Calcium in PDB 5xs8: Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with Two Sulfate Groups at C-4 and C-6 Positions of Galnac

The structure of Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with Two Sulfate Groups at C-4 and C-6 Positions of Galnac, PDB code: 5xs8 was solved by S.Oiki, R.Kamochi, 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)	40.40 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.741, 69.208, 165.967, 89.99, 90.04, 90.03
R / Rfree (%)	17.3 / 21.6

The binding sites of Calcium atom in the Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with Two Sulfate Groups at C-4 and C-6 Positions of Galnac (pdb code 5xs8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with Two Sulfate Groups at C-4 and C-6 Positions of Galnac, PDB code: 5xs8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with Two Sulfate Groups at C-4 and C-6 Positions 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 Two Sulfate Groups at C-4 and C-6 Positions of Galnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:27.1 occ:1.00 OD1 A:ASN191 2.2 29.0 1.0 OD1 A:ASP189 2.2 30.2 1.0 OD1 A:ASP197 2.3 27.8 1.0 O A:LYS195 2.5 28.0 1.0 OE2 A:GLU198 2.5 26.1 1.0 OD1 A:ASN193 2.5 25.4 1.0 OE1 A:GLU198 2.8 23.1 1.0 CD A:GLU198 2.9 24.8 1.0 CG A:ASN191 3.2 27.2 1.0 CG A:ASP189 3.4 30.0 1.0 CG A:ASP197 3.5 26.6 1.0 CG A:ASN193 3.5 25.4 1.0 ND2 A:ASN191 3.6 23.6 1.0 C A:LYS195 3.6 32.7 1.0 CA A:ASP189 4.0 24.7 1.0 OD2 A:ASP197 4.0 23.3 1.0 ND2 A:ASN193 4.0 29.6 1.0 N A:LYS195 4.0 31.8 1.0 N A:ASP197 4.1 28.2 1.0 CB A:ASP189 4.1 28.9 1.0 N A:ASN193 4.2 30.1 1.0 CA A:LYS195 4.2 30.6 1.0 O A:HOH728 4.3 27.0 1.0 CG A:GLU198 4.3 26.8 1.0 OD2 A:ASP189 4.4 30.5 1.0 C A:ASP189 4.4 27.6 1.0 CB A:ASN191 4.5 26.0 1.0 N A:ASN191 4.5 25.5 1.0 CB A:LYS195 4.5 33.5 1.0 N A:LYS196 4.6 30.7 1.0 N A:GLU198 4.6 27.6 1.0 N A:GLY192 4.6 28.8 1.0 CB A:ASN193 4.6 30.0 1.0 CB A:ASP197 4.7 26.1 1.0 C A:ASN191 4.7 29.0 1.0 CA A:ASN191 4.7 26.4 1.0 O A:ASP189 4.8 27.2 1.0 N A:GLY194 4.8 30.9 1.0 CA A:ASN193 4.8 31.3 1.0 CA A:LYS196 4.8 31.6 1.0 CA A:ASP197 4.8 26.6 1.0 C A:ASN193 4.9 28.4 1.0 C A:LYS196 5.0 30.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with Two Sulfate Groups at C-4 and C-6 Positions 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 Two Sulfate Groups at C-4 and C-6 Positions of Galnac within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:26.8 occ:1.00 OD1 B:ASN191 2.2 28.0 1.0 OD1 B:ASP189 2.2 29.6 1.0 OD1 B:ASP197 2.3 28.8 1.0 O B:LYS195 2.4 27.1 1.0 OE2 B:GLU198 2.5 27.8 1.0 OD1 B:ASN193 2.5 27.4 1.0 OE1 B:GLU198 2.8 22.8 1.0 CD B:GLU198 2.9 26.6 1.0 CG B:ASN191 3.1 28.6 1.0 CG B:ASP189 3.4 29.2 1.0 CG B:ASN193 3.5 28.7 1.0 CG B:ASP197 3.5 27.5 1.0 ND2 B:ASN191 3.5 24.9 1.0 C B:LYS195 3.6 32.8 1.0 ND2 B:ASN193 3.9 30.1 1.0 CA B:ASP189 4.0 23.2 1.0 OD2 B:ASP197 4.0 26.4 1.0 N B:LYS195 4.0 32.8 1.0 N B:ASP197 4.1 30.0 1.0 CB B:ASP189 4.1 28.7 1.0 N B:ASN193 4.2 26.9 1.0 O B:HOH715 4.3 27.5 1.0 CA B:LYS195 4.3 30.4 1.0 CG B:GLU198 4.3 24.6 1.0 OD2 B:ASP189 4.4 30.3 1.0 C B:ASP189 4.4 29.2 1.0 N B:ASN191 4.4 26.1 1.0 CB B:ASN191 4.5 25.6 1.0 N B:GLY192 4.6 28.2 1.0 CB B:LYS195 4.6 35.6 1.0 N B:LYS196 4.6 30.1 1.0 N B:GLU198 4.6 27.5 1.0 CB B:ASN193 4.7 29.9 1.0 O B:ASP189 4.7 26.2 1.0 CB B:ASP197 4.7 26.4 1.0 N B:GLY194 4.7 29.0 1.0 C B:ASN191 4.7 27.9 1.0 CA B:ASN191 4.7 26.7 1.0 CA B:LYS196 4.8 31.5 1.0 CA B:ASN193 4.8 30.9 1.0 CA B:ASP197 4.8 28.8 1.0 C B:ASN193 4.9 29.6 1.0 C B:LYS196 5.0 32.