Calcium in PDB 5g60: S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Nystose

The structure of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Nystose, PDB code: 5g60 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)	119.54 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.030, 129.740, 120.280, 90.00, 96.34, 90.00
R / Rfree (%)	16.9 / 22.1

The structure of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Nystose also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with Nystose (pdb code 5g60). 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 Nystose, PDB code: 5g60:
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 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 Nystose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:35.0 occ:1.00 OD1 A:ASP223 2.3 31.2 1.0 OD1 A:ASP215 2.3 38.4 1.0 OD1 A:ASN217 2.3 32.4 1.0 O A:GLU221 2.3 37.0 1.0 OD1 A:ASN219 2.4 39.6 1.0 OE2 A:GLU224 2.4 29.9 1.0 OE1 A:GLU224 2.4 29.2 1.0 CD A:GLU224 2.7 30.3 1.0 CG A:ASN217 3.3 35.2 1.0 CG A:ASP223 3.4 28.7 1.0 C A:GLU221 3.5 33.8 1.0 CG A:ASN219 3.5 41.7 1.0 CG A:ASP215 3.5 43.7 1.0 ND2 A:ASN217 3.8 35.4 1.0 N A:ASP223 3.9 30.1 1.0 N A:GLU221 4.0 37.9 1.0 ND2 A:ASN219 4.0 43.0 1.0 OD2 A:ASP223 4.0 31.7 1.0 CA A:ASP215 4.1 40.9 1.0 CA A:GLU221 4.2 35.9 1.0 CG A:GLU224 4.2 31.6 1.0 CB A:ASP215 4.3 43.3 1.0 O A:HOH2150 4.3 37.4 1.0 N A:ASN219 4.3 44.6 1.0 OD2 A:ASP215 4.4 44.0 1.0 N A:GLY218 4.4 47.6 1.0 N A:ALA222 4.5 31.6 1.0 CB A:GLU221 4.5 37.3 1.0 CB A:ASP223 4.5 28.1 1.0 C A:ASP215 4.6 36.9 1.0 N A:GLU224 4.6 29.4 1.0 N A:ASN217 4.6 33.4 1.0 CB A:ASN217 4.6 35.4 1.0 CA A:ASP223 4.7 30.7 1.0 CB A:ASN219 4.7 43.4 1.0 CA A:ALA222 4.7 30.4 1.0 C A:ASN217 4.8 44.2 1.0 CA A:ASN217 4.8 38.1 1.0 C A:ALA222 4.9 29.9 1.0 CA A:ASN219 4.9 42.7 1.0 N A:GLY220 4.9 39.0 1.0 N A:PRO216 5.0 38.0 1.0 O A:ASP215 5.0 41.5 1.0 C A:ASP223 5.0 31.9 1.0

Calcium binding site 2 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with 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 Nystose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:21.4 occ:1.00 O A:PHE264 2.2 25.8 1.0 O A:HOH2205 2.3 16.6 1.0 OD1 A:ASN268 2.3 19.7 1.0 OD1 A:ASP263 2.3 20.0 1.0 O A:HOH2211 2.4 28.6 1.0 OD1 A:ASP267 2.4 22.3 1.0 O A:HOH2206 2.4 26.3 1.0 N A:PHE264 2.6 31.3 1.0 C A:PHE264 2.7 22.0 1.0 CA A:PHE264 3.2 26.8 1.0 CG A:ASN268 3.4 20.9 1.0 CG A:ASP267 3.5 20.2 1.0 CG A:ASP263 3.5 20.1 1.0 C A:ASP263 3.8 24.9 1.0 OD2 A:ASP267 3.9 21.0 1.0 ND2 A:ASN268 3.9 20.4 1.0 CB A:PHE264 3.9 28.2 1.0 N A:THR265 4.0 19.8 1.0 O A:HOH2212 4.0 28.0 1.0 O A:HOH2207 4.2 21.2 1.0 OD2 A:ASP263 4.2 23.2 1.0 O A:HOH2204 4.2 37.3 1.0 CA A:ASP263 4.4 20.4 1.0 CA A:THR265 4.6 19.7 1.0 CB A:ASP263 4.6 18.6 1.0 N A:ASN268 4.7 22.2 1.0 CB A:ASN268 4.7 20.6 1.0 C A:ASP267 4.8 22.6 1.0 O A:ASP263 4.8 22.0 1.0 CB A:ASP267 4.8 20.2 1.0 CA A:ASN268 4.9 22.8 1.0 CG A:PHE264 4.9 28.1 1.0 C A:THR265 4.9 20.2 1.0

