Calcium in PDB 5gx8: Crystal Structure of Solute-Binding Protein Related to Glycosaminoglycans

The structure of Crystal Structure of Solute-Binding Protein Related to Glycosaminoglycans, PDB code: 5gx8 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)	39.36 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.674, 142.050, 73.676, 90.00, 105.98, 90.00
R / Rfree (%)	19.7 / 22.9

The binding sites of Calcium atom in the Crystal Structure of Solute-Binding Protein Related to Glycosaminoglycans (pdb code 5gx8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Solute-Binding Protein Related to Glycosaminoglycans, PDB code: 5gx8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Solute-Binding Protein Related to Glycosaminoglycans


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 Related to Glycosaminoglycans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:30.7 occ:1.00 OD1 A:ASN191 2.3 27.8 1.0 OD1 A:ASP189 2.3 28.9 1.0 OE2 A:GLU198 2.3 22.4 1.0 O A:LYS195 2.4 28.1 1.0 OD1 A:ASP197 2.4 27.0 1.0 OD1 A:ASN193 2.5 28.4 1.0 OE1 A:GLU198 2.7 26.9 1.0 CD A:GLU198 2.8 26.6 1.0 CG A:ASN191 3.1 30.2 1.0 ND2 A:ASN191 3.4 24.7 1.0 CG A:ASN193 3.5 29.5 1.0 CG A:ASP189 3.5 32.9 1.0 C A:LYS195 3.5 33.0 1.0 CG A:ASP197 3.5 26.6 1.0 N A:LYS195 4.0 33.4 1.0 ND2 A:ASN193 4.0 30.2 1.0 CA A:ASP189 4.0 29.1 1.0 OD2 A:ASP197 4.0 33.2 1.0 N A:ASP197 4.1 25.7 1.0 CG A:GLU198 4.2 20.0 1.0 CB A:ASP189 4.2 26.9 1.0 CA A:LYS195 4.2 30.3 1.0 N A:ASN193 4.2 35.1 1.0 N A:ASN191 4.4 24.3 1.0 O A:HOH803 4.4 27.6 1.0 CB A:ASN191 4.4 21.8 1.0 N A:GLY192 4.4 30.1 1.0 C A:ASP189 4.5 29.3 1.0 OD2 A:ASP189 4.5 31.8 1.0 CB A:LYS195 4.5 34.2 1.0 N A:LYS196 4.6 34.0 1.0 N A:GLU198 4.6 23.0 1.0 CB A:ASN193 4.7 30.1 1.0 CA A:ASN191 4.7 22.9 1.0 CB A:ASP197 4.7 25.6 1.0 O A:ASP189 4.7 26.9 1.0 C A:ASN191 4.7 27.4 1.0 N A:GLY194 4.8 34.7 1.0 CA A:LYS196 4.8 33.2 1.0 CA A:ASN193 4.8 32.4 1.0 CA A:ASP197 4.8 25.2 1.0 C A:ASN193 4.9 33.8 1.0 C A:LYS196 5.0 31.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Solute-Binding Protein Related to Glycosaminoglycans


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 Related to Glycosaminoglycans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:47.2 occ:1.00 OD1 B:ASP189 2.2 46.8 1.0 OD1 B:ASP197 2.4 41.9 1.0 OE2 B:GLU198 2.4 31.2 1.0 O B:LYS195 2.5 41.2 1.0 OD1 B:ASN193 2.6 40.0 1.0 OE1 B:GLU198 2.8 31.7 1.0 CD B:GLU198 2.9 32.6 1.0 OD1 B:ASN191 3.2 45.3 1.0 CG B:ASP189 3.3 44.1 1.0 CG B:ASN193 3.4 48.1 1.0 CG B:ASP197 3.5 30.3 1.0 ND2 B:ASN191 3.5 34.1 1.0 ND2 B:ASN193 3.6 38.2 1.0 C B:LYS195 3.7 44.9 1.0 CG B:ASN191 3.7 40.3 1.0 OD2 B:ASP197 4.0 43.1 1.0 OD2 B:ASP189 4.0 51.9 1.0 N B:ASP197 4.1 35.0 1.0 N B:LYS195 4.1 40.4 1.0 CB B:ASP189 4.3 40.7 1.0 CG B:GLU198 4.4 23.9 1.0 CA B:ASP189 4.4 35.2 1.0 N B:GLU198 4.4 32.8 1.0 CA B:LYS195 4.4 43.6 1.0 N B:GLY194 4.6 53.2 1.0 N B:LYS196 4.6 41.6 1.0 CB B:ASP197 4.6 42.2 1.0 CB B:ASN193 4.7 44.9 1.0 CA B:ASP197 4.7 31.3 1.0 CA B:LYS196 4.8 43.9 1.0 C B:ASP197 4.9 34.4 1.0 C B:LYS196 5.0 33.7 1.0 C B:ASP189 5.0 38.1 1.0 CB B:LYS195 5.0 48.1 1.0 C B:GLY194 5.0 48.5 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