Atomistry » Calcium » PDB 5g3a-5gti » 5g60
Atomistry »
  Calcium »
    PDB 5g3a-5gti »
      5g60 »

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

Protein crystallography data

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

Other elements in 5g60:

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

Calcium Binding Sites:

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 5g60

Go back to Calcium Binding Sites List in 5g60
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 5g60

Go back to Calcium Binding Sites List in 5g60
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 5g60

Go back to Calcium Binding Sites List in 5g60
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 5g60

Go back to Calcium Binding Sites List in 5g60
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 5g60

Go back to Calcium Binding Sites List in 5g60
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 5g60

Go back to Calcium Binding Sites List in 5g60
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 5g60

Go back to Calcium Binding Sites List in 5g60
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 5g60

Go back to Calcium Binding Sites List in 5g60
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

Reference:

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
Page generated: Sun Jul 14 19:30:41 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy