Sodium in PDB 4qqs: Crystal Structure of A Thermostable Family-43 Glycoside Hydrolase

The structure of Crystal Structure of A Thermostable Family-43 Glycoside Hydrolase, PDB code: 4qqs was solved by N.Hassan, L.D.Kori, B.K.C.Patel, C.Divne, T.C.Tan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.01 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.133, 73.882, 87.520, 90.00, 94.27, 90.00
R / Rfree (%)	12.2 / 14.5

The binding sites of Sodium atom in the Crystal Structure of A Thermostable Family-43 Glycoside Hydrolase (pdb code 4qqs). 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 A Thermostable Family-43 Glycoside Hydrolase, PDB code: 4qqs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Thermostable Family-43 Glycoside Hydrolase


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 Thermostable Family-43 Glycoside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:9.8 occ:1.00 HE2 A:HIS256 1.9 14.5 1.0 OE2 A:GLU75 2.1 13.2 1.0 O A:HOH707 2.2 14.0 1.0 O A:HOH582 2.2 14.0 1.0 O A:HOH523 2.4 11.2 1.0 O A:HOH577 2.6 23.2 1.0 NE2 A:HIS256 2.8 12.1 1.0 CD A:GLU75 3.2 12.3 1.0 CD2 A:HIS256 3.6 11.9 1.0 HG3 A:GLU75 3.6 12.7 1.0 HG2 A:GLU75 3.6 12.7 1.0 HD2 A:HIS256 3.7 14.2 1.0 CE1 A:HIS256 3.7 12.6 1.0 CG A:GLU75 3.7 10.6 1.0 HA2 A:GLY196 3.8 7.4 1.0 HE1 A:HIS256 3.9 15.1 1.0 O A:HOH598 3.9 20.1 1.0 O A:PRO197 4.0 7.1 1.0 O A:HOH507 4.0 9.2 1.0 HB1 A:ALA73 4.1 9.8 1.0 HB2 A:HIS128 4.1 8.3 1.0 HD2 A:TYR19 4.1 11.7 1.0 OE1 A:GLU75 4.2 12.0 1.0 O A:ALA127 4.5 8.1 1.0 HD2 A:PHE198 4.5 9.9 1.0 HA A:ASP126 4.6 8.6 1.0 CA A:GLY196 4.6 6.2 1.0 CG A:HIS256 4.7 11.3 1.0 ND1 A:HIS256 4.7 13.0 1.0 HB3 A:ASP126 4.7 9.5 1.0 O A:ASN257 4.7 7.4 1.0 C A:GLY196 4.7 5.9 1.0 HD1 A:HIS128 4.7 9.9 1.0 HB2 A:TYR19 4.8 9.2 1.0 HA3 A:GLY196 4.8 7.4 1.0 O A:ASP126 4.9 8.4 1.0 O A:GLY196 4.9 6.6 1.0 HB2 A:PHE198 4.9 8.4 1.0 HB3 A:ASP17 4.9 10.4 1.0 HD2 A:PRO197 4.9 7.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Thermostable Family-43 Glycoside Hydrolase


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 A Thermostable Family-43 Glycoside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:11.3 occ:1.00 OE2 B:GLU75 1.9 14.3 1.0 O B:HOH1021 2.2 16.5 1.0 HE2 B:HIS256 2.2 23.2 1.0 O B:HOH586 2.3 15.8 1.0 O B:HOH550 2.3 13.3 1.0 O B:HOH598 2.8 16.7 1.0 NE2 B:HIS256 2.9 19.3 1.0 CD B:GLU75 3.1 11.8 1.0 HG3 B:GLU75 3.6 12.8 1.0 CD2 B:HIS256 3.6 18.4 1.0 HG2 B:GLU75 3.6 12.8 1.0 HD2 B:HIS256 3.7 22.1 1.0 CG B:GLU75 3.7 10.7 1.0 HA2 B:GLY196 3.8 9.9 1.0 CE1 B:HIS256 3.8 19.0 1.0 O B:PRO197 4.0 8.9 1.0 HE1 B:HIS256 4.1 22.8 1.0 O B:HOH505 4.1 10.6 1.0 OE1 B:GLU75 4.1 11.8 1.0 HB2 B:HIS128 4.1 10.7 1.0 HD2 B:TYR19 4.1 11.7 1.0 O B:HOH818 4.1 22.1 1.0 HB1 B:ALA73 4.3 11.1 1.0 O B:ALA127 4.5 10.7 1.0 CA B:GLY196 4.6 8.2 1.0 HA B:ASP126 4.6 10.5 1.0 HB3 B:ASP126 4.6 12.1 1.0 O B:ASN257 4.6 9.3 1.0 HD2 B:PHE198 4.6 11.8 1.0 CG B:HIS256 4.7 17.4 1.0 C B:GLY196 4.7 7.9 1.0 HD1 B:HIS128 4.7 12.1 1.0 HA3 B:GLY196 4.8 9.9 1.0 ND1 B:HIS256 4.8 18.9 1.0 HB2 B:TYR19 4.8 11.2 1.0 O B:GLY196 4.8 8.4 1.0 O B:ASP126 4.9 10.5 1.0 HD2 B:PRO197 4.9 9.9 1.0 HB2 B:PHE198 4.9 10.5 1.0 CD2 B:TYR19 5.0 9.8 1.0

N.Hassan, L.D.Kori, R.Gandini, B.K.C.Patel, C.Divne, T.C.Tan. High-Resolution Crystal Structure of A Polyextreme GH43 Glycosidase From Halothermothrix Orenii with [Alpha]-L-Arabino Furanosidase Activity Acta Crystallogr.,Sect.F V. 71 338 2015.
ISSN: ISSN 1744-3091
DOI: 10.1107/S2053230X15003337