Calcium in PDB 4bq2: 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: 4bq2 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)	39.28 / 1.90
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	166.666, 166.666, 114.559, 90.00, 90.00, 90.00
R / Rfree (%)	17.021 / 21.487

The binding sites of Calcium atom in the Structural Analysis of An Exo-Beta-Agarase (pdb code 4bq2). 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: 4bq2:
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:Ca1797 b:22.6 occ:1.00 O A:HOH2007 2.1 21.2 1.0 O A:LYS81 2.3 17.6 1.0 O A:ASP50 2.3 21.4 1.0 OE2 A:GLU52 2.4 24.8 1.0 OD2 A:ASP228 2.5 17.6 1.0 OD1 A:ASP228 2.6 17.9 1.0 OG A:SER80 2.6 22.6 1.0 CG A:ASP228 2.9 19.2 1.0 C A:LYS81 3.4 18.5 1.0 C A:ASP50 3.5 21.6 1.0 CD A:GLU52 3.5 26.7 1.0 N A:LYS81 3.7 20.5 1.0 CB A:SER80 3.8 20.8 1.0 CG A:GLU52 4.0 24.6 1.0 CA A:LYS81 4.0 19.5 1.0 O A:HOH2041 4.1 22.0 1.0 CA A:ASP50 4.2 21.5 1.0 OD1 A:ASN229 4.2 22.6 1.0 CB A:ASP50 4.3 22.0 1.0 C A:SER80 4.3 20.6 1.0 O A:HOH2012 4.4 28.9 1.0 CB A:ASP228 4.4 18.7 1.0 CB A:LYS81 4.4 21.6 1.0 N A:GLY82 4.5 18.3 1.0 N A:PHE51 4.5 23.0 1.0 CA A:SER80 4.5 20.2 1.0 OE1 A:GLU52 4.6 26.1 1.0 O A:HOH2018 4.7 46.4 1.0 CB A:PHE51 4.7 22.3 1.0 N A:GLU52 4.7 25.2 1.0 C A:PHE51 4.8 23.2 1.0 CA A:GLY82 4.8 19.4 1.0 CG A:ASN229 4.8 21.6 1.0 CA A:PHE51 4.8 22.6 1.0 CE1 A:TYR72 4.9 25.1 1.0 OH A:TYR72 4.9 24.4 1.0 ND2 A:ASN229 5.0 20.8 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 B:Ca1799 b:55.4 occ:1.00 OE2 B:GLU52 2.8 42.2 1.0 O B:ASP50 2.9 26.5 1.0 OD2 B:ASP228 3.0 25.7 1.0 O B:LYS81 3.0 30.3 1.0 N B:LYS81 3.1 31.1 1.0 OD1 B:ASP228 3.2 25.7 1.0 CG B:ASP228 3.5 26.1 1.0 CD B:GLU52 3.8 42.3 1.0 C B:LYS81 3.8 30.0 1.0 CA B:SER80 3.8 32.9 1.0 CA B:LYS81 3.9 31.6 1.0 C B:SER80 3.9 30.9 1.0 C B:ASP50 3.9 25.5 1.0 CB B:ASP50 4.0 28.2 1.0 OD1 B:ASN229 4.0 25.9 1.0 CB B:SER80 4.0 31.1 1.0 CG B:GLU52 4.0 39.7 1.0 CB B:LYS81 4.2 34.0 1.0 CA B:ASP50 4.3 25.7 1.0 OG B:SER80 4.4 31.7 1.0 CG B:ASP50 4.7 32.3 1.0 CG B:ASN229 4.7 24.1 1.0 ND2 B:ASN229 4.8 24.2 1.0 O B:PRO79 4.8 37.2 1.0 O B:HOH2030 4.9 44.8 