Calcium in PDB 4bq3: 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: 4bq3 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)	38.98 / 2.10
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	170.594, 170.594, 116.299, 90.00, 90.00, 90.00
R / Rfree (%)	15.949 / 20.886

The binding sites of Calcium atom in the Structural Analysis of An Exo-Beta-Agarase (pdb code 4bq3). 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: 4bq3:
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:Ca1799 b:34.0 occ:1.00 O A:LYS81 2.3 15.9 1.0 O A:ASP50 2.3 15.5 1.0 O A:HOH2009 2.3 19.1 1.0 OD1 A:ASP228 2.6 15.2 1.0 OE2 A:GLU52 2.6 21.3 1.0 OG A:SER80 2.8 26.2 1.0 OD2 A:ASP228 2.8 17.6 1.0 CG A:ASP228 3.0 16.3 1.0 C A:LYS81 3.4 17.7 1.0 C A:ASP50 3.5 15.4 1.0 CD A:GLU52 3.6 22.1 1.0 N A:LYS81 3.7 20.1 1.0 CG A:GLU52 3.8 19.2 1.0 CA A:LYS81 4.0 19.2 1.0 O A:HOH2059 4.1 21.1 1.0 CB A:SER80 4.1 24.4 1.0 CA A:ASP50 4.1 16.1 1.0 OD1 A:ASN229 4.2 17.8 1.0 CB A:ASP50 4.3 18.4 1.0 CB A:LYS81 4.4 19.1 1.0 C A:SER80 4.5 24.1 1.0 N A:GLY82 4.5 17.7 1.0 CB A:ASP228 4.5 14.4 1.0 N A:PHE51 4.6 13.9 1.0 N A:GLU52 4.6 15.7 1.0 C A:PHE51 4.7 14.7 1.0 OE1 A:GLU52 4.7 22.4 1.0 CB A:PHE51 4.8 13.3 1.0 CA A:SER80 4.8 26.0 1.0 CG A:ASN229 4.8 16.9 1.0 CA A:GLY82 4.8 15.7 1.0 CA A:PHE51 4.9 14.3 1.0 ND2 A:ASN229 4.9 15.6 1.0 CG A:ASP50 5.0 20.8 1.0 CB A:GLU52 5.0 18.3 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:Ca1803 b:27.6 occ:1.00 O B:LYS81 2.3 15.6 1.0 O B:ASP50 2.4 19.1 1.0 OE2 B:GLU52 2.5 27.0 1.0 OD2 B:ASP228 2.6 14.1 1.0 OD1 B:ASP228 2.6 14.1 1.0 OG B:SER80 2.6 21.4 1.0 CG B:ASP228 2.9 15.8 1.0 C B:LYS81 3.5 17.4 1.0 C B:ASP50 3.6 18.9 1.0 N B:LYS81 3.6 18.7 1.0 CD B:GLU52 3.6 26.5 1.0 CB B:SER80 3.9 20.6 1.0 CA B:LYS81 4.0 18.8 1.0 O B:HOH2042 4.0 18.7 1.0 CG B:GLU52 4.1 23.8 1.0 OD1 B:ASN229 4.2 14.4 1.0 CA B:ASP50 4.2 18.2 1.0 O B:HOH2009 4.3 26.7 1.0 CB B:ASP50 4.3 19.0 1.0 C B:SER80 4.4 18.8 1.0 CB B:ASP228 4.5 15.4 1.0 CB B:LYS81 4.5 19.3 1.0 CA B:SER80 4.5 19.3 1.0 N B:GLY82 4.6 17.3 1.0 N B:PHE51 4.7 18.2 1.0 OE1 B:GLU52 4.7 24.6 1.0 N B:GLU52 4.7 19.9 1.0 CB B:PHE51 4.8 18.2 1.0 CG B:ASN229 4.8 14.2 1.0 C B:PHE51 4.8 19.2 1.0 ND2 B:ASN229 4.8 13.4 1.0 CA B:PHE51 4.9 18.5 1.0 CE1 B:TYR72 5.0 14.4 1.0 CA B:GLY82 5.0 15.7 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:55.6 occ:1.00 OE2 C:GLU52 2.6 32.4 1.0 O C:ASP50 2.6 27.1 1.0 O C:HOH2025 2.7 32.9 1.0 O C:LYS81 2.8 31.2 1.0 OG C:SER80 2.8 46.3 1.0 OD2 C:ASP228 2.9 28.6 1.0 OD1 C:ASP228 2.9 28.8 1.0 CG C:ASP228 3.3 29.0 1.0 N C:LYS81 3.3 35.4 1.0 O C:HOH2026 3.4 36.7 1.0 CD C:GLU52 3.6 35.1 1.0 C C:LYS81 3.7 32.4 1.0 C C:ASP50 3.7 26.3 1.0 CB C:SER80 3.9 43.7 1.0 OD1 C:ASN229 3.9 30.5 1.0 CG C:GLU52 3.9 33.9 1.0 CA C:LYS81 4.0 36.8 1.0 CB C:ASP50 4.1 27.6 1.0 CA C:ASP50 4.2 26.9 1.0 C C:SER80 4.2 40.9 1.0 CA C:SER80 4.2 41.4 1.0 CB C:LYS81 4.3 36.8 1.0 CG C:ASN229 4.5 30.7 1.0 ND2 C:ASN229 4.6 30.7 1.0 OE1 C:GLU52 4.7 38.5 1.0 CB C:ASP228 4.8 25.1 1.0 N C:GLY82 4.8 30.0 1.0 N C:PHE51 4.9 26.8 1.0 N C:GLU52 4.9 31.7 1.0 CG C:ASP50 4.9 28.3 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:Ca1801 b:44.1 occ:1.00 O D:ASP50 2.5 23.7 1.0 O D:LYS81 2.6 21.5 1.0 OE2 D:GLU52 2.7 32.1 1.0 OG D:SER80 2.7 35.7 1.0 OD1 D:ASP228 2.7 17.5 1.0 OD2 D:ASP228 2.7 17.8 1.0 CG D:ASP228 3.1 17.6 1.0 CD D:GLU52 3.5 28.6 1.0 C D:ASP50 3.6 23.6 1.0 CG D:GLU52 3.6 27.9 1.0 C D:LYS81 3.7 21.7 1.0 O D:HOH2027 3.7 33.7 1.0 OD1 D:ASN229 3.8 19.8 1.0 N D:LYS81 3.8 22.9 1.0 CB D:SER80 4.0 29.7 1.0 CB D:ASP50 4.0 26.2 1.0 CA D:ASP50 4.1 22.9 1.0 CA D:LYS81 4.2 23.4 1.0 CG D:ASN229 4.5 19.4 1.0 C D:SER80 4.5 24.8 1.0 CB D:LYS81 4.5 24.2 1.0 CB D:ASP228 4.6 17.2 1.0 ND2 D:ASN229 4.6 18.9 1.0 CA D:SER80 4.7 26.1 1.0 OE1 D:GLU52 4.7 28.7 1.0 N D:PHE51 4.7 21.4 1.0 CG D:ASP50 4.8 26.4 1.0 N D:GLU52 4.8 25.0 1.0 N D:GLY82 4.9 20.2 1.0 CB D:GLU52 4.9 26.5 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