Sodium in PDB 4c1o: Geobacillus Thermoglucosidasius Gh Family 52 Xylosidase

All present enzymatic activity of Geobacillus Thermoglucosidasius Gh Family 52 Xylosidase:
3.2.1.37;

The structure of Geobacillus Thermoglucosidasius Gh Family 52 Xylosidase, PDB code: 4c1o was solved by G.Espina, K.Eley, T.R.Schneider, S.J.Crennell, M.J.Danson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.782 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.557, 105.143, 195.565, 90.00, 90.00, 90.00
R / Rfree (%)	14.04 / 17.3

The binding sites of Sodium atom in the Geobacillus Thermoglucosidasius Gh Family 52 Xylosidase (pdb code 4c1o). 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 Geobacillus Thermoglucosidasius Gh Family 52 Xylosidase, PDB code: 4c1o:

Sodium binding site 1 out of 1 in the Geobacillus Thermoglucosidasius Gh Family 52 Xylosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Geobacillus Thermoglucosidasius Gh Family 52 Xylosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1731 b:23.4 occ:1.00 O A:VAL499 2.3 18.9 1.0 OD1 A:ASP489 2.3 25.6 1.0 OD1 A:ASN497 2.4 26.6 1.0 O A:HOH2494 2.4 26.9 1.0 O A:HOH2500 2.5 27.8 1.0 O A:ASP489 2.5 23.7 1.0 HA A:ASP489 3.2 21.8 1.0 C A:ASP489 3.2 17.3 1.0 CG A:ASN497 3.3 26.1 1.0 H A:VAL499 3.3 26.8 1.0 H A:ASN497 3.3 30.0 1.0 CG A:ASP489 3.4 21.0 1.0 C A:VAL499 3.4 20.9 1.0 HD22 A:ASN497 3.5 33.2 1.0 CA A:ASP489 3.6 18.2 1.0 HB2 A:HIS490 3.6 32.8 1.0 HA3 A:GLY501 3.7 26.0 1.0 ND2 A:ASN497 3.8 27.7 1.0 HB A:VAL499 3.8 28.8 1.0 N A:VAL499 4.0 22.4 1.0 N A:GLY501 4.1 21.1 1.0 CB A:ASP489 4.1 22.6 1.0 H A:GLY501 4.1 25.3 1.0 N A:ASN497 4.1 25.0 1.0 CA A:VAL499 4.1 19.6 1.0 HA A:ARG496 4.1 38.5 1.0 HO1 A:GOL1753 4.2 48.9 1.0 N A:HIS490 4.3 22.4 1.0 C A:MET500 4.3 17.6 1.0 OD2 A:ASP489 4.4 27.9 1.0 CA A:GLY501 4.4 21.6 1.0 CB A:VAL499 4.4 24.0 1.0 CB A:ASN497 4.4 26.4 1.0 HD2 A:HIS490 4.5 35.2 1.0 N A:MET500 4.5 21.6 1.0 O1 A:GOL1753 4.5 40.7 1.0 CB A:HIS490 4.5 27.3 1.0 HD21 A:ASN497 4.6 33.2 1.0 HB2 A:ASP489 4.6 27.1 1.0 HA A:MET500 4.6 27.6 1.0 H A:GLY498 4.6 24.6 1.0 HB3 A:ASN497 4.6 31.7 1.0 CA A:ASN497 4.7 22.4 1.0 HG13 A:VAL499 4.7 30.1 1.0 CA A:MET500 4.7 23.0 1.0 HA2 A:GLY501 4.8 26.0 1.0 HB3 A:ASP489 4.8 27.1 1.0 N A:GLY498 4.8 20.5 1.0 O A:MET500 4.8 21.0 1.0 C A:ASN497 4.9 21.1 1.0 CA A:HIS490 4.9 27.7 1.0 O A:HOH2520 4.9 42.3 1.0 H A:HIS490 4.9 26.9 1.0 O A:LYS495 5.0 25.6 1.0 N A:ASP489 5.0 21.3 1.0 HA A:HIS490 5.0 33.2 1.0 CA A:ARG496 5.0 32.1 1.0 O A:ARG488 5.0 20.4 1.0

G.Espina, K.Eley, G.Pompidor, T.R.Schneider, S.J.Crennell, M.J.Danson. A Novel Beta-Xylosidase Structure From Geobacillus Thermoglucosidasius: the First Crystal Structure of A Glycoside Hydrolase Family GH52 Enzyme Reveals Unpredicted Similarity to Other Glycoside Hydrolase Folds Acta Crystallogr.,Sect.D V. 70 1366 2014.
ISSN: ISSN 0907-4449
PubMed: 24816105
DOI: 10.1107/S1399004714002788