Sodium in PDB 4atf: Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose

All present enzymatic activity of Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose:
3.2.1.81;

The structure of Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose, PDB code: 4atf was solved by T.Bernard, J.H.Hehemann, G.Correc, M.Jam, G.Michel, M.Czjzek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.35 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.187, 106.234, 96.983, 90.00, 93.22, 90.00
R / Rfree (%)	13.4 / 19

The binding sites of Sodium atom in the Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose (pdb code 4atf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose, PDB code: 4atf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na500 b:14.8 occ:1.00 O A:GLY127 2.2 18.5 1.0 O A:ASN83 2.3 16.6 1.0 O A:ASP343 2.3 14.6 1.0 OD1 A:ASP343 2.4 18.9 1.0 O A:HOH2024 2.4 29.9 1.0 OE2 A:GLU85 2.9 32.5 0.7 C A:ASP343 3.3 14.6 1.0 C A:GLY127 3.4 19.8 1.0 C A:ASN83 3.4 16.6 1.0 CG A:ASP343 3.5 16.1 1.0 CA A:ASP343 3.8 14.2 1.0 O A:HOH2239 3.8 37.2 1.0 CD A:GLU85 3.9 31.6 0.7 CA A:GLY127 4.1 20.8 1.0 CA A:ASN83 4.2 16.5 1.0 O A:PHE84 4.2 19.2 1.0 CB A:ASP343 4.3 14.6 1.0 CG A:GLU85 4.3 26.2 0.7 CB A:ASN83 4.3 17.1 1.0 C A:PHE84 4.3 19.0 1.0 CB A:PHE84 4.4 15.3 1.0 N A:GLU128 4.4 18.3 1.0 N A:PHE84 4.4 16.5 1.0 N A:TRP344 4.5 13.5 1.0 OD2 A:ASP343 4.5 15.6 1.0 CA A:PHE84 4.6 16.5 1.0 CA A:GLU128 4.6 16.9 1.0 CB A:TRP344 4.7 13.7 1.0 CD1 A:TRP344 4.7 14.8 1.0 OE1 A:GLU85 4.9 32.9 0.7 N A:GLU85 4.9 20.2 1.0 CA A:TRP344 4.9 13.6 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na500 b:14.1 occ:1.00 O B:GLY127 2.2 18.2 1.0 O B:ASP343 2.3 12.8 1.0 O B:HOH2025 2.3 31.3 1.0 OD1 B:ASP343 2.3 16.6 1.0 O B:ASN83 2.4 16.3 1.0 OE2 B:GLU85 2.9 32.3 0.7 C B:ASP343 3.2 12.7 1.0 C B:GLY127 3.4 18.7 1.0 CG B:ASP343 3.5 15.3 1.0 C B:ASN83 3.5 15.3 1.0 CA B:ASP343 3.7 11.7 1.0 O B:HOH2072 3.9 36.2 1.0 CD B:GLU85 3.9 31.4 0.7 CA B:GLY127 4.2 19.1 1.0 CB B:ASP343 4.2 13.1 1.0 CA B:ASN83 4.2 15.9 1.0 O B:PHE84 4.3 19.2 1.0 CB B:ASN83 4.3 15.5 1.0 CB B:PHE84 4.4 14.8 1.0 N B:TRP344 4.4 11.8 1.0 CG B:GLU85 4.4 25.2 0.7 C B:PHE84 4.4 18.4 1.0 OD2 B:ASP343 4.4 18.4 1.0 N B:GLU128 4.5 17.3 1.0 N B:PHE84 4.5 15.6 1.0 CB B:TRP344 4.6 13.0 1.0 CA B:GLU128 4.7 16.9 1.0 CA B:PHE84 4.7 15.9 1.0 O B:HOH2246 4.7 35.3 1.0 CD1 B:TRP344 4.8 16.9 1.0 CA B:TRP344 4.8 11.8 1.0 OE1 B:GLU85 4.9 31.7 0.7 N B:GLU85 5.0 19.