Calcium in PDB 5gx7: Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with A Sulfate Group at C-6 Position of Galnac

The structure of Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with A Sulfate Group at C-6 Position of Galnac, PDB code: 5gx7 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)	45.67 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.275, 112.444, 166.614, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.9

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-6 Position of Galnac (pdb code 5gx7). 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-6 Position of Galnac, PDB code: 5gx7:
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-6 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-6 Position of Galnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:22.4 occ:1.00 OD1 A:ASP189 2.3 24.4 1.0 OD1 A:ASP197 2.3 18.3 1.0 O A:LYS195 2.3 20.5 1.0 OD1 A:ASN191 2.4 22.2 1.0 OD1 A:ASN193 2.5 25.7 1.0 OE2 A:GLU198 2.6 22.2 1.0 OE1 A:GLU198 2.7 19.3 1.0 CD A:GLU198 3.0 20.7 1.0 CG A:ASN191 3.1 22.9 1.0 ND2 A:ASN191 3.3 21.4 1.0 CG A:ASN193 3.4 26.8 1.0 CG A:ASP197 3.5 24.5 1.0 CG A:ASP189 3.5 25.1 1.0 C A:LYS195 3.5 28.7 1.0 ND2 A:ASN193 3.8 25.2 1.0 N A:LYS195 3.9 23.7 1.0 N A:ASP197 3.9 23.0 1.0 CA A:ASP189 4.0 21.9 1.0 OD2 A:ASP197 4.1 22.0 1.0 CA A:LYS195 4.2 24.9 1.0 CB A:ASP189 4.2 22.9 1.0 N A:ASN193 4.3 24.5 1.0 CG A:GLU198 4.4 15.1 1.0 OD2 A:ASP189 4.4 26.2 1.0 CB A:LYS195 4.5 28.6 1.0 O A:HOH728 4.5 21.1 1.0 CB A:ASN191 4.5 18.4 1.0 C A:ASP189 4.5 21.2 1.0 CB A:ASP197 4.6 23.6 1.0 N A:LYS196 4.6 22.3 1.0 N A:GLU198 4.6 19.1 1.0 CB A:ASN193 4.6 23.7 1.0 N A:ASN191 4.6 17.9 1.0 N A:GLY192 4.7 24.6 1.0 CA A:ASP197 4.7 24.7 1.0 N A:GLY194 4.7 22.8 1.0 CA A:LYS196 4.8 23.8 1.0 CA A:ASN193 4.8 23.4 1.0 O A:ASP189 4.9 20.4 1.0 C A:ASN191 4.9 26.7 1.0 C A:ASN193 4.9 28.1 1.0 CA A:ASN191 4.9 23.8 1.0 C A:LYS196 4.9 26.1 1.0 C A:ASP197 5.0 20.8 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-6 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-6 Position of Galnac within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:18.3 occ:1.00 OD1 B:ASN191 2.3 19.2 1.0 OD1 B:ASP189 2.3 25.2 1.0 O B:LYS195 2.3 22.5 1.0 OE2 B:GLU198 2.4 19.5 1.0 OD1 B:ASN193 2.5 20.7 1.0 OD1 B:ASP197 2.5 17.2 1.0 OE1 B:GLU198 2.7 21.7 1.0 CD B:GLU198 2.9 16.5 1.0 CG B:ASN191 3.2 19.8 1.0 CG B:ASN193 3.4 21.8 1.0 ND2 B:ASN191 3.5 18.8 1.0 C B:LYS195 3.5 24.7 1.0 CG B:ASP189 3.5 21.4 1.0 CG B:ASP197 3.6 21.4 1.0 ND2 B:ASN193 3.9 19.1 1.0 N B:LYS195 4.0 24.8 1.0 OD2 B:ASP197 4.1 22.9 1.0 N B:ASP197 4.1 20.1 1.0 CA B:ASP189 4.2 23.3 1.0 CA B:LYS195 4.2 20.8 1.0 CG B:GLU198 4.3 15.5 1.0 CB B:ASP189 4.3 21.0 1.0 N B:ASN193 4.3 24.6 1.0 OD2 B:ASP189 4.3 22.7 1.0 CB B:ASN191 4.5 19.9 1.0 N B:LYS196 4.5 23.3 1.0 O B:HOH722 4.6 21.1 1.0 N B:ASN191 4.6 20.2 1.0 N B:GLU198 4.6 17.9 1.0 CB B:LYS195 4.6 25.0 1.0 C B:ASP189 4.6 22.9 1.0 N B:GLY192 4.6 22.1 1.0 CB B:ASN193 4.7 20.8 1.0 N B:GLY194 4.7 24.1 1.0 CB B:ASP197 4.8 21.2 1.0 CA B:LYS196 4.8 25.4 1.0 C B:ASN191 4.8 24.1 1.0 CA B:ASN191 4.8 21.2 1.0 CA B:ASN193 4.8 24.2 1.0 CA B:ASP197 4.9 22.7 1.0 O B:ASP189 4.9 20.2 1.0 C B:ASN193 4.9 22.9 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-6 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-6 Position of Galnac within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:25.4 occ:1.00 O C:LYS195 2.2 27.7 1.0 OD1 C:ASN191 2.3 23.1 1.0 OD1 C:ASP189 2.4 29.1 1.0 OE2 C:GLU198 2.4 20.5 1.0 OD1 C:ASP197 2.5 26.5 1.0 OD1 C:ASN193 2.5 25.2 1.0 OE1 C:GLU198 2.7 20.5 1.0 CD C:GLU198 2.9 22.5 1.0 CG C:ASN191 3.2 22.5 1.0 CG C:ASN193 3.4 31.1 1.0 C C:LYS195 3.4 23.9 1.0 CG C:ASP189 3.6 32.0 1.0 ND2 C:ASN191 3.6 22.7 1.0 CG C:ASP197 3.6 26.8 1.0 N C:LYS195 3.9 32.3 1.0 ND2 C:ASN193 3.9 28.5 1.0 N C:ASP197 4.1 22.6 1.0 CA C:LYS195 4.1 25.0 1.0 OD2 C:ASP197 4.1 20.0 1.0 CA C:ASP189 4.2 26.8 1.0 N C:ASN193 4.3 32.4 1.0 CB C:ASP189 4.3 22.3 1.0 CG C:GLU198 4.3 22.2 1.0 O C:HOH776 4.4 22.0 1.0 OD2 C:ASP189 4.5 37.3 1.0 N C:LYS196 4.5 24.5 1.0 CB C:LYS195 4.6 28.4 1.0 N C:GLU198 4.6 19.9 1.0 CB C:ASN191 4.6 24.8 1.0 C C:ASP189 4.6 23.0 1.0 N C:ASN191 4.6 23.0 1.0 N C:GLY194 4.6 29.9 1.0 CB C:ASN193 4.6 33.8 1.0 N C:GLY192 4.7 30.2 1.0 CA C:LYS196 4.8 31.2 1.0 CB C:ASP197 4.8 27.3 1.0 CA C:ASN193 4.8 32.4 1.0 CA C:ASP197 4.8 23.8 1.0 C C:ASN193 4.8 31.3 1.0 CA C:ASN191 4.9 26.1 1.0 O C:ASP189 4.9 21.8 1.0 C C:ASN191 4.9 30.4 1.0 C C:GLY194 5.0 32.9 1.0 C C:LYS196 5.0 24.3 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