Calcium binding site 3 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with 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 Nystose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:24.5 occ:1.00 OD1 B:ASP215 2.3 25.1 1.0 OD1 B:ASP223 2.3 29.0 1.0 O B:GLU221 2.3 28.5 1.0 OD1 B:ASN217 2.3 23.4 1.0 OE2 B:GLU224 2.4 21.5 1.0 OD1 B:ASN219 2.4 28.6 1.0 OE1 B:GLU224 2.4 22.1 1.0 CD B:GLU224 2.7 22.0 1.0 CG B:ASN217 3.2 22.7 1.0 CG B:ASN219 3.3 27.8 1.0 C B:GLU221 3.5 31.3 1.0 CG B:ASP223 3.5 27.5 1.0 CG B:ASP215 3.5 27.3 1.0 ND2 B:ASN217 3.6 24.0 1.0 ND2 B:ASN219 3.7 28.4 1.0 N B:GLU221 4.0 30.9 1.0 OD2 B:ASP223 4.0 29.1 1.0 CA B:ASP215 4.1 26.3 1.0 N B:ASP223 4.1 25.9 1.0 CG B:GLU224 4.2 23.1 1.0 CA B:GLU221 4.2 34.0 1.0 CB B:ASP215 4.3 27.8 1.0 N B:ASN219 4.3 28.3 1.0 OD2 B:ASP215 4.4 26.3 1.0 N B:GLU224 4.5 22.2 1.0 CB B:ASN217 4.5 23.1 1.0 O B:HOH2208 4.5 29.5 1.0 N B:ALA222 4.5 31.5 1.0 CB B:GLU221 4.6 38.6 1.0 C B:ASP215 4.6 24.7 1.0 N B:ASN217 4.6 25.2 1.0 CB B:ASN219 4.6 29.0 1.0 CB B:ASP223 4.7 26.3 1.0 N B:GLY220 4.7 27.1 1.0 N B:GLY218 4.7 26.4 1.0 CA B:ASN219 4.8 27.9 1.0 CA B:ASN217 4.8 24.2 1.0 CA B:ALA222 4.8 29.9 1.0 CA B:ASP223 4.8 26.6 1.0 C B:ASN217 4.8 29.1 1.0 C B:ASN219 4.9 29.2 1.0 O B:ASP215 4.9 23.3 1.0 C B:ASP223 5.0 24.9 1.0

Calcium binding site 4 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with 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 Nystose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:21.3 occ:1.00 OD1 B:ASN268 2.3 19.9 1.0 OD1 B:ASP263 2.3 21.6 1.0 OD1 B:ASP267 2.3 23.0 1.0 O B:HOH2266 2.3 19.9 1.0 O B:PHE264 2.3 19.6 1.0 O B:HOH2269 2.3 23.3 1.0 O B:HOH2265 2.4 23.8 1.0 CG B:ASN268 3.3 19.6 1.0 CG B:ASP267 3.4 21.4 1.0 C B:PHE264 3.5 20.5 1.0 CG B:ASP263 3.5 22.9 1.0 OD2 B:ASP267 3.7 25.3 1.0 ND2 B:ASN268 3.8 20.1 1.0 N B:PHE264 4.0 22.5 1.0 O B:HOH2264 4.1 24.6 1.0 O B:HOH2270 4.1 22.8 1.0 CA B:PHE264 4.1 20.6 1.0 OD2 B:ASP263 4.2 24.3 1.0 CB B:PHE264 4.3 22.2 1.0 N B:ASN268 4.4 19.7 1.0 O B:HOH2263 4.4 33.7 1.0 C B:ASP267 4.5 21.5 1.0 N B:THR265 4.5 19.0 1.0 CB B:ASN268 4.5 19.8 1.0 C B:ASP263 4.6 22.3 1.0 CA B:ASN268 4.6 19.9 1.0 CB B:ASP267 4.7 23.4 1.0 O B:HOH2268 4.7 31.2 1.0 CB B:ASP263 4.7 21.1 1.0 CA B:ASP263 4.7 22.1 1.0 CA B:THR265 4.8 16.8 1.0 O B:ASP267 4.8 23.5 1.0 N B:ASP267 4.9 20.5 1.0 CA B:ASP267 4.9 23.2 1.0 C B:THR265 5.0 17.4 1.0