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose within 5.0Å range: probe atom residue distance (Å) B Occ C:Na500 b:22.3 occ:1.00 O C:GLY127 2.2 19.5 1.0 O C:ASP343 2.3 14.3 1.0 O C:ASN83 2.3 16.0 1.0 OD1 C:ASP343 2.4 15.7 1.0 O C:HOH2022 2.4 23.4 1.0 C C:ASP343 3.3 13.9 1.0 C C:ASN83 3.4 16.1 1.0 C C:GLY127 3.4 19.7 1.0 CG C:ASP343 3.5 14.8 1.0 CA C:ASP343 3.7 13.8 1.0 CA C:ASN83 4.1 15.5 1.0 CA C:GLY127 4.2 21.5 1.0 CB C:ASP343 4.2 12.7 1.0 CB C:ASN83 4.3 15.3 1.0 CB C:PHE84 4.4 13.9 1.0 N C:TRP344 4.4 12.4 1.0 N C:GLU128 4.4 19.3 1.0 N C:PHE84 4.4 15.0 1.0 OD2 C:ASP343 4.5 16.1 1.0 CA C:GLU128 4.6 17.9 1.0 CD C:GLU85 4.6 31.9 0.7 C C:PHE84 4.6 17.7 1.0 CB C:TRP344 4.6 12.6 1.0 CA C:PHE84 4.6 15.8 1.0 O C:PHE84 4.7 18.0 1.0 CG C:GLU85 4.7 25.3 0.7 CD1 C:TRP344 4.7 11.7 1.0 OE1 C:GLU85 4.7 33.0 0.7 CA C:TRP344 4.8 12.8 1.0 OE2 C:GLU85 4.9 33.7 0.7 N C:GLU85 5.0 18.9 1.0 O C:VAL342 5.0 14.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Inactivated Mutant Beta-Agarase B in Complex with Agaro-Octaose within 5.0Å range: probe atom residue distance (Å) B Occ D:Na500 b:13.2 occ:1.00 O D:GLY127 2.2 18.6 1.0 O D:ASP343 2.2 15.2 1.0 O D:HOH2027 2.3 27.5 1.0 O D:ASN83 2.3 15.3 1.0 OD1 D:ASP343 2.4 18.8 1.0 C D:ASP343 3.3 14.5 1.0 C D:GLY127 3.4 19.6 1.0 C D:ASN83 3.4 15.2 1.0 CG D:ASP343 3.6 17.2 1.0 CA D:ASP343 3.8 13.9 1.0 CA D:ASN83 4.1 14.8 1.0 CA D:GLY127 4.1 20.7 1.0 CB D:ASN83 4.2 15.4 1.0 CB D:ASP343 4.3 14.5 1.0 CB D:PHE84 4.4 13.2 1.0 N D:GLU128 4.4 18.8 1.0 N D:TRP344 4.4 13.4 1.0 N D:PHE84 4.5 13.4 1.0 O D:PHE84 4.5 16.6 1.0 OD2 D:ASP343 4.5 19.8 1.0 CD D:GLU85 4.5 32.1 0.7 C D:PHE84 4.5 17.4 1.0 CG D:GLU85 4.5 25.1 0.7 CA D:GLU128 4.6 18.0 1.0 CA D:PHE84 4.7 14.7 1.0 CB D:TRP344 4.7 13.6 1.0 OE1 D:GLU85 4.7 33.4 0.7 CD1 D:TRP344 4.8 15.6 1.0 CA D:TRP344 4.8 12.4 1.0 OE2 D:GLU85 4.8 34.6 0.7 N D:GLU85 5.0 19.1 1.0

J.H.Hehemann, G.Correc, F.Thomas, T.Bernard, T.Barbeyron, M.Jam, W.Helbert, G.Michel, M.Czjzek. Biochemical and Structural Characterization of the Complex Agarolytic Enzyme System From the Marine Bacterium Zobellia Galactanivorans. J.Biol.Chem. V. 287 30571 2012.
ISSN: ISSN 0021-9258
PubMed: 22778272
DOI: 10.1074/JBC.M112.377184