Calcium in PDB 5a59: The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with T-Antigen

The structure of The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with T-Antigen, PDB code: 5a59 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)	91.74 / 2.50
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.200, 121.890, 139.340, 90.00, 90.00, 90.00
R / Rfree (%)	16.654 / 22.875

The structure of The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with 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 T-Antigen (pdb code 5a59). 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 T-Antigen, PDB code: 5a59:
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 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 T-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2427 b:19.4 occ:1.00 OD1 A:ASP581 2.3 25.2 1.0 OD1 A:ASN579 2.3 19.6 1.0 OD1 A:ASP577 2.3 23.2 1.0 O A:ASN583 2.3 32.9 1.0 OD1 A:ASP588 2.4 16.4 1.0 O A:HOH3261 2.4 15.6 1.0 OD2 A:ASP588 2.6 16.0 1.0 CG A:ASP588 2.8 16.2 1.0 CG A:ASP581 3.1 24.7 1.0 CG A:ASN579 3.3 19.7 1.0 OD2 A:ASP581 3.5 24.3 1.0 CG A:ASP577 3.5 22.9 1.0 C A:ASN583 3.5 30.3 1.0 ND2 A:ASN579 3.7 20.6 1.0 N A:ASN583 4.0 33.9 1.0 N A:ALA578 4.2 20.3 1.0 N A:ASN579 4.2 19.6 1.0 CA A:ASN583 4.3 34.2 1.0 CA A:ASP577 4.3 20.5 1.0 CB A:ASP577 4.3 21.3 1.0 N A:ASP581 4.3 21.7 1.0 CB A:ASP581 4.3 24.0 1.0 CB A:ASP588 4.3 15.4 1.0 OD2 A:ASP577 4.4 23.7 1.0 N A:VAL584 4.5 24.7 1.0 CB A:ASN583 4.5 38.0 1.0 CB A:ASN579 4.6 19.7 1.0 OD1 A:ASP585 4.6 18.1 1.0 CA A:VAL584 4.6 22.3 1.0 C A:ASP577 4.7 20.4 1.0 CA A:ASP581 4.7 23.5 1.0 N A:LYS582 4.8 28.9 1.0 C A:ASP581 4.8 25.5 1.0 CA A:ASN579 4.8 19.7 1.0 C A:ASN579 4.9 19.9 1.0 N A:ALA580 4.9 19.7 1.0 N A:ASP585 4.9 18.9 1.0 N A:ASP588 5.0 15.4 1.0

Calcium binding site 2 out of 3 in the The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with 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 T-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2429 b:13.2 occ:1.00 O A:GLU1281 2.2 17.8 1.0 OE2 A:GLU1235 2.3 16.6 1.0 O A:TRP1284 2.4 16.0 1.0 OD2 A:ASP1411 2.4 11.6 1.0 O A:HOH3886 2.4 13.9 1.0 O A:ASP1233 2.5 13.3 1.0 OD1 A:ASP1411 2.6 11.7 1.0 CG A:ASP1411 2.9 12.6 1.0 C A:GLU1281 3.4 18.7 1.0 CD A:GLU1235 3.4 15.9 1.0 C A:TRP1284 3.6 15.9 1.0 C A:ASP1233 3.7 13.4 1.0 CG A:GLU1235 3.9 15.2 1.0 OG A:SER1285 4.2 15.7 1.0 CA A:GLU1281 4.2 19.9 1.0 N A:GLU1281 4.2 18.4 1.0 OD1 A:ASN1412 4.3 16.6 1.0 N A:TRP1284 4.3 15.1 1.0 N A:GLY1282 4.3 17.2 1.0 CA A:ASP1233 4.4 13.6 1.0 CB A:ASP1411 4.4 13.7 1.0 CB A:ASP1233 4.4 13.3 1.0 CA A:TRP1284 4.5 15.4 1.0 CA A:GLY1282 4.5 17.0 1.0 OE1 A:GLU1235 4.5 15.6 1.0 CB A:GLU1281 4.5 21.3 1.0 N A:SER1285 4.6 15.8 1.0 N A:PHE1234 4.7 13.2 1.0 CB A:PHE1234 4.7 13.2 1.0 CA A:SER1285 4.8 15.2 1.0 N A:ASN1283 4.8 16.3 1.0 C A:GLY1282 4.9 16.9 1.0 CB A:TRP1284 4.9 15.9 1.0 N A:GLU1235 5.0 14.6 1.0

Calcium binding site 3 out of 3 in the The Structure of GH101 E796Q Mutant From Streptococcus Pneumoniae TIGR4 in Complex with 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 T-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2430 b:21.1 occ:1.00 OD1 A:ASN1090 2.3 15.3 1.0 O A:ASP1091 2.4 21.9 1.0 OD2 A:ASP1207 2.4 15.0 1.0 O A:GLY1063 2.5 16.3 1.0 O A:HOH3858 2.6 13.3 1.0 OD1 A:ASP1207 2.8 14.9 1.0 O A:HOH3716 2.8 24.3 1.0 CG A:ASP1207 2.9 14.8 1.0 CG A:ASN1090 3.5 15.5 1.0 C A:GLY1063 3.5 17.1 1.0 C A:ASP1091 3.5 19.6 1.0 N A:ASP1091 3.8 19.2 1.0 CA A:GLY1063 3.9 17.4 1.0 CA A:ASP1091 4.1 19.7 1.0 ND2 A:ASN1090 4.1 15.0 1.0 O A:HOH3747 4.3 24.2 1.0 C A:ASN1090 4.3 18.4 1.0 OD1 A:ASN1065 4.4 17.1 1.0 CB A:ASP1207 4.4 15.0 1.0 CB A:ASP1091 4.5 20.0 1.0 N A:MET1092 4.6 18.1 1.0 N A:PHE1064 4.7 17.2 1.0 CB A:ASN1090 4.7 16.3 1.0 O A:HOH3717 4.7 19.9 1.0 CA A:ASN1090 4.8 17.2 1.0 NE2 A:HIS1160 4.8 15.8 1.0 C1 A:EDO2455 4.9 37.2 1.0 O A:ASN1090 4.9 18.5 1.0 ND2 A:ASN1065 5.0 16.7 1.0 CB A:PHE1064 5.0 16.8 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