Calcium in PDB 5gx6: Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with A Sulfate Group at C-4 Position of Galnac

The structure of Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with A Sulfate Group at C-4 Position of Galnac, PDB code: 5gx6 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)	39.45 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.983, 112.590, 165.928, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 21.1

The binding sites of Calcium atom in the Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with A Sulfate Group at C-4 Position of Galnac (pdb code 5gx6). 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 Unsaturated Chondroitin Disaccharide with A Sulfate Group at C-4 Position of Galnac, PDB code: 5gx6:
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 Unsaturated Chondroitin Disaccharide with A Sulfate Group at C-4 Position of Galnac


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 Unsaturated Chondroitin Disaccharide with A Sulfate Group at C-4 Position of Galnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:19.9 occ:1.00 OD1 A:ASN191 2.3 20.0 1.0 OD1 A:ASP189 2.3 21.1 1.0 OD1 A:ASP197 2.4 19.9 1.0 O A:LYS195 2.4 22.9 1.0 OE2 A:GLU198 2.5 16.4 1.0 OD1 A:ASN193 2.5 21.3 1.0 OE1 A:GLU198 2.7 18.3 1.0 CD A:GLU198 2.9 16.6 1.0 CG A:ASN191 3.2 20.6 1.0 CG A:ASN193 3.5 25.6 1.0 CG A:ASP197 3.5 19.8 1.0 C A:LYS195 3.5 21.7 1.0 CG A:ASP189 3.5 23.5 1.0 ND2 A:ASN191 3.6 20.8 1.0 ND2 A:ASN193 3.9 22.3 1.0 N A:LYS195 3.9 20.9 1.0 OD2 A:ASP197 4.0 22.4 1.0 N A:ASP197 4.1 21.1 1.0 CA A:ASP189 4.1 17.6 1.0 CA A:LYS195 4.2 25.6 1.0 CB A:ASP189 4.3 19.4 1.0 CG A:GLU198 4.3 13.6 1.0 N A:ASN193 4.3 21.3 1.0 CB A:LYS195 4.4 27.6 1.0 O A:HOH1078 4.4 18.1 1.0 N A:ASN191 4.4 18.3 1.0 OD2 A:ASP189 4.5 18.4 1.0 CB A:ASN191 4.5 19.3 1.0 C A:ASP189 4.5 18.0 1.0 N A:GLY192 4.6 21.0 1.0 N A:LYS196 4.6 20.0 1.0 N A:GLU198 4.6 16.4 1.0 CB A:ASP197 4.7 19.0 1.0 CB A:ASN193 4.7 26.5 1.0 N A:GLY194 4.7 24.0 1.0 CA A:ASN191 4.8 17.7 1.0 C A:ASN191 4.8 21.8 1.0 CA A:ASP197 4.8 19.7 1.0 CA A:ASN193 4.8 23.8 1.0 CA A:LYS196 4.9 20.6 1.0 C A:ASN193 4.9 25.2 1.0 O A:ASP189 4.9 17.4 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with A Sulfate Group at C-4 Position of Galnac


