Calcium in PDB 5g61: S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Fructo-Nystose

The structure of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Fructo-Nystose, PDB code: 5g61 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)	90.37 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.370, 135.910, 121.190, 90.00, 93.28, 90.00
R / Rfree (%)	18.6 / 25.1

The binding sites of Calcium atom in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Fructo-Nystose (pdb code 5g61). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Fructo-Nystose, PDB code: 5g61:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Fructo-Nystose


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 Fructo-Nystose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca600 b:30.7 occ:1.00 OD1 A:ASN217 2.1 36.9 1.0 ND2 A:ASN217 2.3 32.5 1.0 O A:GLU221 2.3 25.8 1.0 OD1 A:ASP223 2.4 28.1 1.0 OD1 A:ASP215 2.4 35.2 1.0 OD1 A:ASN219 2.4 31.9 1.0 OE2 A:GLU224 2.5 32.6 1.0 CG A:ASN217 2.5 29.6 1.0 OE1 A:GLU224 2.6 27.0 1.0 CD A:GLU224 2.8 28.7 1.0 CG A:ASP223 3.4 29.9 1.0 CG A:ASN219 3.4 30.4 1.0 C A:GLU221 3.5 34.3 1.0 CG A:ASP215 3.6 32.6 1.0 OD2 A:ASP223 3.8 28.5 1.0 ND2 A:ASN219 3.9 26.1 1.0 CB A:ASN217 4.0 33.2 1.0 N A:GLU221 4.0 35.3 1.0 N A:ASP223 4.1 32.7 1.0 CA A:ASP215 4.2 30.6 1.0 CG A:GLU224 4.2 31.0 1.0 CA A:GLU221 4.3 42.8 1.0 N A:ASN219 4.3 33.3 1.0 CB A:ASP215 4.4 33.0 1.0 N A:GLU224 4.5 28.8 1.0 OD2 A:ASP215 4.5 34.5 1.0 N A:GLY218 4.5 27.4 1.0 N A:ALA222 4.5 35.5 1.0 CB A:ASP223 4.6 30.5 1.0 N A:ASN217 4.6 35.4 1.0 O A:HOH2134 4.6 31.9 1.0 C A:ASP215 4.6 31.8 1.0 CB A:ASN219 4.6 24.3 1.0 CA A:ASN217 4.7 33.0 1.0 N A:GLY220 4.7 30.8 1.0 CA A:ALA222 4.8 39.1 1.0 CA A:ASP223 4.8 31.1 1.0 CA A:ASN219 4.8 24.5 1.0 C A:ASN217 4.8 30.3 1.0 CB A:GLU221 4.8 39.9 1.0 C A:ASN219 4.9 33.8 1.0 C A:ALA222 4.9 34.8 1.0 O A:ASP215 4.9 37.3 1.0 CB A:GLU224 5.0 25.8 1.0 C A:ASP223 5.0 33.1 1.0

Calcium binding site 2 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Fructo-Nystose


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 Fructo-Nystose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:23.7 occ:1.00 OD1 A:ASP263 2.1 30.4 1.0 OD1 A:ASP267 2.3 22.6 1.0 OD1 A:ASN268 2.3 21.9 1.0 O A:HOH2179 2.4 21.2 1.0 O A:HOH2183 2.4 28.3 1.0 O A:PHE264 2.6 25.0 1.0 O A:HOH2178 2.6 24.5 1.0 CG A:ASP263 3.1 26.4 1.0 OD2 A:ASP263 3.4 28.4 1.0 CG A:ASP267 3.5 25.9 1.0 CG A:ASN268 3.5 23.6 1.0 C A:PHE264 3.6 28.2 1.0 N A:PHE264 3.9 24.8 1.0 OD2 A:ASP267 3.9 30.9 1.0 ND2 A:ASN268 4.1 23.8 1.0 O A:HOH2184 4.1 33.6 1.0 CA A:PHE264 4.2 28.5 1.0 O A:HOH2181 4.4 29.2 1.0 N A:ASN268 4.4 24.0 1.0 CB A:ASP263 4.4 22.9 1.0 C A:ASP263 4.5 25.4 1.0 CB A:PHE264 4.5 25.5 1.0 C A:ASP267 4.6 26.8 1.0 CA A:ASP263 4.6 24.4 1.0 N A:THR265 4.6 30.7 1.0 CB A:ASN268 4.7 19.9 1.0 CA A:ASN268 4.7 23.9 1.0 O A:HOH2177 4.7 31.6 1.0 CB A:ASP267 4.8 28.0 1.0 CA A:THR265 4.8 25.2 1.0 N A:ASP267 4.8 24.8 1.0 CA A:ASP267 4.9 27.3 1.0 C A:THR265 5.0 26.0 1.0

