Calcium in PDB 5g5z: S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose

The structure of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose, PDB code: 5g5z was solved by S.Culurgioni, G.Harris, A.K.Singh, S.J.King, M.A.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.15 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.610, 127.820, 120.550, 90.00, 96.58, 90.00
R / Rfree (%)	16.8 / 22.2

The binding sites of Calcium atom in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose (pdb code 5g5z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose, PDB code: 5g5z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca545 b:45.8 occ:1.00 O A:GLU221 2.2 49.9 1.0 OD1 A:ASP223 2.4 47.4 1.0 OD1 A:ASN217 2.4 44.0 1.0 OD1 A:ASP215 2.4 50.4 1.0 OD1 A:ASN219 2.5 48.6 1.0 OE2 A:GLU224 2.5 44.1 1.0 OE1 A:GLU224 2.6 38.8 1.0 CD A:GLU224 2.9 43.0 1.0 CG A:ASN217 3.3 51.3 1.0 C A:GLU221 3.3 52.5 1.0 CG A:ASN219 3.5 54.9 1.0 CG A:ASP223 3.5 47.8 1.0 CG A:ASP215 3.5 52.6 1.0 ND2 A:ASN217 3.6 49.8 1.0 N A:GLU221 3.8 62.5 1.0 ND2 A:ASN219 3.9 55.1 1.0 N A:ASP223 4.1 45.5 1.0 CA A:ASP215 4.1 53.0 1.0 OD2 A:ASP223 4.1 49.5 1.0 CA A:GLU221 4.1 58.0 1.0 CB A:ASP215 4.2 48.6 1.0 N A:ASN219 4.4 57.3 1.0 N A:ALA222 4.4 49.9 1.0 CG A:GLU224 4.4 42.3 1.0 OD2 A:ASP215 4.5 45.7 1.0 C A:ASP215 4.6 50.4 1.0 N A:GLU224 4.6 39.3 1.0 CB A:ASN217 4.6 49.2 1.0 N A:ASN217 4.6 50.4 1.0 CA A:ALA222 4.6 47.8 1.0 CB A:GLU221 4.7 55.7 1.0 N A:GLY218 4.7 41.2 1.0 CB A:ASP223 4.7 43.1 1.0 N A:GLY220 4.7 57.2 1.0 CB A:ASN219 4.7 52.5 1.0 C A:ASN219 4.8 58.8 1.0 CA A:ASP223 4.8 41.6 1.0 C A:ASN217 4.8 54.3 1.0 CA A:ASN219 4.9 57.6 1.0 C A:ALA222 4.9 50.5 1.0 CA A:ASN217 4.9 54.7 1.0 O A:ASP215 5.0 52.8 1.0 C A:GLY220 5.0 65.5 1.0

Calcium binding site 2 out of 9 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca546 b:30.1 occ:1.00 O A:HOH2167 2.3 32.3 1.0 OD1 A:ASN268 2.3 26.3 1.0 O A:HOH2163 2.4 24.6 1.0 OD1 A:ASP263 2.4 33.5 1.0 OD1 A:ASP267 2.4 34.5 1.0 O A:PHE264 2.5 28.7 1.0 O A:HOH2162 2.5 30.7 1.0 CG A:ASN268 3.4 27.8 1.0 CG A:ASP267 3.5 35.7 1.0 C A:PHE264 3.5 25.0 1.0 CG A:ASP263 3.6 26.6 1.0 N A:PHE264 3.8 27.2 1.0 ND2 A:ASN268 3.9 30.6 1.0 OD2 A:ASP267 3.9 37.8 1.0 O A:HOH2169 4.1 33.9 1.0 OD2 A:ASP263 4.1 32.8 1.0 CA A:PHE264 4.1 25.0 1.0 O A:HOH2164 4.2 35.3 1.0 CB A:PHE264 4.4 26.7 1.0 N A:ASN268 4.4 28.2 1.0 C A:ASP267 4.5 27.9 1.0 C A:ASP263 4.5 29.2 1.0 O A:HOH2161 4.5 42.7 1.0 N A:THR265 4.6 22.7 1.0 CB A:ASN268 4.6 28.1 1.0 CA A:ASN268 4.7 33.1 1.0 O A:ASP267 4.7 29.5 1.0 CA A:ASP263 4.7 27.2 1.0 CB A:ASP263 4.8 21.4 1.0 CB A:ASP267 4.8 25.3 1.0 CA A:THR265 4.8 23.7 1.0 N A:ASP267 4.9 21.6 1.0 CA A:ASP267 4.9 19.1 1.0

