Calcium in PDB 5a55: The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4

All present enzymatic activity of The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4:
3.2.1.97;

The structure of The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4, PDB code: 5a55 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)	89.09 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.260, 89.130, 88.570, 90.00, 110.91, 90.00
R / Rfree (%)	14.3 / 17.9

The structure of The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4 also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4 (pdb code 5a55). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4, PDB code: 5a55:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2419 b:9.2 occ:1.00 OD1 A:ASP577 2.3 11.4 1.0 O A:ASN583 2.4 12.0 1.0 OD1 A:ASN579 2.4 8.8 1.0 OD1 A:ASP581 2.4 12.7 1.0 O A:HOH3479 2.4 9.8 1.0 OD1 A:ASP588 2.4 8.1 1.0 OD2 A:ASP588 2.5 7.7 1.0 CG A:ASP588 2.8 7.8 1.0 CG A:ASP581 3.3 13.9 1.0 CG A:ASN579 3.4 9.2 1.0 CG A:ASP577 3.4 11.5 1.0 C A:ASN583 3.5 13.0 1.0 OD2 A:ASP581 3.6 14.1 1.0 ND2 A:ASN579 3.9 8.9 1.0 N A:ASN583 4.1 15.1 1.0 CA A:ASP577 4.3 9.9 1.0 N A:ASN579 4.3 9.4 1.0 OD2 A:ASP577 4.3 12.1 1.0 CB A:ASP588 4.3 7.6 1.0 CB A:ASP577 4.3 10.6 1.0 N A:ALA578 4.3 10.0 1.0 CA A:ASN583 4.3 14.6 1.0 N A:ASP581 4.4 13.7 1.0 OD1 A:ASP585 4.4 9.1 1.0 N A:VAL584 4.5 11.0 1.0 CA A:VAL584 4.5 9.4 1.0 CB A:ASP581 4.5 13.6 1.0 CB A:ASN583 4.5 18.9 1.0 CB A:ASN579 4.7 9.3 1.0 N A:LYS582 4.8 14.9 1.0 N A:ASP585 4.8 8.7 1.0 CA A:ASP581 4.8 14.0 1.0 CA A:ASN579 4.8 9.9 1.0 C A:ASP577 4.8 10.1 1.0 N A:ALA580 4.9 12.0 1.0 O A:HOH3485 4.9 29.0 1.0 N A:ASP588 4.9 7.7 1.0 C A:ASP581 4.9 14.6 1.0 C A:ASN579 5.0 11.0 1.0

Calcium binding site 2 out of 4 in the The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2421 b:8.8 occ:1.00 O A:HOH4454 2.3 7.2 1.0 OE2 A:GLU1235 2.3 9.1 1.0 O A:TRP1284 2.4 7.9 1.0 O A:GLU1281 2.4 9.3 1.0 O A:ASP1233 2.4 7.5 1.0 OD2 A:ASP1411 2.5 7.9 1.0 OD1 A:ASP1411 2.6 7.2 1.0 CG A:ASP1411 2.9 7.8 1.0 CD A:GLU1235 3.4 9.2 1.0 C A:GLU1281 3.5 10.1 1.0 C A:TRP1284 3.6 8.1 1.0 C A:ASP1233 3.6 7.9 1.0 CG A:GLU1235 3.9 8.5 1.0 N A:TRP1284 4.2 8.7 1.0 CA A:ASP1233 4.3 8.2 1.0 O A:HOH3822 4.3 19.6 1.0 CA A:TRP1284 4.3 8.1 1.0 N A:GLY1282 4.4 9.9 1.0 CA A:GLU1281 4.4 10.4 1.0 N A:GLU1281 4.4 9.5 1.0 OG A:SER1285 4.4 8.3 1.0 CB A:ASP1411 4.4 7.6 1.0 CA A:GLY1282 4.4 10.3 1.0 CB A:ASP1233 4.4 8.7 1.0 OD1 A:ASN1412 4.5 9.8 1.0 OE1 A:GLU1235 4.5 8.8 1.0 N A:SER1285 4.6 7.6 1.0 N A:PHE1234 4.6 8.0 1.0 CB A:GLU1281 4.6 11.9 1.0 CB A:PHE1234 4.7 7.7 1.0 CB A:TRP1284 4.7 8.1 1.0 CA A:SER1285 4.8 7.5 1.0 C A:GLY1282 4.9 9.7 1.0 N A:ASN1283 4.9 9.7 1.0 N A:GLU1235 4.9 8.3 1.0 C A:PHE1234 4.9 8.0 1.0 CA A:PHE1234 4.9 7.8 1.0

Calcium binding site 3 out of 4 in the The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2422 b:7.1 occ:1.00 O A:ASP1091 2.3 10.7 1.0 O A:HOH4222 2.3 7.3 1.0 OD2 A:ASP1207 2.3 9.0 1.0 OD1 A:ASN1090 2.4 9.7 1.0 O A:GLY1063 2.4 7.6 1.0 O A:HOH4223 2.5 8.1 1.0 OD1 A:ASP1207 2.6 8.8 1.0 CG A:ASP1207 2.8 8.9 1.0 C A:GLY1063 3.4 8.0 1.0 C A:ASP1091 3.4 10.1 1.0 CG A:ASN1090 3.6 10.0 1.0 CA A:GLY1063 3.8 8.3 1.0 N A:ASP1091 3.9 10.4 1.0 CA A:ASP1091 4.1 10.9 1.0 O A:HOH4260 4.2 12.9 1.0 ND2 A:ASN1090 4.2 9.9 1.0 CB A:ASP1207 4.3 8.6 1.0 C A:ASN1090 4.4 10.1 1.0 CB A:ASP1091 4.5 11.8 1.0 O A:HOH4221 4.5 12.7 1.0 N A:MET1092 4.5 9.8 1.0 N A:PHE1064 4.6 7.7 1.0 NE2 A:HIS1160 4.7 7.1 1.0 CB A:ASN1090 4.7 9.8 1.0 OD1 A:ASN1065 4.8 8.0 1.0 CB A:PHE1064 4.8 7.8 1.0 CA A:MET1092 4.9 9.4 1.0 CA A:ASN1090 4.9 10.2 1.0 O A:ASN1090 4.9 10.1 1.0

Calcium binding site 4 out of 4 in the The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Native Structure of GH101 From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2425 b:13.0 occ:1.00 ND1 A:HIS315 2.0 25.4 1.0 N A:SER314 2.0 22.7 1.0 N A:HIS315 2.1 24.3 1.0 O A:HOH3003 2.2 34.1 1.0 O A:HOH3002 2.8 25.6 1.0 C A:SER314 2.9 23.8 1.0 CA A:SER314 2.9 23.5 1.0 CG A:HIS315 2.9 26.0 1.0 CE1 A:HIS315 3.0 26.9 1.0 CA A:HIS315 3.2 25.0 1.0 CB A:HIS315 3.3 25.0 1.0 N A:MET316 4.0 25.4 1.0 CB A:SER314 4.0 25.9 1.0 OG A:SER314 4.0 25.1 1.0 NE2 A:HIS315 4.0 25.9 1.0 CD2 A:HIS315 4.1 26.4 1.0 C A:HIS315 4.1 25.5 1.0 O A:SER314 4.1 24.9 1.0 O A:HOH3004 4.1 26.5 1.0 O A:HOH3001 4.3 40.6 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