Calcium in PDB 5g5y: S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure

The structure of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure, PDB code: 5g5y 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)	70.76 / 1.73
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	66.070, 72.170, 77.660, 108.02, 104.99, 92.49
R / Rfree (%)	16.1 / 19.3

The structure of S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure also contains other interesting chemical elements:

Zinc

(Zn)

10 atoms

The binding sites of Calcium atom in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure (pdb code 5g5y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure, PDB code: 5g5y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


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 Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:35.1 occ:1.00 OD1 A:ASP215 2.1 35.4 1.0 OD1 A:ASP223 2.1 30.1 1.0 O A:GLU221 2.4 38.8 1.0 OD1 A:ASN219 2.5 41.8 1.0 OD1 A:ASN217 2.5 36.1 1.0 OE2 A:GLU224 2.6 29.3 1.0 OE1 A:GLU224 2.6 30.5 1.0 CD A:GLU224 2.9 33.5 1.0 CG A:ASP215 3.3 38.1 1.0 CG A:ASP223 3.3 29.1 1.0 CG A:ASN217 3.4 38.1 1.0 CG A:ASN219 3.4 39.8 1.0 C A:GLU221 3.5 45.1 1.0 ND2 A:ASN217 3.7 38.6 1.0 ND2 A:ASN219 3.9 36.0 1.0 N A:GLU221 4.0 49.1 1.0 OD2 A:ASP223 4.0 31.9 1.0 N A:ASP223 4.1 32.9 1.0 CA A:ASP215 4.1 34.9 1.0 CB A:ASP215 4.1 37.2 1.0 CA A:GLU221 4.2 48.5 1.0 OD2 A:ASP215 4.2 38.9 1.0 CG A:GLU224 4.3 30.1 1.0 N A:ASN219 4.3 41.7 1.0 CB A:GLU221 4.4 50.8 1.0 O A:HOH2306 4.5 36.7 1.0 CB A:ASP223 4.5 30.9 1.0 C A:ASP215 4.5 39.6 1.0 N A:ALA222 4.6 40.8 1.0 N A:GLU224 4.6 28.7 1.0 CB A:ASN217 4.6 36.2 1.0 N A:ASN217 4.6 35.0 1.0 CB A:ASN219 4.7 40.0 1.0 N A:GLY218 4.7 38.6 1.0 CA A:ASP223 4.7 30.6 1.0 N A:GLY220 4.8 46.5 1.0 CA A:ASN219 4.8 41.0 1.0 CA A:ALA222 4.8 38.9 1.0 C A:ASN217 4.9 38.7 1.0 C A:ASN219 4.9 41.6 1.0 CA A:ASN217 4.9 37.5 1.0 O A:ASP215 4.9 37.9 1.0 C A:ALA222 5.0 36.5 1.0

Calcium binding site 2 out of 4 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


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 Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:24.7 occ:1.00 OD1 A:ASN268 2.3 18.1 1.0 O A:HOH2392 2.3 34.6 1.0 O A:PHE264 2.4 15.8 1.0 OD1 A:ASP263 2.4 19.9 1.0 OD1 A:ASP267 2.5 17.1 1.0 O A:HOH2396 2.5 28.5 1.0 O A:HOH2391 2.6 14.3 1.0 CG A:ASN268 3.3 17.6 1.0 C A:PHE264 3.5 14.8 1.0 CG A:ASP267 3.6 18.6 1.0 CG A:ASP263 3.6 18.0 1.0 N A:PHE264 3.7 14.3 1.0 ND2 A:ASN268 3.8 17.0 1.0 OD2 A:ASP267 4.0 18.6 1.0 CA A:PHE264 4.0 15.2 1.0 O A:HOH2398 4.1 21.5 1.0 O A:HOH2390 4.1 26.7 1.0 OD2 A:ASP263 4.2 19.5 1.0 CB A:PHE264 4.3 16.2 1.0 N A:ASN268 4.4 14.1 1.0 C A:ASP263 4.5 14.7 1.0 O A:HOH2389 4.5 42.5 1.0 C A:ASP267 4.5 15.9 1.0 CB A:ASN268 4.5 16.0 1.0 N A:THR265 4.6 14.2 1.0 O A:HOH2179 4.6 41.8 1.0 CA A:ASN268 4.6 15.3 1.0 O A:HOH2395 4.7 40.4 1.0 CA A:ASP263 4.7 14.7 1.0 CB A:ASP263 4.8 15.5 1.0 CA A:THR265 4.8 14.4 1.0 O A:ASP267 4.8 15.3 1.0 CB A:ASP267 4.8 16.8 1.0 N A:ASP267 4.9 14.8 1.0 CA A:ASP267 5.0 15.7 1.0

