Calcium in PDB 5a58: The Structure of GH101 D764N Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Serinyl T-Antigen

The structure of The Structure of GH101 D764N Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Serinyl T-Antigen, PDB code: 5a58 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)	39.03 / 1.80
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.069, 121.964, 139.605, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.9

The structure of The Structure of GH101 D764N Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Serinyl T-Antigen also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the The Structure of GH101 D764N Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Serinyl T-Antigen (pdb code 5a58). 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 D764N Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Serinyl T-Antigen, PDB code: 5a58:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The Structure of GH101 D764N Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Serinyl 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 D764N Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Serinyl T-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2427 b:14.2 occ:1.00 O A:ASN583 2.3 17.8 1.0 OD1 A:ASP581 2.3 16.1 1.0 OD1 A:ASP577 2.4 17.5 1.0 O A:HOH3454 2.4 14.0 1.0 OD1 A:ASN579 2.4 14.6 1.0 OD1 A:ASP588 2.5 11.9 1.0 OD2 A:ASP588 2.5 11.8 1.0 CG A:ASP588 2.9 10.9 1.0 CG A:ASP581 3.3 16.5 1.0 CG A:ASN579 3.5 15.3 1.0 C A:ASN583 3.5 18.3 1.0 CG A:ASP577 3.5 16.8 1.0 OD2 A:ASP581 3.6 15.8 1.0 ND2 A:ASN579 3.9 13.8 1.0 N A:ASN583 4.1 20.2 1.0 N A:ASN579 4.3 15.4 1.0 N A:ALA578 4.3 15.5 1.0 OD2 A:ASP577 4.3 16.2 1.0 CA A:ASN583 4.3 20.2 1.0 CA A:ASP577 4.3 15.4 1.0 CB A:ASP588 4.4 11.0 1.0 CB A:ASP577 4.4 15.9 1.0 N A:ASP581 4.4 17.7 1.0 OD1 A:ASP585 4.4 13.5 1.0 N A:VAL584 4.4 14.7 1.0 CA A:VAL584 4.5 13.7 1.0 CB A:ASP581 4.5 16.6 1.0 CB A:ASN583 4.6 23.6 1.0 CB A:ASN579 4.7 15.1 1.0 N A:LYS582 4.8 18.9 1.0 C A:ASP577 4.8 15.9 1.0 CA A:ASP581 4.8 17.5 1.0 N A:ASP585 4.8 12.9 1.0 CA A:ASN579 4.8 16.0 1.0 N A:ASP588 4.9 10.7 1.0 C A:ASP581 4.9 17.9 1.0 N A:ALA580 5.0 17.9 1.0 C A:ASN579 5.0 17.4 1.0

Calcium binding site 2 out of 3 in the The Structure of GH101 D764N Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Serinyl 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 D764N Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Serinyl T-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2429 b:11.5 occ:1.00 OE2 A:GLU1235 2.3 11.2 1.0 O A:TRP1284 2.4 10.0 1.0 O A:HOH4443 2.4 9.9 1.0 O A:GLU1281 2.4 11.7 1.0 O A:ASP1233 2.4 10.3 1.0 OD2 A:ASP1411 2.5 10.8 1.0 OD1 A:ASP1411 2.6 10.1 1.0 CG A:ASP1411 2.9 10.8 1.0 CD A:GLU1235 3.5 11.4 1.0 C A:GLU1281 3.5 12.3 1.0 C A:TRP1284 3.6 10.1 1.0 C A:ASP1233 3.6 10.8 1.0 CG A:GLU1235 4.0 11.6 1.0 N A:TRP1284 4.2 10.5 1.0 CA A:ASP1233 4.3 11.3 1.0 CA A:TRP1284 4.4 10.2 1.0 CB A:ASP1411 4.4 10.3 1.0 N A:GLU1281 4.4 12.2 1.0 CA A:GLU1281 4.4 12.7 1.0 CB A:ASP1233 4.4 12.1 1.0 OG A:SER1285 4.4 10.3 1.0 N A:GLY1282 4.4 12.2 1.0 O A:HOH3787 4.5 23.1 1.0 OE1 A:GLU1235 4.5 10.8 1.0 CA A:GLY1282 4.5 12.1 1.0 OD1 A:ASN1412 4.6 14.9 1.0 N A:SER1285 4.6 10.0 1.0 CB A:PHE1234 4.6 9.8 1.0 CB A:GLU1281 4.6 14.7 1.0 N A:PHE1234 4.7 10.2 1.0 CA A:SER1285 4.7 9.7 1.0 CB A:TRP1284 4.8 10.0 1.0 C A:GLY1282 4.9 12.0 1.0 N A:ASN1283 4.9 11.2 1.0 N A:GLU1235 4.9 9.8 1.0 CA A:PHE1234 4.9 9.8 1.0 C A:PHE1234 4.9 10.1 1.0

Calcium binding site 3 out of 3 in the The Structure of GH101 D764N Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Serinyl 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 D764N Mutant From Streptococcus Pneumoniae TIGR4 in Complex with Serinyl T-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2430 b:13.0 occ:1.00 O A:ASP1091 2.4 13.4 1.0 O A:HOH4188 2.4 11.0 1.0 OD1 A:ASN1090 2.4 13.4 1.0 O A:HOH4189 2.4 16.3 1.0 OD2 A:ASP1207 2.4 12.9 1.0 O A:GLY1063 2.5 11.1 1.0 OD1 A:ASP1207 2.6 12.1 1.0 CG A:ASP1207 2.8 12.4 1.0 C A:GLY1063 3.4 11.2 1.0 C A:ASP1091 3.5 14.2 1.0 CG A:ASN1090 3.6 13.5 1.0 CA A:GLY1063 3.8 10.9 1.0 N A:ASP1091 3.9 14.9 1.0 CA A:ASP1091 4.2 14.8 1.0 ND2 A:ASN1090 4.3 13.6 1.0 O A:HOH4240 4.3 13.2 1.0 CB A:ASP1207 4.4 11.7 1.0 O A:HOH4191 4.4 16.8 1.0 C A:ASN1090 4.5 14.2 1.0 N A:PHE1064 4.6 10.9 1.0 CB A:ASP1091 4.6 16.1 1.0 N A:MET1092 4.6 13.5 1.0 NE2 A:HIS1160 4.7 11.7 1.0 O A:HOH3567 4.7 20.2 1.0 OD1 A:ASN1065 4.7 11.3 1.0 CB A:ASN1090 4.8 13.0 1.0 CA A:MET1092 4.9 13.2 1.0 CA A:ASN1090 4.9 13.8 1.0 O A:HOH3559 4.9 21.9 1.0 CB A:PHE1064 4.9 11.2 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