Calcium in PDB 4bq4: Structural Analysis of An Exo-Beta-Agarase

All present enzymatic activity of Structural Analysis of An Exo-Beta-Agarase:
3.2.1.81;

The structure of Structural Analysis of An Exo-Beta-Agarase, PDB code: 4bq4 was solved by B.Pluvinage, J.H.Hehemann, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.29 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.230, 116.010, 208.760, 90.00, 90.00, 90.00
R / Rfree (%)	16.288 / 20.88

The binding sites of Calcium atom in the Structural Analysis of An Exo-Beta-Agarase (pdb code 4bq4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structural Analysis of An Exo-Beta-Agarase, PDB code: 4bq4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structural Analysis of An Exo-Beta-Agarase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Analysis of An Exo-Beta-Agarase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1802 b:42.5 occ:1.00 O A:LYS81 2.3 24.0 1.0 O A:ASP50 2.4 24.3 1.0 O A:HOH2008 2.6 44.0 1.0 OE2 A:GLU52 2.6 34.7 1.0 OD1 A:ASP228 2.7 18.1 1.0 OD2 A:ASP228 2.8 17.1 1.0 OG A:SER80 2.8 37.0 1.0 CG A:ASP228 3.1 18.8 1.0 C A:LYS81 3.4 27.2 1.0 C A:ASP50 3.5 21.2 1.0 CD A:GLU52 3.5 34.9 1.0 N A:LYS81 3.7 31.1 1.0 CG A:GLU52 3.7 33.5 1.0 OD1 A:ASN229 3.9 22.5 1.0 CA A:LYS81 4.0 28.9 1.0 CA A:ASP50 4.1 21.6 1.0 CB A:ASP50 4.1 23.1 1.0 CB A:SER80 4.1 33.0 1.0 O A:HOH2036 4.2 26.9 1.0 O A:HOH2007 4.2 38.7 1.0 CB A:LYS81 4.3 31.2 1.0 C A:SER80 4.4 31.5 1.0 N A:GLY82 4.5 26.5 1.0 N A:PHE51 4.6 21.2 1.0 N A:GLU52 4.6 28.4 1.0 CB A:ASP228 4.6 17.4 1.0 CA A:SER80 4.7 33.2 1.0 OE1 A:GLU52 4.7 35.3 1.0 CG A:ASN229 4.7 22.5 1.0 C A:PHE51 4.8 28.1 1.0 CB A:GLU52 4.9 32.6 1.0 CA A:GLY82 4.9 25.3 1.0 CB A:PHE51 4.9 22.9 1.0 CA A:GLU52 4.9 32.4 1.0 CG A:ASP50 4.9 24.9 1.0 CA A:PHE51 4.9 24.0 1.0 ND2 A:ASN229 5.0 21.7 1.0

Calcium binding site 2 out of 4 in the Structural Analysis of An Exo-Beta-Agarase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Analysis of An Exo-Beta-Agarase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1803 b:21.0 occ:1.00 O A:HOH2317 3.0 19.8 1.0 O A:HOH2316 3.2 15.1 1.0 ND2 A:ASN336 3.2 13.7 1.0 N A:TYR754 3.3 15.1 1.0 CA A:ASN336 3.5 15.0 1.0 CB A:TYR754 3.5 16.6 1.0 N A:ALA753 3.6 17.0 1.0 CB A:ARG752 3.7 14.1 1.0 CG A:ARG752 3.8 12.5 1.0 CB A:ASN336 3.9 14.3 1.0 O A:ASN336 4.0 13.0 1.0 CG A:ASN336 4.0 14.6 1.0 C A:ASN336 4.0 14.2 1.0 CA A:TYR754 4.1 15.7 1.0 CD A:ARG752 4.1 12.3 1.0 C A:ARG752 4.1 16.0 1.0 O A:SER335 4.1 15.7 1.0 C A:ALA753 4.3 16.9 1.0 CA A:ALA753 4.3 17.2 1.0 CA A:ARG752 4.3 15.2 1.0 CB A:ALA753 4.3 17.4 1.0 O A:HOH2128 4.6 24.1 1.0 N A:ASN336 4.6 16.4 1.0 O A:ASP362 4.8 18.6 1.0 C A:SER335 4.8 16.7 1.0 O A:SER338 4.8 16.4 1.0 NE A:ARG752 4.8 11.8 1.0 CG A:TYR754 4.8 17.7 1.0 O A:ARG752 4.9 16.2 1.0