Calcium binding site 3 out of 9 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca545 b:45.9 occ:1.00 OD1 B:ASN217 2.3 40.1 1.0 OD1 B:ASP215 2.3 48.5 1.0 O B:GLU221 2.4 55.4 1.0 OD1 B:ASP223 2.4 44.9 1.0 OE2 B:GLU224 2.4 42.2 1.0 OD1 B:ASN219 2.5 41.2 1.0 OE1 B:GLU224 2.5 36.5 1.0 CD B:GLU224 2.8 39.9 1.0 CG B:ASN217 3.2 43.2 1.0 CG B:ASN219 3.4 47.5 1.0 CG B:ASP215 3.5 42.8 1.0 C B:GLU221 3.6 53.7 1.0 CG B:ASP223 3.6 44.6 1.0 ND2 B:ASN217 3.7 44.0 1.0 ND2 B:ASN219 3.7 50.6 1.0 N B:GLU221 4.0 49.6 1.0 N B:ASP223 4.0 37.0 1.0 CA B:ASP215 4.1 43.2 1.0 N B:ASN219 4.2 59.7 1.0 CB B:ASP215 4.2 35.4 1.0 CG B:GLU224 4.3 41.8 1.0 OD2 B:ASP223 4.3 48.4 1.0 CA B:GLU221 4.3 58.5 1.0 N B:GLY218 4.4 48.6 1.0 O B:HOH2119 4.5 49.0 1.0 N B:GLU224 4.5 41.5 1.0 OD2 B:ASP215 4.5 48.3 1.0 C B:ASP215 4.5 42.0 1.0 CB B:ASN217 4.6 41.6 1.0 N B:ALA222 4.6 49.4 1.0 N B:ASN217 4.6 47.3 1.0 CB B:ASN219 4.6 44.1 1.0 CB B:ASP223 4.7 36.4 1.0 N B:GLY220 4.7 52.2 1.0 CA B:ALA222 4.8 43.0 1.0 CA B:ASP223 4.8 37.9 1.0 CA B:ASN219 4.8 47.8 1.0 C B:ASN217 4.8 49.9 1.0 CA B:ASN217 4.8 40.4 1.0 C B:ASN219 4.9 54.0 1.0 O B:ASP215 4.9 50.2 1.0 CB B:GLU221 4.9 68.8 1.0 C B:ALA222 5.0 43.0 1.0 N B:PRO216 5.0 45.9 1.0 C B:ASP223 5.0 41.7 1.0

Calcium binding site 4 out of 9 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca546 b:28.2 occ:1.00 OD1 B:ASP263 2.3 26.0 1.0 OD1 B:ASN268 2.4 31.4 1.0 O B:HOH2160 2.4 22.1 1.0 O B:HOH2164 2.4 37.4 1.0 O B:PHE264 2.4 26.2 1.0 OD1 B:ASP267 2.4 25.8 1.0 O B:HOH2159 2.5 28.9 1.0 CG B:ASN268 3.4 31.1 1.0 CG B:ASP263 3.5 29.3 1.0 CG B:ASP267 3.5 28.1 1.0 C B:PHE264 3.5 30.8 1.0 OD2 B:ASP267 3.8 28.3 1.0 N B:PHE264 3.8 31.8 1.0 ND2 B:ASN268 3.9 31.8 1.0 OD2 B:ASP263 4.0 33.0 1.0 CA B:PHE264 4.1 26.8 1.0 O B:HOH2165 4.2 38.2 1.0 O B:HOH2158 4.2 33.8 1.0 O B:HOH2156 4.3 33.1 1.0 CB B:PHE264 4.3 29.4 1.0 N B:ASN268 4.5 29.5 1.0 C B:ASP263 4.5 33.4 1.0 N B:THR265 4.6 30.2 1.0 C B:ASP267 4.6 26.1 1.0 CB B:ASP263 4.7 27.5 1.0 CA B:ASP263 4.7 28.6 1.0 CB B:ASN268 4.7 28.9 1.0 O B:HOH2163 4.7 36.0 1.0 CA B:ASN268 4.8 34.2 1.0 O B:HOH2069 4.8 49.5 1.0 CA B:THR265 4.8 31.4 1.0 CB B:ASP267 4.8 22.9 1.0 O B:ASP267 4.9 32.9 1.0 N B:ASP267 4.9 30.4 1.0