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with Two Sulfate Groups at C-4 and C-6 Positions 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 Two Sulfate Groups at C-4 and C-6 Positions of Galnac within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:27.6 occ:1.00 OD1 C:ASN191 2.2 28.5 1.0 OD1 C:ASP197 2.3 27.9 1.0 OD1 C:ASP189 2.3 32.5 1.0 O C:LYS195 2.4 26.1 1.0 OD1 C:ASN193 2.5 26.4 1.0 OE1 C:GLU198 2.5 26.2 1.0 OE2 C:GLU198 2.8 24.2 1.0 CD C:GLU198 2.9 25.6 1.0 CG C:ASN191 3.2 27.7 1.0 CG C:ASP197 3.4 27.1 1.0 CG C:ASN193 3.4 27.8 1.0 CG C:ASP189 3.5 29.4 1.0 C C:LYS195 3.6 32.1 1.0 ND2 C:ASN191 3.6 26.2 1.0 ND2 C:ASN193 3.9 30.8 1.0 OD2 C:ASP197 3.9 23.6 1.0 N C:LYS195 4.0 31.2 1.0 CA C:ASP189 4.0 24.3 1.0 N C:ASP197 4.1 30.4 1.0 CB C:ASP189 4.2 28.1 1.0 CA C:LYS195 4.2 29.9 1.0 N C:ASN193 4.2 28.5 1.0 CG C:GLU198 4.4 26.1 1.0 O C:HOH736 4.4 27.3 1.0 C C:ASP189 4.4 26.9 1.0 OD2 C:ASP189 4.4 34.1 1.0 N C:ASN191 4.4 27.2 1.0 CB C:LYS195 4.4 32.6 1.0 CB C:ASN191 4.5 24.6 1.0 N C:GLY192 4.6 30.0 1.0 N C:LYS196 4.6 28.1 1.0 CB C:ASN193 4.6 31.5 1.0 N C:GLU198 4.6 27.5 1.0 CB C:ASP197 4.6 26.0 1.0 O C:ASP189 4.6 23.8 1.0 C C:ASN191 4.7 29.0 1.0 CA C:ASN191 4.7 25.4 1.0 N C:GLY194 4.7 31.1 1.0 CA C:ASN193 4.8 31.6 1.0 CA C:LYS196 4.8 31.0 1.0 CA C:ASP197 4.8 27.3 1.0 C C:ASN193 4.9 31.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with Two Sulfate Groups at C-4 and C-6 Positions of Galnac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Solute-Binding Protein Complexed with Unsaturated Chondroitin Disaccharide with Two Sulfate Groups at C-4 and C-6 Positions of Galnac within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca601 b:27.1 occ:1.00 OD1 D:ASN191 2.2 30.1 1.0 OD1 D:ASP189 2.3 32.1 1.0 OD1 D:ASP197 2.3 28.3 1.0 O D:LYS195 2.4 25.4 1.0 OE2 D:GLU198 2.5 27.1 1.0 OD1 D:ASN193 2.6 26.5 1.0 OE1 D:GLU198 2.7 22.7 1.0 CD D:GLU198 2.9 26.1 1.0 CG D:ASN191 3.1 28.5 1.0 CG D:ASP197 3.4 27.5 1.0 CG D:ASP189 3.5 29.8 1.0 CG D:ASN193 3.5 28.7 1.0 ND2 D:ASN191 3.5 28.0 1.0 C D:LYS195 3.6 33.6 1.0 ND2 D:ASN193 3.9 28.2 1.0 OD2 D:ASP197 4.0 26.3 1.0 CA D:ASP189 4.0 24.1 1.0 N D:LYS195 4.0 32.5 1.0 N D:ASP197 4.1 26.9 1.0 CB D:ASP189 4.1 27.9 1.0 N D:ASN193 4.3 27.2 1.0 CA D:LYS195 4.3 34.1 1.0 CG D:GLU198 4.3 26.4 1.0 O D:HOH724 4.4 26.0 1.0 OD2 D:ASP189 4.4 31.4 1.0 C D:ASP189 4.4 28.5 1.0 CB D:ASN191 4.4 26.0 1.0 N D:ASN191 4.5 27.7 1.0 N D:GLU198 4.6 28.7 1.0 N D:LYS196 4.6 27.6 1.0 N D:GLY192 4.6 27.3 1.0 CB D:ASP197 4.6 27.9 1.0 O D:ASP189 4.7 25.2 1.0 CB D:ASN193 4.7 27.1 1.0 CA D:ASN191 4.7 26.8 1.0 N D:GLY194 4.8 28.0 1.0 C D:ASN191 4.8 27.8 1.0 CA D:ASP197 4.8 26.9 1.0 CA D:LYS196 4.8 32.1 1.0 CA D:ASN193 4.9 30.0 1.0 CB D:LYS195 4.9 38.7 1.0 C D:ASN193 5.0 30.4 1.0

S.Oiki, R.Kamochi, B.Mikami, K.Murata, W.Hashimoto. Alternative Substrate-Bound Conformation of Bacterial Solute-Binding Protein Involved in the Import of Mammalian Host Glycosaminoglycans. Sci Rep V. 7 17005 2017.
ISSN: ESSN 2045-2322
PubMed: 29208901
DOI: 10.1038/S41598-017-16801-8