Calcium binding site 3 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Fructo-Nystose


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 Fructo-Nystose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca600 b:41.1 occ:1.00 OD1 B:ASN217 2.1 42.2 1.0 OD1 B:ASP215 2.4 44.1 1.0 OE2 B:GLU224 2.5 33.0 1.0 OD1 B:ASP223 2.5 39.5 1.0 O B:GLU221 2.5 35.8 1.0 OE1 B:GLU224 2.6 31.8 1.0 OD1 B:ASN219 2.6 45.3 1.0 CD B:GLU224 2.8 36.9 1.0 CG B:ASN217 3.1 41.4 1.0 CG B:ASN219 3.4 44.3 1.0 CG B:ASP223 3.5 35.4 1.0 CG B:ASP215 3.6 46.4 1.0 ND2 B:ASN217 3.6 37.9 1.0 C B:GLU221 3.6 44.5 1.0 N B:GLU221 3.9 52.3 1.0 OD2 B:ASP223 3.9 32.2 1.0 ND2 B:ASN219 3.9 42.6 1.0 N B:ASN219 4.1 49.6 1.0 CA B:ASP215 4.2 37.4 1.0 CA B:GLU221 4.3 51.9 1.0 N B:GLY218 4.3 46.9 1.0 N B:ASP223 4.3 34.5 1.0 CG B:GLU224 4.3 35.5 1.0 CB B:ASP215 4.4 35.5 1.0 CB B:ASN217 4.4 40.2 1.0 OD2 B:ASP215 4.5 54.7 1.0 CB B:ASN219 4.5 51.7 1.0 C B:ASP215 4.6 40.4 1.0 N B:ASN217 4.6 43.6 1.0 N B:GLY220 4.6 47.7 1.0 C B:ASN217 4.7 46.9 1.0 N B:GLU224 4.7 32.7 1.0 CA B:ASN219 4.7 38.4 1.0 CB B:GLU221 4.7 48.0 1.0 N B:ALA222 4.7 42.5 1.0 CA B:ASN217 4.7 44.7 1.0 CB B:ASP223 4.8 32.5 1.0 O B:ASP215 4.8 43.7 1.0 C B:GLY220 4.8 53.1 1.0 C B:ASN219 4.9 48.5 1.0 CA B:ALA222 5.0 36.7 1.0

Calcium binding site 4 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Fructo-Nystose


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 Fructo-Nystose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:22.6 occ:1.00 OD1 B:ASP267 2.3 30.0 1.0 OD1 B:ASP263 2.4 30.1 1.0 O B:HOH2146 2.4 22.9 1.0 OD1 B:ASN268 2.4 25.4 1.0 O B:HOH2152 2.4 23.0 1.0 O B:PHE264 2.5 25.6 1.0 O B:HOH2148 2.6 19.4 1.0 CG B:ASP267 3.5 32.1 1.0 CG B:ASN268 3.5 22.8 1.0 C B:PHE264 3.5 24.1 1.0 CG B:ASP263 3.5 22.7 1.0 O B:HOH2153 3.9 26.3 1.0 N B:PHE264 3.9 24.7 1.0 OD2 B:ASP267 3.9 31.8 1.0 OD2 B:ASP263 4.1 28.2 1.0 ND2 B:ASN268 4.1 21.0 1.0 CA B:PHE264 4.2 22.2 1.0 O B:HOH2147 4.2 29.6 1.0 CB B:PHE264 4.4 23.2 1.0 N B:ASN268 4.4 24.7 1.0 C B:ASP267 4.5 24.7 1.0 C B:ASP263 4.5 24.8 1.0 N B:THR265 4.6 26.3 1.0 CB B:ASP263 4.7 23.1 1.0 CB B:ASN268 4.7 21.8 1.0 CA B:ASP263 4.7 21.8 1.0 CA B:ASN268 4.7 26.1 1.0 CB B:ASP267 4.8 28.0 1.0 CA B:THR265 4.8 31.3 1.0 O B:HOH2151 4.8 30.5 1.0 N B:ASP267 4.8 27.0 1.0 O B:ASP267 4.8 28.7 1.0 CA B:ASP267 4.9 26.9 1.0 CD2 B:PHE264 5.0 29.5 1.0