Calcium binding site 5 out of 9 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca545 b:39.5 occ:1.00 OD1 C:ASN217 2.2 48.8 1.0 ND2 C:ASN217 2.3 52.2 1.0 OD1 C:ASP223 2.3 48.0 1.0 O C:GLU221 2.3 53.4 1.0 OD1 C:ASP215 2.3 48.7 1.0 OE2 C:GLU224 2.4 40.4 1.0 CG C:ASN217 2.5 49.5 1.0 OE1 C:GLU224 2.5 40.3 1.0 OD1 C:ASN219 2.6 53.7 1.0 CD C:GLU224 2.7 40.7 1.0 CG C:ASN219 3.4 55.5 1.0 CG C:ASP223 3.5 46.3 1.0 C C:GLU221 3.5 55.9 1.0 CG C:ASP215 3.6 43.6 1.0 ND2 C:ASN219 3.7 54.7 1.0 N C:ASP223 4.0 37.3 1.0 CB C:ASN217 4.0 45.3 1.0 OD2 C:ASP223 4.1 50.6 1.0 N C:GLU221 4.1 55.2 1.0 CA C:ASP215 4.1 44.1 1.0 CG C:GLU224 4.1 40.1 1.0 CA C:GLU221 4.3 54.4 1.0 O C:HOH2119 4.3 47.0 1.0 CB C:ASP215 4.3 47.2 1.0 N C:ASN219 4.4 63.2 1.0 N C:GLU224 4.4 40.5 1.0 N C:ASN217 4.4 43.8 1.0 OD2 C:ASP215 4.5 40.9 1.0 C C:ASP215 4.5 48.4 1.0 N C:ALA222 4.5 50.0 1.0 CB C:ASP223 4.6 37.1 1.0 N C:GLY218 4.6 50.5 1.0 CA C:ALA222 4.7 47.5 1.0 CA C:ASN217 4.7 46.6 1.0 N C:GLY220 4.7 60.0 1.0 CA C:ASP223 4.7 42.8 1.0 CB C:ASN219 4.7 55.2 1.0 CB C:GLU221 4.7 58.6 1.0 C C:ALA222 4.9 41.9 1.0 O C:ASP215 4.9 44.0 1.0 CA C:ASN219 4.9 60.7 1.0 N C:PRO216 4.9 42.4 1.0 C C:ASP223 5.0 40.8 1.0 C C:ASN219 5.0 61.3 1.0 C C:ASN217 5.0 49.2 1.0

Calcium binding site 6 out of 9 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca546 b:32.3 occ:1.00 OD1 C:ASP263 2.3 37.8 1.0 OD1 C:ASN268 2.4 33.0 1.0 O C:HOH2162 2.4 29.7 1.0 OD1 C:ASP267 2.4 36.0 1.0 O C:PHE264 2.4 31.2 1.0 O C:HOH2166 2.5 45.5 1.0 O C:HOH2160 2.6 28.3 1.0 CG C:ASP267 3.4 39.6 1.0 CG C:ASN268 3.4 29.1 1.0 CG C:ASP263 3.5 37.3 1.0 C C:PHE264 3.5 33.9 1.0 OD2 C:ASP267 3.8 40.2 1.0 O C:HOH2167 3.9 45.5 1.0 N C:PHE264 3.9 27.8 1.0 ND2 C:ASN268 4.0 28.6 1.0 O C:HOH2161 4.1 28.6 1.0 OD2 C:ASP263 4.1 36.5 1.0 CA C:PHE264 4.1 33.2 1.0 CB C:PHE264 4.4 39.9 1.0 N C:ASN268 4.4 29.6 1.0 C C:ASP263 4.5 32.6 1.0 N C:THR265 4.6 39.2 1.0 C C:ASP267 4.6 27.5 1.0 CA C:ASP263 4.7 27.9 1.0 O C:HOH2159 4.7 41.5 1.0 CB C:ASP263 4.7 29.6 1.0 CB C:ASN268 4.7 30.5 1.0 CA C:ASN268 4.7 31.3 1.0 O C:HOH2165 4.8 44.4 1.0 CB C:ASP267 4.8 34.3 1.0 CA C:THR265 4.8 19.7 1.0 O C:ASP267 4.9 36.8 1.0 N C:ASP267 5.0 31.4 1.0