Calcium binding site 5 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with 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 Nystose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:28.5 occ:1.00 OD1 C:ASP223 2.3 28.2 1.0 O C:GLU221 2.3 26.9 1.0 OD1 C:ASN217 2.3 26.3 1.0 OD1 C:ASP215 2.3 29.9 1.0 OD1 C:ASN219 2.4 32.5 1.0 OE2 C:GLU224 2.4 28.4 1.0 OE1 C:GLU224 2.4 25.5 1.0 CD C:GLU224 2.7 26.0 1.0 CG C:ASN217 3.2 28.5 1.0 CG C:ASN219 3.4 32.8 1.0 CG C:ASP223 3.4 31.6 1.0 CG C:ASP215 3.5 29.3 1.0 C C:GLU221 3.5 32.4 1.0 ND2 C:ASN217 3.6 28.8 1.0 N C:ASP223 3.9 29.2 1.0 ND2 C:ASN219 4.0 32.6 1.0 CA C:ASP215 4.0 28.0 1.0 N C:GLU221 4.0 37.6 1.0 OD2 C:ASP223 4.0 30.2 1.0 CB C:ASP215 4.2 26.9 1.0 CG C:GLU224 4.2 25.2 1.0 CA C:GLU221 4.2 37.5 1.0 N C:ASN219 4.3 34.0 1.0 OD2 C:ASP215 4.4 29.4 1.0 N C:GLY218 4.4 33.1 1.0 C C:ASP215 4.5 28.2 1.0 N C:ALA222 4.5 30.2 1.0 N C:GLU224 4.5 26.1 1.0 CB C:ASN217 4.6 29.7 1.0 O C:HOH2204 4.6 29.9 1.0 CB C:ASN219 4.6 34.7 1.0 CB C:ASP223 4.6 27.5 1.0 N C:ASN217 4.6 30.8 1.0 CB C:GLU221 4.7 44.7 1.0 CA C:ASP223 4.7 26.9 1.0 CA C:ALA222 4.8 32.5 1.0 CA C:ASN219 4.8 33.0 1.0 C C:ASN217 4.8 32.7 1.0 C C:ALA222 4.8 29.1 1.0 N C:GLY220 4.8 32.8 1.0 CA C:ASN217 4.9 30.7 1.0 C C:ASN219 4.9 30.5 1.0 O C:ASP215 4.9 27.3 1.0 N C:PRO216 5.0 29.4 1.0

Calcium binding site 6 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with 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 Nystose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca602 b:23.6 occ:1.00 OD1 C:ASN268 2.3 22.9 1.0 OD1 C:ASP263 2.3 23.5 1.0 OD1 C:ASP267 2.3 23.5 1.0 O C:HOH2256 2.3 19.0 1.0 O C:HOH2262 2.3 24.2 1.0 O C:PHE264 2.4 25.7 1.0 O C:HOH2258 2.4 23.0 1.0 CG C:ASN268 3.4 23.1 1.0 CG C:ASP267 3.4 23.2 1.0 CG C:ASP263 3.5 20.8 1.0 C C:PHE264 3.5 22.7 1.0 N C:PHE264 3.9 21.8 1.0 OD2 C:ASP267 3.9 20.8 1.0 ND2 C:ASN268 3.9 21.8 1.0 O C:HOH2257 4.1 30.2 1.0 O C:HOH2264 4.1 26.8 1.0 OD2 C:ASP263 4.2 22.4 1.0 CA C:PHE264 4.2 23.1 1.0 N C:ASN268 4.4 24.5 1.0 O C:HOH2255 4.4 34.8 1.0 C C:ASP267 4.4 22.9 1.0 CB C:PHE264 4.5 24.1 1.0 C C:ASP263 4.6 22.8 1.0 CB C:ASN268 4.6 23.4 1.0 N C:THR265 4.6 22.7 1.0 CA C:ASN268 4.6 23.7 1.0 CB C:ASP263 4.6 20.4 1.0 CA C:ASP263 4.7 20.7 1.0 CB C:ASP267 4.7 22.4 1.0 O C:HOH2261 4.8 45.5 1.0 N C:ASP267 4.8 23.4 1.0 O C:ASP267 4.8 23.4 1.0 CA C:THR265 4.8 22.6 1.0 CA C:ASP267 4.8 23.0 1.0 C C:THR265 5.0 22.5 1.0

