Sodium in PDB 7esm: Crystal Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex

The structure of Crystal Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex, PDB code: 7esm 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)	41.52 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.19, 65.039, 107.714, 90, 90, 90
R / Rfree (%)	18.8 / 21.5

The binding sites of Sodium atom in the Crystal Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex (pdb code 7esm). 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, L-Rha Complex, PDB code: 7esm:

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, L-Rha Complex


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, L-Rha Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:13.8 occ:1.00 O A:GLU221 2.3 14.2 1.0 O A:HOH846 2.3 21.5 1.0 O A:HOH905 2.4 22.6 1.0 O A:GLY171 2.4 12.2 1.0 O A:ASP198 2.4 13.9 1.0 OD1 A:ASP198 2.8 21.0 0.5 C A:ASP198 3.3 14.7 1.0 CG A:ASP198 3.4 17.6 0.5 C A:GLY171 3.4 13.4 1.0 C A:GLU221 3.5 13.2 1.0 CA A:GLY171 3.8 12.2 1.0 OD2 A:ASP198 3.8 18.9 0.5 N A:ASN199 4.0 12.7 1.0 CA A:ASP198 4.1 14.9 0.5 CA A:ASP198 4.1 14.9 0.5 CA A:ASN199 4.2 11.2 1.0 CB A:ASP198 4.3 16.9 0.5 CA A:GLU221 4.4 11.9 1.0 CB A:ASP198 4.4 17.1 0.5 N A:THR222 4.4 11.7 1.0 CA A:THR222 4.5 13.4 1.0 O A:HOH842 4.5 19.6 1.0 N A:SER172 4.6 11.6 1.0 CG2 A:THR222 4.8 15.8 1.0 CB A:ASN199 4.9 11.7 1.0 OE1 A:GLU221 4.9 15.5 1.0 CB A:SER172 4.9 11.6 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