Calcium binding site 7 out of 9 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca545 b:43.6 occ:1.00 OD1 D:ASP215 2.2 46.4 1.0 OD1 D:ASN217 2.2 63.1 1.0 ND2 D:ASN217 2.2 54.6 1.0 OD1 D:ASP223 2.2 42.4 1.0 O D:GLU221 2.3 47.9 1.0 OD1 D:ASN219 2.4 60.1 1.0 OE2 D:GLU224 2.5 43.3 1.0 CG D:ASN217 2.5 55.5 1.0 OE1 D:GLU224 2.6 44.0 1.0 CD D:GLU224 2.8 44.2 1.0 CG D:ASP223 3.3 47.9 1.0 CG D:ASN219 3.4 66.5 1.0 CG D:ASP215 3.4 53.9 1.0 C D:GLU221 3.5 50.2 1.0 OD2 D:ASP223 3.8 54.3 1.0 ND2 D:ASN219 3.9 67.1 1.0 CB D:ASN217 4.0 49.5 1.0 N D:GLU221 4.0 52.2 1.0 CA D:ASP215 4.1 47.7 1.0 N D:ASP223 4.1 45.8 1.0 CB D:ASP215 4.2 47.3 1.0 N D:ASN219 4.2 50.7 1.0 CA D:GLU221 4.3 55.0 1.0 CG D:GLU224 4.3 44.3 1.0 OD2 D:ASP215 4.3 57.9 1.0 O D:HOH2106 4.4 40.1 1.0 N D:ALA222 4.5 38.8 1.0 N D:ASN217 4.5 45.6 1.0 C D:ASP215 4.5 51.9 1.0 CB D:ASN219 4.6 62.7 1.0 N D:GLY218 4.6 51.8 1.0 N D:GLU224 4.6 39.9 1.0 CB D:ASP223 4.6 37.2 1.0 CA D:ALA222 4.7 41.0 1.0 N D:GLY220 4.7 57.0 1.0 CA D:ASN217 4.7 49.3 1.0 CA D:ASN219 4.7 59.8 1.0 CB D:GLU221 4.8 61.4 1.0 C D:ASN219 4.8 59.4 1.0 CA D:ASP223 4.8 41.3 1.0 C D:ASN217 4.9 56.3 1.0 C D:ALA222 4.9 44.2 1.0 O D:ASP215 5.0 55.4 1.0

Calcium binding site 8 out of 9 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca546 b:30.2 occ:1.00 OD1 D:ASN268 2.2 25.6 1.0 O D:HOH2152 2.3 25.2 1.0 OD1 D:ASP267 2.3 27.3 1.0 OD1 D:ASP263 2.4 34.6 1.0 O D:PHE264 2.4 27.0 1.0 O D:HOH2156 2.5 40.5 1.0 O D:HOH2150 2.6 28.7 1.0 CG D:ASN268 3.3 29.3 1.0 CG D:ASP267 3.4 35.2 1.0 C D:PHE264 3.5 28.2 1.0 CG D:ASP263 3.6 34.5 1.0 OD2 D:ASP267 3.7 30.6 1.0 O D:HOH2157 3.8 33.1 1.0 ND2 D:ASN268 3.9 20.0 1.0 N D:PHE264 4.0 26.2 1.0 CA D:PHE264 4.2 24.5 1.0 OD2 D:ASP263 4.2 34.8 1.0 O D:HOH2151 4.2 31.0 1.0 O D:HOH2149 4.3 56.6 1.0 N D:ASN268 4.4 28.6 1.0 CB D:PHE264 4.4 27.3 1.0 O D:HOH2155 4.5 38.4 1.0 C D:ASP267 4.5 30.2 1.0 CB D:ASN268 4.5 28.8 1.0 C D:ASP263 4.6 28.7 1.0 CA D:ASN268 4.6 31.9 1.0 N D:THR265 4.6 33.5 1.0 CB D:ASP267 4.7 32.5 1.0 O D:HOH2060 4.7 65.9 1.0 CB D:ASP263 4.8 28.3 1.0 CA D:ASP263 4.8 26.1 1.0 CA D:THR265 4.9 25.9 1.0 O D:ASP267 4.9 26.4 1.0 N D:ASP267 4.9 34.0 1.0 CA D:ASP267 4.9 32.3 1.0

Calcium binding site 9 out of 9 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Kestose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca547 b:56.3 occ:1.00 O D:SER402 2.4 55.7 1.0 O D:HOH2289 2.5 44.6 1.0 O D:HOH2234 2.5 47.2 1.0 O D:HOH2244 2.5 51.4 1.0 O C:HOH2241 2.6 44.8 1.0 O D:HOH2235 2.6 46.2 1.0 O C:HOH2240 2.6 47.9 1.0 C D:SER402 3.5 59.6 1.0 CA D:SER402 4.0 60.1 1.0 OD2 C:ASP432 4.1 50.0 1.0 CB D:SER402 4.2 59.5 1.0 O D:HOH2236 4.4 51.2 1.0 N D:ASN403 4.6 59.1 1.0 OD1 C:ASP432 4.6 49.3 1.0 O D:LYS437 4.7 65.5 1.0 CG C:ASP432 4.8 40.0 1.0 CB D:ASN403 4.8 49.3 1.0 O D:ASN403 4.8 45.6 1.0 C D:ASN403 4.9 43.1 1.0 CA D:ASN403 5.0 46.4 1.0

S.Culurgioni, G.Harris, A.K.Singh, S.J.King, M.A.Walsh. Structural Basis For Regulation and Specificity of Fructooligosaccharide Import in Streptococcus Pneumoniae. Structure V. 25 79 2017.
ISSN: ISSN 1878-4186
PubMed: 27939783
DOI: 10.1016/J.STR.2016.11.008