Calcium binding site 3 out of 4 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


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 Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:23.8 occ:1.00 OD1 B:ASN217 2.1 23.9 1.0 OD1 B:ASP215 2.3 28.5 1.0 OD1 B:ASP223 2.3 25.8 1.0 O B:GLU221 2.4 26.9 1.0 OD1 B:ASN219 2.5 24.6 1.0 OE2 B:GLU224 2.5 20.9 1.0 OE1 B:GLU224 2.6 19.7 1.0 CD B:GLU224 2.8 20.7 1.0 CG B:ASN217 3.2 26.2 1.0 CG B:ASN219 3.4 26.2 1.0 CG B:ASP223 3.5 24.2 1.0 CG B:ASP215 3.5 29.6 1.0 C B:GLU221 3.6 26.2 1.0 ND2 B:ASN217 3.7 27.7 1.0 ND2 B:ASN219 3.8 25.7 1.0 OD2 B:ASP223 4.0 24.4 1.0 N B:GLU221 4.0 29.5 1.0 N B:ASP223 4.1 20.9 1.0 CA B:ASP215 4.1 24.9 1.0 N B:ASN219 4.3 32.0 1.0 CB B:ASP215 4.3 27.1 1.0 CA B:GLU221 4.3 26.9 1.0 O B:HOH2244 4.3 30.4 1.0 CG B:GLU224 4.3 20.6 1.0 N B:GLY218 4.4 28.9 1.0 OD2 B:ASP215 4.4 30.2 1.0 C B:ASP215 4.5 26.4 1.0 N B:ASN217 4.5 25.0 1.0 CB B:ASN217 4.5 26.3 1.0 CB B:GLU221 4.6 29.6 1.0 N B:ALA222 4.6 24.3 1.0 N B:GLU224 4.6 19.6 1.0 CB B:ASN219 4.6 29.5 1.0 CB B:ASP223 4.7 21.2 1.0 N B:GLY220 4.7 30.5 1.0 CA B:ASN217 4.8 25.1 1.0 C B:ASN217 4.8 26.3 1.0 CA B:ASN219 4.8 29.9 1.0 CA B:ALA222 4.8 24.4 1.0 O B:ASP215 4.8 25.1 1.0 CA B:ASP223 4.8 21.6 1.0 C B:ASN219 4.9 30.9 1.0 C B:ALA222 5.0 22.2 1.0

Calcium binding site 4 out of 4 in the S.Pneumoniae Abc-Transporter Substrate Binding Protein Fusa Apo Structure


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 Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:29.2 occ:1.00 O B:PHE264 2.3 18.0 1.0 OD1 B:ASP267 2.4 21.4 1.0 OD1 B:ASN268 2.4 20.4 1.0 O B:HOH2330 2.4 32.3 1.0 OD1 B:ASP263 2.5 23.8 1.0 O B:HOH2328 2.5 16.1 1.0 O B:HOH2334 2.6 38.9 1.0 CG B:ASN268 3.4 19.0 1.0 C B:PHE264 3.4 16.5 1.0 CG B:ASP267 3.5 21.9 1.0 CG B:ASP263 3.6 21.3 1.0 N B:PHE264 3.7 16.0 1.0 OD2 B:ASP267 3.9 23.1 1.0 ND2 B:ASN268 3.9 18.9 1.0 O B:HOH2335 3.9 25.5 1.0 CA B:PHE264 4.0 16.6 1.0 OD2 B:ASP263 4.2 22.9 1.0 CB B:PHE264 4.2 17.3 1.0 O B:HOH2329 4.2 32.6 1.0 C B:ASP263 4.4 16.1 1.0 N B:ASN268 4.4 18.0 1.0 N B:THR265 4.5 15.6 1.0 C B:ASP267 4.6 19.4 1.0 CB B:ASN268 4.6 18.1 1.0 O B:HOH2332 4.7 48.9 1.0 CA B:ASN268 4.7 19.0 1.0 CA B:ASP263 4.7 16.8 1.0 O B:HOH2128 4.7 40.8 1.0 CB B:ASP263 4.8 18.8 1.0 CB B:ASP267 4.8 20.0 1.0 CA B:THR265 4.8 16.1 1.0 N B:ASP267 4.9 18.0 1.0 O B:ASP267 5.0 18.5 1.0 CA B:ASP267 5.0 19.2 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