Sodium in PDB 3wdq: Crystal Structure of Beta-Mannanase From A Symbiotic Protist of the Termite Reticulitermes Speratus

All present enzymatic activity of Crystal Structure of Beta-Mannanase From A Symbiotic Protist of the Termite Reticulitermes Speratus:
3.2.1.78;

The structure of Crystal Structure of Beta-Mannanase From A Symbiotic Protist of the Termite Reticulitermes Speratus, PDB code: 3wdq was solved by H.Tsukagoshi, T.Ishida, K.K.Touhara, K.Igarashi, M.Samejima, S.Fushinobu, K.Kitamoto, M.Arioka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.87 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.503, 61.405, 57.806, 90.00, 92.74, 90.00
R / Rfree (%)	14.4 / 16.4

The structure of Crystal Structure of Beta-Mannanase From A Symbiotic Protist of the Termite Reticulitermes Speratus also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Beta-Mannanase From A Symbiotic Protist of the Termite Reticulitermes Speratus (pdb code 3wdq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Beta-Mannanase From A Symbiotic Protist of the Termite Reticulitermes Speratus, PDB code: 3wdq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Beta-Mannanase From A Symbiotic Protist of the Termite Reticulitermes Speratus


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 Beta-Mannanase From A Symbiotic Protist of the Termite Reticulitermes Speratus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:12.7 occ:1.00 O A:HOH649 3.2 18.5 1.0 O A:HOH650 3.3 22.2 1.0 N A:LEU323 3.3 12.4 1.0 O A:HOH845 3.5 39.3 1.0 CB A:PRO314 3.8 13.2 1.0 CA A:SER322 3.8 11.9 1.0 CB A:SER322 3.8 12.5 1.0 CG A:PRO319 3.9 14.4 1.0 CB A:LEU323 4.0 13.8 1.0 CG A:PRO314 4.0 12.5 1.0 C A:SER322 4.1 12.2 1.0 CA A:LEU323 4.3 13.5 1.0 CB A:PRO319 4.7 13.8 1.0 CD A:PRO319 4.9 15.1 1.0 OG A:SER322 4.9 13.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Beta-Mannanase From A Symbiotic Protist of the Termite Reticulitermes Speratus


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 Beta-Mannanase From A Symbiotic Protist of the Termite Reticulitermes Speratus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:14.1 occ:1.00 OH A:TYR270 3.0 17.1 1.0 O A:HOH550 3.0 17.7 1.0 O A:HOH809 3.0 30.0 1.0 N A:ILE237 3.4 12.5 1.0 CA A:PRO236 3.6 11.4 1.0 CE1 A:TYR270 3.6 14.2 1.0 CZ A:TYR270 3.7 14.1 1.0 CG2 A:THR235 3.7 11.4 1.0 CB A:THR235 3.8 11.5 1.0 CG2 A:ILE237 4.0 13.2 1.0 C A:PRO236 4.0 12.1 1.0 CB A:PRO236 4.2 11.9 1.0 CA A:THR235 4.3 10.7 1.0 CB A:ILE237 4.3 12.9 1.0 CA A:ILE237 4.4 12.6 1.0 O A:HOH710 4.5 30.9 1.0 N A:PRO236 4.6 11.5 1.0 O A:HOH711 4.8 33.5 1.0 CD1 A:TYR270 4.9 13.4 1.0 N A:GLU238 4.9 14.6 0.5 N A:GLU238 5.0 14.5 0.5 C A:THR235 5.0 11.7 1.0 OG1 A:THR235 5.0 11.9 1.0 O A:HOH715 5.0 31.9 1.0

H.Tsukagoshi, A.Nakamura, T.Ishida, K.K.Touhara, M.Otagiri, S.Moriya, M.Samejima, K.Igarashi, S.Fushinobu, K.Kitamoto, M.Arioka. Structural and Biochemical Analyses of Glycoside Hydrolase Family 26 Beta-Mannanase From A Symbiotic Protist of the Termite Reticulitermes Speratus J.Biol.Chem. V. 289 10843 2014.
ISSN: ISSN 0021-9258
PubMed: 24570006
DOI: 10.1074/JBC.M114.555383