Sodium in PDB 7esk: Crystal Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, Ligand Free Form

The structure of Crystal Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, Ligand Free Form, PDB code: 7esk was solved by T.Kondo, T.Arakawa, S.Fushinobu, T.Sakamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.30 / 1.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.113, 65.267, 107.008, 90, 90, 90
R / Rfree (%)	15.1 / 17.1

The structure of Crystal Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, Ligand Free Form also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Crystal Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, Ligand Free Form (pdb code 7esk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, Ligand Free Form, PDB code: 7esk:

Sodium binding site 1 out of 1 in the Crystal Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, Ligand Free Form


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 A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:14.1 occ:1.00 O A:GLU221 2.2 14.7 1.0 O A:GLY171 2.4 12.8 1.0 O A:HOH889 2.4 19.4 1.0 O A:ASP198 2.4 13.0 1.0 O A:HOH1072 2.4 21.7 1.0 OD1 A:ASP198 2.8 18.4 0.5 C A:ASP198 3.2 12.2 1.0 CG A:ASP198 3.4 15.8 0.5 C A:GLY171 3.4 12.4 1.0 C A:GLU221 3.5 13.2 1.0 O A:HOH784 3.8 32.7 1.0 CA A:GLY171 3.8 12.5 1.0 OD2 A:ASP198 3.8 19.1 0.5 N A:ASN199 4.0 11.8 1.0 CA A:ASP198 4.0 13.5 0.5 CA A:ASP198 4.0 13.0 0.5 CA A:ASN199 4.1 11.3 1.0 CB A:ASP198 4.2 15.7 0.5 O A:HOH705 4.2 23.4 1.0 CB A:ASP198 4.2 14.0 0.5 CA A:GLU221 4.3 11.7 1.0 O A:HOH1176 4.4 34.3 1.0 N A:THR222 4.5 12.6 1.0 O A:HOH1167 4.5 35.1 1.0 CA A:THR222 4.5 13.4 1.0 O A:HOH821 4.5 25.6 1.0 N A:SER172 4.6 12.1 1.0 CG2 A:THR222 4.8 16.5 1.0 CB A:ASN199 4.8 12.2 1.0 OE1 A:GLU221 4.8 15.4 1.0 CB A:SER172 4.9 13.4 1.0 CB A:GLU221 5.0 13.3 1.0

T.Kondo, M.Kichijo, A.Maruta, M.Nakaya, S.Takenaka, T.Arakawa, S.Fushinobu, T.Sakamoto. Structural and Functional Analysis of Gum Arabic L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase Establishes A Novel Polysaccharide Lyase Family. J.Biol.Chem. 01001 2021.
ISSN: ESSN 1083-351X
PubMed: 34303708
DOI: 10.1016/J.JBC.2021.101001