Calcium binding site 3 out of 4 in the Structural Analysis of An Exo-Beta-Agarase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Analysis of An Exo-Beta-Agarase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1802 b:32.3 occ:1.00 O B:LYS81 2.2 16.2 1.0 O B:HOH2004 2.3 25.9 1.0 O B:ASP50 2.4 18.2 1.0 OD1 B:ASP228 2.5 16.4 1.0 OD2 B:ASP228 2.7 15.0 1.0 OE2 B:GLU52 2.7 28.1 1.0 OG B:SER80 2.8 26.1 1.0 CG B:ASP228 2.9 17.0 1.0 C B:LYS81 3.3 19.6 1.0 C B:ASP50 3.6 19.2 1.0 CD B:GLU52 3.6 25.7 1.0 N B:LYS81 3.6 22.0 1.0 CG B:GLU52 3.9 25.4 1.0 CA B:LYS81 3.9 20.7 1.0 CB B:SER80 3.9 22.4 1.0 O B:HOH2039 4.1 17.5 1.0 OD1 B:ASN229 4.2 17.3 1.0 CA B:ASP50 4.2 19.9 1.0 C B:SER80 4.3 22.1 1.0 CB B:LYS81 4.3 21.5 1.0 CB B:ASP50 4.4 21.2 1.0 N B:GLY82 4.4 19.7 1.0 CB B:ASP228 4.5 16.6 1.0 CA B:SER80 4.6 23.6 1.0 N B:PHE51 4.6 21.0 1.0 OE1 B:GLU52 4.7 27.8 1.0 CA B:GLY82 4.8 19.4 1.0 N B:GLU52 4.8 23.9 1.0 CG B:ASN229 4.8 16.6 1.0 ND2 B:ASN229 4.8 14.8 1.0 C B:PHE51 4.9 23.1 1.0 CB B:PHE51 4.9 21.0 1.0 CE1 B:TYR72 5.0 18.5 1.0

Calcium binding site 4 out of 4 in the Structural Analysis of An Exo-Beta-Agarase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Analysis of An Exo-Beta-Agarase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1803 b:25.5 occ:1.00 O B:HOH2304 3.0 25.7 1.0 O B:HOH2305 3.1 18.6 1.0 N B:TYR754 3.3 20.8 1.0 ND2 B:ASN336 3.4 16.4 1.0 CB B:TYR754 3.5 22.7 1.0 CA B:ASN336 3.6 18.8 1.0 CB B:ARG752 3.6 18.4 1.0 N B:ALA753 3.7 18.6 1.0 CG B:ARG752 3.8 18.2 1.0 CB B:ASN336 3.9 17.2 1.0 O B:ASN336 4.0 17.6 1.0 CA B:TYR754 4.0 20.8 1.0 CD B:ARG752 4.0 19.4 1.0 C B:ARG752 4.1 19.0 1.0 C B:ASN336 4.1 18.1 1.0 O B:SER335 4.1 19.1 1.0 CG B:ASN336 4.2 18.1 1.0 C B:ALA753 4.2 20.6 1.0 CA B:ALA753 4.2 20.4 1.0 CB B:ALA753 4.3 21.0 1.0 CA B:ARG752 4.3 19.4 1.0 N B:ASN336 4.7 18.8 1.0 CG B:TYR754 4.8 24.3 1.0 NE B:ARG752 4.8 18.3 1.0 C B:SER335 4.8 19.4 1.0 O B:ARG752 4.8 18.6 1.0 O B:SER338 4.9 18.5 1.0 O B:ASP362 4.9 23.9 1.0

B.Pluvinage, J.H.Hehemann, A.B.Boraston. Substrate Recognition and Hydrolysis By A Family 50 Exo-Beta-Agarase AGA50D From the Marine Bacterium Saccharophagus Degradans J.Biol.Chem. V. 288 28078 2013.
ISSN: ISSN 0021-9258
PubMed: 23921382
DOI: 10.1074/JBC.M113.491068