Calcium in PDB 4qb2: Structure of CBM35 in Complex with Glucuronic Acid

All present enzymatic activity of Structure of CBM35 in Complex with Glucuronic Acid:
3.2.1.8;

The structure of Structure of CBM35 in Complex with Glucuronic Acid, PDB code: 4qb2 was solved by M.A.Sainz-Polo, J.Sanz-Aparicio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.37 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.891, 47.552, 102.735, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 16.9

The binding sites of Calcium atom in the Structure of CBM35 in Complex with Glucuronic Acid (pdb code 4qb2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of CBM35 in Complex with Glucuronic Acid, PDB code: 4qb2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of CBM35 in Complex with Glucuronic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of CBM35 in Complex with Glucuronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:11.9 occ:1.00 OE1 A:GLU18 2.3 14.1 1.0 OD1 A:ASP134 2.3 12.5 1.0 O A:THR38 2.4 13.2 1.0 O A:GLY41 2.4 12.1 1.0 OE2 A:GLU20 2.4 13.0 1.0 OE1 A:GLU20 2.5 13.7 1.0 O A:ASP134 2.6 11.8 1.0 CD A:GLU20 2.8 14.2 1.0 CD A:GLU18 3.4 16.2 1.0 C A:THR38 3.4 14.3 1.0 CG A:ASP134 3.4 11.4 1.0 C A:ASP134 3.5 10.9 1.0 C A:GLY41 3.6 11.4 1.0 OG1 A:THR38 3.6 15.6 1.0 CA A:ASP134 3.9 10.2 1.0 OE2 A:GLU18 4.1 20.7 1.0 N A:THR38 4.1 12.7 1.0 CB A:GLU18 4.2 13.2 1.0 CA A:THR38 4.2 13.2 1.0 N A:GLY41 4.3 13.9 1.0 OD2 A:ASP134 4.3 13.8 1.0 CG A:GLU18 4.3 14.6 1.0 CB A:ASP134 4.3 10.3 1.0 CG A:GLU20 4.3 16.0 1.0 N A:GLY39 4.4 16.0 1.0 CA A:TYR42 4.4 11.8 1.0 N A:TYR42 4.4 11.5 1.0 CA A:GLY39 4.4 15.9 1.0 CB A:TYR37 4.5 12.6 1.0 N A:ALA19 4.5 12.1 1.0 CA A:GLY41 4.5 13.6 1.0 CB A:THR38 4.6 13.7 1.0 N A:ASN135 4.7 10.4 1.0 CA A:GLU18 4.7 11.7 1.0 CB A:ASN135 4.7 10.9 1.0 C A:GLY39 4.8 17.1 1.0 N A:SER40 4.8 15.5 1.0 CB A:TYR42 4.9 11.3 1.0 C A:TYR37 4.9 13.9 1.0

Calcium binding site 2 out of 2 in the Structure of CBM35 in Complex with Glucuronic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of CBM35 in Complex with Glucuronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:11.9 occ:1.00 O A:PHE45 2.4 12.6 1.0 O6A A:GCU201 2.4 12.6 1.0 OE2 A:GLU129 2.4 12.3 1.0 O A:HOH306 2.4 13.7 1.0 OD1 A:ASN44 2.4 12.2 1.0 O A:HOH304 2.5 11.7 1.0 O4 A:GCU201 2.5 11.6 1.0 OE1 A:GLU129 2.6 11.3 1.0 CD A:GLU129 2.9 11.8 1.0 C6 A:GCU201 3.4 11.8 1.0 CG A:ASN44 3.5 12.2 1.0 C A:PHE45 3.6 11.6 1.0 C4 A:GCU201 3.6 11.2 1.0 C5 A:GCU201 3.7 12.4 1.0 N A:PHE45 4.0 11.2 1.0 ND2 A:ASN44 4.1 13.8 1.0 NH1 A:ARG79 4.2 12.7 1.0 OD1 A:ASN132 4.2 12.3 1.0 CA A:PHE45 4.3 11.2 1.0 O A:GLY130 4.3 11.3 1.0 CG A:GLU129 4.4 11.4 1.0 C A:ASN44 4.5 11.1 1.0 O6B A:GCU201 4.5 13.3 1.0 O A:HOH318 4.5 18.8 1.0 N A:ASN46 4.6 11.8 1.0 CB A:PHE45 4.6 11.3 1.0 O A:HOH364 4.6 21.3 1.0 CA A:ASN46 4.7 13.3 1.0 CB A:ASN44 4.7 12.0 1.0 C3 A:GCU201 4.7 11.9 1.0 CA A:ASN44 4.7 11.4 1.0 O A:HOH317 4.8 17.8 1.0 OD1 A:ASN46 4.9 24.7 1.0

M.A.Sainz-Polo, S.V.Valenzuela, B.Gonzalez, F.I.Pastor, J.Sanz-Aparicio. Structural Analysis of Glucuronoxylan Specific XYN30D and Its Attached CBM35 Domain Give Insights Into the Role of Modularity in Specificity. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25202007
DOI: 10.1074/JBC.M114.597732