Calcium binding site 7 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with 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 Nystose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca601 b:26.9 occ:1.00 OD1 D:ASP223 2.3 23.2 1.0 OD1 D:ASP215 2.3 27.8 1.0 OD1 D:ASN217 2.3 35.2 1.0 O D:GLU221 2.3 31.1 1.0 ND2 D:ASN217 2.3 37.3 1.0 OE2 D:GLU224 2.4 21.4 1.0 OD1 D:ASN219 2.4 27.6 1.0 OE1 D:GLU224 2.4 24.7 1.0 CG D:ASN217 2.6 31.4 1.0 CD D:GLU224 2.7 23.4 1.0 CG D:ASN219 3.3 28.5 1.0 CG D:ASP223 3.4 27.2 1.0 CG D:ASP215 3.5 30.1 1.0 C D:GLU221 3.6 32.8 1.0 ND2 D:ASN219 3.7 27.5 1.0 OD2 D:ASP223 4.0 26.8 1.0 CB D:ASN217 4.0 31.9 1.0 N D:ASP223 4.1 26.8 1.0 CA D:ASP215 4.1 28.2 1.0 CG D:GLU224 4.1 24.2 1.0 N D:GLU221 4.2 31.7 1.0 N D:ASN219 4.2 33.8 1.0 CB D:ASP215 4.3 28.7 1.0 CA D:GLU221 4.4 33.5 1.0 OD2 D:ASP215 4.4 29.5 1.0 N D:ASN217 4.5 28.9 1.0 C D:ASP215 4.5 27.1 1.0 CB D:ASN219 4.5 29.8 1.0 N D:GLY218 4.5 30.5 1.0 O D:HOH2167 4.6 29.1 1.0 N D:ALA222 4.6 29.7 1.0 N D:GLU224 4.6 26.6 1.0 CB D:ASP223 4.6 24.6 1.0 CA D:ASN217 4.6 31.2 1.0 CA D:ASN219 4.7 32.1 1.0 O D:ASP215 4.8 25.1 1.0 CA D:ALA222 4.8 32.2 1.0 C D:ASN217 4.8 32.3 1.0 CA D:ASP223 4.8 27.7 1.0 N D:GLY220 4.8 33.4 1.0 C D:ASN219 4.9 33.7 1.0 CB D:GLU221 5.0 36.6 1.0 C D:ALA222 5.0 29.3 1.0

Calcium binding site 8 out of 8 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa in Complex with 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 Nystose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca602 b:24.6 occ:0.98 OD1 D:ASP263 2.3 23.7 1.0 O D:HOH2222 2.3 24.1 1.0 O D:HOH2228 2.3 29.1 1.0 OD1 D:ASP267 2.3 24.6 1.0 OD1 D:ASN268 2.3 25.5 1.0 O D:PHE264 2.3 25.2 1.0 O D:HOH2223 2.4 28.5 1.0 CG D:ASN268 3.4 23.0 1.0 CG D:ASP267 3.4 24.9 1.0 C D:PHE264 3.4 23.5 1.0 CG D:ASP263 3.5 26.7 1.0 N D:PHE264 3.9 26.9 1.0 OD2 D:ASP267 3.9 25.1 1.0 ND2 D:ASN268 4.0 25.1 1.0 O D:HOH2230 4.1 35.5 1.0 CA D:PHE264 4.1 28.4 1.0 OD2 D:ASP263 4.1 28.2 1.0 O D:HOH2224 4.4 27.4 1.0 CB D:PHE264 4.4 28.8 1.0 N D:ASN268 4.4 25.7 1.0 C D:ASP267 4.5 24.8 1.0 N D:THR265 4.5 24.6 1.0 O D:HOH2227 4.6 38.2 1.0 C D:ASP263 4.6 24.6 1.0 CB D:ASN268 4.7 23.0 1.0 CB D:ASP267 4.7 25.7 1.0 CB D:ASP263 4.7 26.2 1.0 CA D:ASN268 4.7 25.3 1.0 CA D:THR265 4.8 23.1 1.0 CA D:ASP263 4.8 25.9 1.0 N D:ASP267 4.8 26.1 1.0 O D:ASP267 4.9 26.6 1.0 CA D:ASP267 4.9 24.4 1.0 C D:THR265 5.0 25.3 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