Calcium binding site 5 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Fructo-Nystose


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 Fructo-Nystose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca600 b:41.5 occ:1.00 OD1 C:ASN217 1.2 47.9 1.0 OD1 C:ASP223 2.1 35.2 1.0 OD1 C:ASP215 2.2 33.6 1.0 CG C:ASN217 2.3 40.8 1.0 O C:GLU221 2.6 33.4 1.0 OD1 C:ASN219 2.7 45.5 1.0 OE2 C:GLU224 2.7 39.9 1.0 ND2 C:ASN217 2.7 36.7 1.0 OE1 C:GLU224 2.8 39.0 1.0 CD C:GLU224 2.9 34.5 1.0 CG C:ASP223 3.0 38.3 1.0 CG C:ASN219 3.2 39.7 1.0 OD2 C:ASP223 3.3 35.8 1.0 ND2 C:ASN219 3.3 43.3 1.0 CG C:ASP215 3.5 36.5 1.0 C C:GLU221 3.6 38.8 1.0 CB C:ASN217 3.7 37.2 1.0 N C:GLU221 4.0 43.7 1.0 N C:ASP223 4.1 29.5 1.0 CB C:GLU221 4.1 41.7 1.0 CA C:GLU221 4.1 39.4 1.0 CG C:GLU224 4.2 35.7 1.0 OD2 C:ASP215 4.2 34.2 1.0 N C:ASN219 4.3 37.4 1.0 CB C:ASP223 4.3 33.0 1.0 CB C:ASN219 4.4 39.1 1.0 CA C:ASN217 4.5 34.6 1.0 CB C:ASP215 4.5 35.5 1.0 C C:ASN217 4.6 31.8 1.0 N C:GLU224 4.6 30.8 1.0 CA C:ASP215 4.6 36.2 1.0 N C:ASN217 4.7 37.8 1.0 N C:ALA222 4.7 38.7 1.0 CA C:ASP223 4.7 32.9 1.0 CA C:ASN219 4.7 44.2 1.0 O C:HOH2099 4.7 29.6 1.0 N C:GLY220 4.7 43.7 1.0 O C:ASN217 4.8 43.7 1.0 N C:GLY218 4.9 42.1 1.0 C C:ASN219 4.9 38.8 1.0 C C:ASP223 4.9 33.4 1.0 CA C:ALA222 5.0 34.2 1.0

Calcium binding site 6 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Fructo-Nystose


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 Fructo-Nystose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:30.4 occ:1.00 OD1 C:ASP263 2.3 25.6 1.0 OD1 C:ASN268 2.3 29.0 1.0 OD1 C:ASP267 2.3 26.8 1.0 O C:HOH2141 2.4 24.9 1.0 O C:HOH2145 2.6 29.5 1.0 O C:PHE264 2.6 26.0 1.0 O C:HOH2147 2.8 24.3 1.0 CG C:ASP267 3.4 30.3 1.0 CG C:ASN268 3.4 28.4 1.0 CG C:ASP263 3.5 28.7 1.0 O C:HOH2140 3.7 31.8 1.0 C C:PHE264 3.7 25.2 1.0 OD2 C:ASP267 3.8 22.8 1.0 ND2 C:ASN268 4.0 20.1 1.0 OD2 C:ASP263 4.0 27.9 1.0 N C:PHE264 4.1 32.3 1.0 O C:HOH2138 4.2 21.5 1.0 CA C:PHE264 4.3 23.8 1.0 O C:HOH2146 4.3 24.7 1.0 N C:ASN268 4.4 25.6 1.0 O C:HOH2144 4.4 28.8 1.0 C C:ASP267 4.5 25.8 1.0 CB C:PHE264 4.5 24.5 1.0 C C:ASP263 4.6 27.1 1.0 CB C:ASN268 4.6 22.6 1.0 CA C:ASN268 4.6 28.8 1.0 CB C:ASP263 4.6 28.1 1.0 CB C:ASP267 4.7 26.1 1.0 N C:THR265 4.7 29.5 1.0 CA C:ASP263 4.8 24.7 1.0 O C:ASP267 4.8 30.8 1.0 N C:ASP267 4.9 27.3 1.0 CA C:ASP267 4.9 28.1 1.0 CA C:THR265 4.9 29.8 1.0

