Calcium in PDB 5a5a: The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Pnp-T-Antigen

The structure of The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Pnp-T-Antigen, PDB code: 5a5a was solved by K.J.Gregg, M.D.L.Suits, L.Deng, D.J.Vocadlo, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.64 / 1.75
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.861, 121.618, 139.403, 90.00, 90.00, 90.00
R / Rfree (%)	14.73 / 17.401

The structure of The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Pnp-T-Antigen also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Pnp-T-Antigen (pdb code 5a5a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Pnp-T-Antigen, PDB code: 5a5a:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Pnp-T-Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Pnp-T-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2427 b:15.8 occ:1.00 OD1 A:ASP577 2.3 19.7 1.0 OD1 A:ASP581 2.3 18.4 1.0 O A:ASN583 2.3 19.6 1.0 OD1 A:ASN579 2.4 15.7 1.0 O A:HOH3408 2.4 16.1 1.0 OD1 A:ASP588 2.4 14.2 1.0 OD2 A:ASP588 2.5 14.2 1.0 CG A:ASP588 2.8 13.0 1.0 CG A:ASP581 3.2 18.9 1.0 CG A:ASN579 3.4 17.1 1.0 CG A:ASP577 3.5 18.0 1.0 C A:ASN583 3.5 20.8 1.0 OD2 A:ASP581 3.6 18.0 1.0 ND2 A:ASN579 3.9 15.9 1.0 N A:ASN583 4.1 22.3 1.0 N A:ALA578 4.2 17.0 1.0 N A:ASN579 4.2 17.6 1.0 CA A:ASP577 4.3 16.4 1.0 CA A:ASN583 4.3 22.2 1.0 OD2 A:ASP577 4.3 18.3 1.0 CB A:ASP577 4.3 17.1 1.0 CB A:ASP588 4.3 12.9 1.0 N A:ASP581 4.4 19.8 1.0 N A:VAL584 4.4 16.6 1.0 CB A:ASP581 4.5 19.0 1.0 CA A:VAL584 4.5 15.2 1.0 OD1 A:ASP585 4.5 15.4 1.0 CB A:ASN583 4.5 25.9 1.0 CB A:ASN579 4.7 16.5 1.0 C A:ASP577 4.8 16.9 1.0 N A:LYS582 4.8 20.7 1.0 CA A:ASP581 4.8 19.5 1.0 CA A:ASN579 4.8 17.9 1.0 N A:ALA580 4.9 19.4 1.0 C A:ASP581 4.9 19.8 1.0 C A:ASN579 4.9 19.1 1.0 N A:ASP585 4.9 14.8 1.0 N A:ASP588 4.9 12.5 1.0

Calcium binding site 2 out of 3 in the The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Pnp-T-Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Pnp-T-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2429 b:12.6 occ:1.00 O A:TRP1284 2.3 11.2 1.0 OE2 A:GLU1235 2.3 12.3 1.0 O A:GLU1281 2.4 13.3 1.0 O A:HOH4334 2.4 12.9 1.0 O A:ASP1233 2.4 12.2 1.0 OD2 A:ASP1411 2.5 13.6 1.0 OD1 A:ASP1411 2.6 12.3 1.0 CG A:ASP1411 2.9 13.5 1.0 CD A:GLU1235 3.5 13.8 1.0 C A:GLU1281 3.5 13.7 1.0 C A:TRP1284 3.6 12.1 1.0 C A:ASP1233 3.6 12.0 1.0 CG A:GLU1235 4.0 13.5 1.0 N A:TRP1284 4.2 11.9 1.0 CA A:ASP1233 4.3 12.9 1.0 CA A:TRP1284 4.4 12.3 1.0 OG A:SER1285 4.4 12.5 1.0 CA A:GLU1281 4.4 14.6 1.0 N A:GLU1281 4.4 14.2 1.0 N A:GLY1282 4.4 14.0 1.0 CB A:ASP1233 4.4 14.4 1.0 CB A:ASP1411 4.4 12.1 1.0 O A:HOH3710 4.4 24.4 1.0 CA A:GLY1282 4.5 12.9 1.0 OD1 A:ASN1412 4.5 16.9 1.0 OE1 A:GLU1235 4.5 12.6 1.0 N A:SER1285 4.6 12.2 1.0 CB A:GLU1281 4.6 16.9 1.0 CB A:PHE1234 4.6 11.8 1.0 N A:PHE1234 4.6 11.7 1.0 CA A:SER1285 4.7 12.2 1.0 CB A:TRP1284 4.8 12.3 1.0 C A:GLY1282 4.9 13.3 1.0 N A:ASN1283 4.9 12.3 1.0 CA A:PHE1234 4.9 11.8 1.0 N A:GLU1235 4.9 11.2 1.0 C A:PHE1234 4.9 11.9 1.0

Calcium binding site 3 out of 3 in the The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Pnp-T-Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Pnp-T-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2430 b:13.7 occ:1.00 O A:ASP1091 2.4 14.4 1.0 O A:HOH4098 2.4 14.2 1.0 OD1 A:ASN1090 2.4 14.1 1.0 O A:GLY1063 2.4 12.6 1.0 O A:HOH4097 2.4 12.8 1.0 OD2 A:ASP1207 2.5 14.8 1.0 OD1 A:ASP1207 2.6 13.4 1.0 CG A:ASP1207 2.8 13.9 1.0 C A:GLY1063 3.4 12.4 1.0 C A:ASP1091 3.5 15.3 1.0 CG A:ASN1090 3.6 14.9 1.0 CA A:GLY1063 3.8 12.0 1.0 N A:ASP1091 3.9 16.4 1.0 CA A:ASP1091 4.2 16.1 1.0 ND2 A:ASN1090 4.2 14.6 1.0 O A:HOH4145 4.3 14.3 1.0 CB A:ASP1207 4.4 13.1 1.0 C A:ASN1090 4.4 16.3 1.0 O A:HOH4100 4.5 19.3 1.0 CB A:ASP1091 4.6 17.7 1.0 N A:PHE1064 4.6 12.3 1.0 N A:MET1092 4.6 14.8 1.0 NE2 A:HIS1160 4.7 14.0 1.0 O A:HOH3516 4.7 23.3 1.0 OD1 A:ASN1065 4.7 12.9 1.0 CB A:ASN1090 4.7 14.7 1.0 CA A:MET1092 4.9 14.2 1.0 CB A:PHE1064 4.9 13.3 1.0 CA A:ASN1090 4.9 15.3 1.0 O A:HOH3508 4.9 25.5 1.0 C1 A:EDO2455 5.0 31.8 1.0

K.J.Gregg, M.D.L.Suits, L.Deng, D.J.Vocadlo, A.B.Boraston. Structural Analysis of A Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights Into Its Mechanism. J.Biol.Chem. V. 290 25657 2015.
ISSN: ISSN 0021-9258
PubMed: 26304114
DOI: 10.1074/JBC.M115.680470