1.0 N B:GLU52 4.9 31.7 1.0 OE1 B:GLU52 4.9 47.6 1.0 N B:GLY82 4.9 26.8 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 C:Ca1798 b:22.6 occ:1.00 OE2 C:GLU52 2.2 22.9 1.0 O C:ASP50 2.3 19.1 1.0 O C:LYS81 2.3 17.5 1.0 OG C:SER80 2.5 24.1 1.0 OD2 C:ASP228 2.5 17.3 1.0 O C:HOH2006 2.6 22.7 1.0 OD1 C:ASP228 2.6 17.7 1.0 CG C:ASP228 2.9 17.1 1.0 CD C:GLU52 3.4 23.1 1.0 C C:ASP50 3.4 19.5 1.0 C C:LYS81 3.4 20.4 1.0 N C:LYS81 3.6 22.3 1.0 CB C:SER80 3.7 23.0 1.0 CG C:GLU52 3.9 23.9 1.0 CA C:LYS81 4.0 21.7 1.0 CA C:ASP50 4.0 19.1 1.0 O C:HOH2046 4.1 21.9 1.0 CB C:ASP50 4.2 20.2 1.0 C C:SER80 4.2 20.8 1.0 OD1 C:ASN229 4.3 16.5 1.0 OE1 C:GLU52 4.4 22.8 1.0 CB C:ASP228 4.4 16.5 1.0 CA C:SER80 4.4 21.3 1.0 CB C:LYS81 4.4 24.5 1.0 O C:HOH2010 4.4 24.3 1.0 N C:PHE51 4.5 19.1 1.0 N C:GLY82 4.6 16.8 1.0 O C:HOH2018 4.6 34.2 1.0 C C:PHE51 4.7 21.9 1.0 CB C:PHE51 4.7 20.5 1.0 N C:GLU52 4.8 22.1 1.0 CE1 C:TYR72 4.8 20.7 1.0 CA C:PHE51 4.8 20.6 1.0 CG C:ASN229 4.9 17.0 1.0 OH C:TYR72 4.9 20.4 1.0 ND2 C:ASN229 4.9 17.5 1.0 CA C:GLY82 4.9 16.7 1.0 CG C:ASP50 5.0 22.4 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 D:Ca1795 b:21.0 occ:1.00 OE2 D:GLU52 2.3 19.6 1.0 O D:ASP50 2.3 19.1 1.0 O D:HOH2006 2.3 18.5 1.0 O D:LYS81 2.4 16.5 1.0 OD2 D:ASP228 2.5 15.4 1.0 OG D:SER80 2.5 23.6 1.0 OD1 D:ASP228 2.5 15.2 1.0 CG D:ASP228 2.9 15.6 1.0 CD D:GLU52 3.4 22.7 1.0 C D:ASP50 3.4 18.7 1.0 C D:LYS81 3.5 18.3 1.0 N D:LYS81 3.6 19.1 1.0 CB D:SER80 3.8 22.0 1.0 CG D:GLU52 3.9 21.9 1.0 CA D:LYS81 4.0 19.7 1.0 CA D:ASP50 4.1 17.6 1.0 OD1 D:ASN229 4.2 15.9 1.0 CB D:ASP50 4.3 19.1 1.0 C D:SER80 4.3 19.1 1.0 O D:HOH2011 4.4 26.7 1.0 CB D:ASP228 4.4 15.6 1.0 O D:HOH2058 4.4 24.9 1.0 OE1 D:GLU52 4.5 20.0 1.0 O D:HOH2019 4.5 29.9 1.0 CB D:LYS81 4.5 21.3 1.0 CA D:SER80 4.5 19.7 1.0 N D:PHE51 4.5 18.8 1.0 N D:GLY82 4.6 17.8 1.0 C D:PHE51 4.7 20.6 1.0 CE1 D:TYR72 4.8 16.5 1.0 CB D:PHE51 4.8 19.5 1.0 N D:GLU52 4.8 22.5 1.0 CG D:ASN229 4.8 16.6 1.0 CA D:PHE51 4.9 18.7 1.0 OH D:TYR72 4.9 18.1 1.0 ND2 D:ASN229 4.9 16.8 1.0 CA D:GLY82 4.9 17.3 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