Calcium binding site 7 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Fructo-Nystose


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 Fructo-Nystose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca600 b:35.2 occ:1.00 OD1 D:ASN217 1.5 37.7 1.0 CG D:ASN217 2.2 32.0 1.0 OD1 D:ASP223 2.3 32.5 1.0 OD1 D:ASP215 2.4 33.6 1.0 O D:GLU221 2.4 30.1 1.0 ND2 D:ASN217 2.4 25.9 1.0 OD1 D:ASN219 2.6 40.4 1.0 OE2 D:GLU224 2.6 40.8 1.0 OE1 D:GLU224 2.8 38.0 1.0 CD D:GLU224 2.9 34.3 1.0 CG D:ASN219 3.2 37.1 1.0 CG D:ASP223 3.4 35.5 1.0 ND2 D:ASN219 3.5 47.3 1.0 C D:GLU221 3.5 36.4 1.0 CG D:ASP215 3.6 35.8 1.0 CB D:ASN217 3.7 37.2 1.0 OD2 D:ASP223 3.8 33.4 1.0 N D:GLU221 4.0 47.4 1.0 CA D:GLU221 4.1 45.4 1.0 N D:ASN219 4.1 36.9 1.0 CB D:GLU221 4.1 46.0 1.0 CG D:GLU224 4.2 33.6 1.0 N D:ASP223 4.2 34.6 1.0 CB D:ASN219 4.4 38.7 1.0 OD2 D:ASP215 4.4 34.8 1.0 N D:GLY218 4.4 35.8 1.0 CA D:ASN217 4.5 39.3 1.0 N D:ASN217 4.5 37.8 1.0 CA D:ASP215 4.5 35.5 1.0 CB D:ASP215 4.5 33.0 1.0 CB D:ASP223 4.6 32.2 1.0 N D:ALA222 4.6 39.4 1.0 CA D:ASN219 4.6 38.1 1.0 N D:GLU224 4.7 36.2 1.0 N D:GLY220 4.8 43.7 1.0 O D:HOH2100 4.8 27.7 1.0 C D:ASN217 4.8 39.5 1.0 C D:ASP215 4.8 37.1 1.0 CA D:ASP223 4.9 29.3 1.0 CA D:ALA222 4.9 39.8 1.0 C D:ASN219 4.9 37.8 1.0

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


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 Fructo-Nystose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca601 b:29.6 occ:1.00 OD1 D:ASN268 2.3 26.1 1.0 OD1 D:ASP263 2.3 27.3 1.0 O D:HOH2141 2.4 28.3 1.0 OD1 D:ASP267 2.5 35.3 1.0 O D:PHE264 2.6 27.8 1.0 O D:HOH2254 2.6 27.2 1.0 O D:HOH2140 2.7 25.3 1.0 CG D:ASN268 3.4 25.6 1.0 CG D:ASP263 3.5 26.9 1.0 CG D:ASP267 3.6 30.8 1.0 C D:PHE264 3.7 29.9 1.0 ND2 D:ASN268 4.0 18.7 1.0 OD2 D:ASP267 4.1 27.5 1.0 OD2 D:ASP263 4.1 25.4 1.0 O D:HOH2145 4.1 22.5 1.0 N D:PHE264 4.1 26.7 1.0 N D:ASN268 4.3 26.2 1.0 O D:HOH2139 4.3 24.5 1.0 CA D:PHE264 4.3 26.4 1.0 O D:HOH2143 4.4 31.7 1.0 C D:ASP267 4.5 29.6 1.0 CB D:PHE264 4.5 26.2 1.0 CB D:ASN268 4.6 18.3 1.0 CA D:ASN268 4.6 24.4 1.0 C D:ASP263 4.7 26.2 1.0 N D:THR265 4.7 28.8 1.0 CB D:ASP263 4.7 21.0 1.0 O D:ASP267 4.8 27.8 1.0 CA D:ASP263 4.8 23.0 1.0 CB D:ASP267 4.9 25.6 1.0 N D:ASP267 4.9 27.5 1.0 CA D:THR265 4.9 25.8 1.0 CA D:ASP267 5.0 25.5 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