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 Unsaturated Chondroitin Disaccharide with A Sulfate Group at C-4 Position of Galnac within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:17.7 occ:1.00 OD1 B:ASP189 2.3 19.3 1.0 OD1 B:ASN191 2.3 18.6 1.0 O B:LYS195 2.4 18.5 1.0 OD1 B:ASP197 2.4 15.5 1.0 OD1 B:ASN193 2.5 20.0 1.0 OE2 B:GLU198 2.5 15.5 1.0 OE1 B:GLU198 2.7 15.2 1.0 CD B:GLU198 2.9 14.9 1.0 CG B:ASN191 3.2 17.2 1.0 CG B:ASN193 3.5 22.4 1.0 CG B:ASP197 3.5 17.3 1.0 CG B:ASP189 3.5 24.2 1.0 C B:LYS195 3.5 19.1 1.0 ND2 B:ASN191 3.6 14.7 1.0 ND2 B:ASN193 3.9 18.5 1.0 N B:LYS195 4.0 20.4 1.0 OD2 B:ASP197 4.0 18.1 1.0 N B:ASP197 4.1 15.7 1.0 CA B:ASP189 4.1 18.8 1.0 CA B:LYS195 4.2 22.2 1.0 N B:ASN193 4.2 24.2 1.0 CB B:ASP189 4.3 21.0 1.0 CG B:GLU198 4.3 13.5 1.0 OD2 B:ASP189 4.4 22.2 1.0 O B:HOH800 4.4 15.1 1.0 CB B:LYS195 4.5 22.5 1.0 N B:GLY192 4.5 21.1 1.0 N B:LYS196 4.6 21.1 1.0 CB B:ASN191 4.6 17.3 1.0 N B:ASN191 4.6 15.1 1.0 C B:ASP189 4.6 21.1 1.0 N B:GLU198 4.6 15.3 1.0 CB B:ASP197 4.7 16.1 1.0 CB B:ASN193 4.7 23.6 1.0 N B:GLY194 4.7 22.9 1.0 CA B:LYS196 4.8 17.3 1.0 CA B:ASN193 4.8 22.9 1.0 CA B:ASP197 4.8 16.0 1.0 C B:ASN191 4.8 18.1 1.0 C B:ASN193 4.9 23.8 1.0 CA B:ASN191 4.9 16.2 1.0 O B:ASP189 5.0 19.0 1.0 C B:LYS196 5.0 16.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with A Sulfate Group at C-4 Position of Galnac


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 Unsaturated Chondroitin Disaccharide with A Sulfate Group at C-4 Position of Galnac within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:18.5 occ:1.00 OD1 C:ASP189 2.3 19.8 1.0 O C:LYS195 2.3 23.0 1.0 OD1 C:ASP197 2.3 18.7 1.0 OD1 C:ASN191 2.4 20.2 1.0 OD1 C:ASN193 2.5 21.0 1.0 OE2 C:GLU198 2.5 19.0 1.0 OE1 C:GLU198 2.7 18.1 1.0 CD C:GLU198 2.9 18.2 1.0 CG C:ASN191 3.3 19.8 1.0 CG C:ASN193 3.4 21.9 1.0 C C:LYS195 3.4 21.1 1.0 CG C:ASP197 3.4 24.9 1.0 CG C:ASP189 3.5 23.1 1.0 ND2 C:ASN191 3.6 16.8 1.0 ND2 C:ASN193 3.8 22.3 1.0 N C:LYS195 3.8 23.0 1.0 OD2 C:ASP197 4.0 19.9 1.0 CA C:LYS195 4.0 23.9 1.0 N C:ASP197 4.1 18.1 1.0 CA C:ASP189 4.2 17.7 1.0 CB C:LYS195 4.2 23.2 1.0 N C:ASN193 4.3 24.2 1.0 CB C:ASP189 4.3 16.8 1.0 CG C:GLU198 4.4 15.4 1.0 OD2 C:ASP189 4.4 22.4 1.0 N C:LYS196 4.5 20.4 1.0 O C:HOH755 4.5 20.7 1.0 N C:GLY192 4.6 22.2 1.0 CB C:ASN191 4.6 21.0 1.0 CB C:ASP197 4.6 19.8 1.0 CB C:ASN193 4.6 23.1 1.0 C C:ASP189 4.6 18.6 1.0 N C:ASN191 4.6 19.9 1.0 N C:GLU198 4.6 16.8 1.0 N C:GLY194 4.6 22.8 1.0 CA C:ASP197 4.8 15.8 1.0 CA C:LYS196 4.8 22.6 1.0 CA C:ASN193 4.8 24.8 1.0 C C:ASN193 4.9 26.8 1.0 C C:ASN191 4.9 22.9 1.0 CA C:ASN191 4.9 22.3 1.0 C C:GLY194 4.9 26.1 1.0 O C:ASP189 5.0 20.4 1.0 C C:LYS196 5.0 19.6 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