CA A:ASP189 4.1 13.2 1.0 CA A:LYS195 4.2 17.8 1.0 CB A:ASP189 4.2 13.1 1.0 N A:ASN193 4.3 18.5 1.0 CG A:GLU198 4.3 9.1 1.0 OD2 A:ASP189 4.4 14.7 1.0 CB A:LYS195 4.5 19.8 1.0 N A:ASN191 4.5 13.0 1.0 CB A:ASN191 4.5 14.0 1.0 O A:HOH818 4.5 13.4 1.0 C A:ASP189 4.5 14.2 1.0 N A:LYS196 4.6 15.6 1.0 N A:GLY192 4.6 18.8 1.0 N A:GLU198 4.6 10.1 1.0 CB A:ASP197 4.6 14.1 1.0 N A:GLY194 4.7 20.7 1.0 CB A:ASN193 4.7 20.5 1.0 CA A:ASP197 4.8 13.9 1.0 CA A:ASN191 4.8 12.8 1.0 C A:ASN191 4.8 15.7 1.0 CA A:LYS196 4.8 14.9 1.0 CA A:ASN193 4.8 19.7 1.0 O A:ASP189 4.9 15.5 1.0 C A:ASN193 4.9 20.5 1.0 C A:LYS196 5.0 11.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Solute-Binding Protein Complexed with Sulfate Group-Free Unsaturated Chondroitin Disaccharide


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 Solute-Binding Protein Complexed with Sulfate Group-Free Unsaturated Chondroitin Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:14.3 occ:1.00 OD1 B:ASP189 2.3 16.9 1.0 OD1 B:ASP197 2.4 15.2 1.0 OD1 B:ASN191 2.4 15.7 1.0 O B:LYS195 2.4 15.7 1.0 OD1 B:ASN193 2.5 15.4 1.0 OE2 B:GLU198 2.5 12.5 1.0 OE1 B:GLU198 2.6 10.8 1.0 CD B:GLU198 2.9 11.0 1.0 CG B:ASN191 3.3 16.0 1.0 CG B:ASN193 3.5 21.3 1.0 CG B:ASP197 3.5 13.5 1.0 CG B:ASP189 3.5 21.9 1.0 C B:LYS195 3.5 14.2 1.0 ND2 B:ASN191 3.6 14.8 1.0 ND2 B:ASN193 4.0 15.9 1.0 N B:LYS195 4.0 18.0 1.0 OD2 B:ASP197 4.0 14.6 1.0 N B:ASP197 4.0 12.7 1.0 CA B:ASP189 4.1 17.4 1.0 N B:ASN193 4.2 22.3 1.0 CB B:ASP189 4.3 19.0 1.0 CA B:LYS195 4.3 15.7 1.0 CG B:GLU198 4.3 8.3 1.0 OD2 B:ASP189 4.4 19.7 1.0 O B:HOH807 4.4 12.3 1.0 N B:GLY192 4.6 19.9 1.0 C B:ASP189 4.6 17.1 1.0 N B:LYS196 4.6 15.6 1.0 CB B:ASN191 4.6 17.1 1.0 N B:ASN191 4.6 12.6 1.0 CB B:ASP197 4.6 14.8 1.0 CB B:LYS195 4.6 19.3 1.0 N B:GLU198 4.6 10.2 1.0 N B:GLY194 4.7 19.7 1.0 CB B:ASN193 4.7 22.8 1.0 CA B:LYS196 4.8 14.2 1.0 CA B:ASP197 4.8 13.4 1.0 CA B:ASN193 4.8 22.2 1.0 C B:ASN191 4.8 17.1 1.0 CA B:ASN191 4.9 16.1 1.0 C B:ASN193 4.9 21.3 1.0 O B:ASP189 4.9 16.3 1.0 C B:LYS196 4.9 11.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Solute-Binding Protein Complexed with Sulfate Group-Free Unsaturated Chondroitin Disaccharide


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 Solute-Binding Protein Complexed with Sulfate Group-Free Unsaturated Chondroitin Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:19.6 occ:1.00 OD1 C:ASP189 2.2 20.0 1.0 O C:LYS195 2.3 20.4 1.0 OD1 C:ASN191 2.3 17.4 1.0 OD1 C:ASP197 2.4 19.6 1.0 OD1 C:ASN193 2.5 23.1 1.0 OE2 C:GLU198 2.6 18.8 1.0 OE1 C:GLU198 2.6 14.3 1.0 CD C:GLU198 2.9 14.3 1.0 CG C:ASN191 3.2 18.9 1.0 CG C:ASP197 3.4 18.8 1.0 CG C:ASP189 3.5 25.3 1.0 C C:LYS195 3.5 20.9 1.0 CG C:ASN193 3.5 23.8 1.0 ND2 C:ASN191 3.6 19.2 1.0 N C:LYS195 3.9 23.9 1.0 ND2 C:ASN193 4.0 20.6 1.0 OD2 C:ASP197 4.0 19.6 1.0 N C:ASP197 4.0 18.5 1.0 CA C:ASP189 4.1 18.6 1.0 CA C:LYS195 4.2 20.4 1.0 N C:ASN193 4.2 23.5 1.0 CB C:ASP189 4.3 19.2 1.0 CG C:GLU198 4.3 13.4 1.0 OD2 C:ASP189 4.4 19.8 1.0 O C:HOH786 4.4 20.5 1.0 CB C:LYS195 4.5 22.6 1.0 N C:GLY192 4.5 24.2 1.0 N C:LYS196 4.5 23.2 1.0 N C:GLU198 4.6 14.9 1.0 CB C:ASN191 4.6 20.4 1.0 CB C:ASP197 4.6 16.9 1.0 N C:GLY194 4.6 23.6 1.0 C C:ASP189 4.6 19.4 1.0 N C:ASN191 4.7 22.4 1.0 CB C:ASN193 4.7 24.5 1.0 CA C:ASP197 4.8 17.9 1.0 CA C:LYS196 4.8 21.8 1.0 CA C:ASN193 4.8 22.5 1.0 C C:ASN191 4.8 25.5 1.0 C C:ASN193 4.9 25.3 1.0 CA C:ASN191 4.9 23.0 1.0 C C:LYS196 4.9 17.6 1.0 O C:ASP189 5.0 19.1 1.0

S.Oiki, B.Mikami, Y.Maruyama, K.Murata, W.Hashimoto. A Bacterial Abc Transporter Enables Import of Mammalian Host Glycosaminoglycans Sci Rep V. 7 1069 2017.
ISSN: ESSN 2045-2322
PubMed: 28432302
DOI: 10.1038/S41598-017-00917-Y