Sodium in PDB 3kl0: Crystal Structure of the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis

All present enzymatic activity of Crystal Structure of the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis:
3.2.1.136;

The structure of Crystal Structure of the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis, PDB code: 3kl0 was solved by F.J.St John, J.C.Hurlbert, E.Pozharski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.64
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	138.490, 195.796, 66.246, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.1

The binding sites of Sodium atom in the Crystal Structure of the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis (pdb code 3kl0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis, PDB code: 3kl0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis


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 the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:18.9 occ:1.00 O A:HOH952 2.3 19.4 1.0 O A:HOH541 2.4 18.1 1.0 O A:HOH950 2.4 18.1 1.0 O C:HOH481 2.5 20.6 1.0 O A:HOH490 2.5 18.3 1.0 O A:HOH556 2.5 20.5 1.0 OD2 A:ASP197 4.2 17.3 1.0 NZ C:LYS308 4.2 20.5 1.0 O A:HOH1394 4.2 34.4 1.0 CE C:LYS308 4.3 19.1 1.0 O A:ASN195 4.5 15.2 1.0 OD1 A:ASN195 4.5 16.8 1.0 CA A:ASN195 4.5 13.7 1.0 CA A:GLY164 4.6 13.0 1.0 O C:HOH409 4.6 30.5 1.0 O A:GLY164 4.7 13.8 1.0 O A:ILE166 4.7 16.0 1.0 O A:ALA194 4.7 14.8 1.0 OD1 A:ASP197 4.8 20.9 1.0 O A:ALA163 4.8 13.2 1.0 C A:ASN195 4.8 13.4 1.0 O A:ALA168 4.8 15.2 1.0 CG A:ASP197 4.9 17.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis


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 the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:20.4 occ:1.00 O B:HOH426 2.4 21.0 1.0 O B:HOH955 2.4 20.0 1.0 O B:HOH484 2.4 21.0 1.0 O B:HOH563 2.4 21.3 1.0 O B:HOH2148 2.4 19.2 1.0 O B:HOH1597 4.1 35.4 1.0 OD2 B:ASP197 4.2 14.8 1.0 O B:HOH970 4.3 31.0 1.0 O B:HOH1794 4.3 41.0 1.0 O B:HOH672 4.3 28.1 1.0 O B:ASN195 4.5 16.4 1.0 O B:GLY164 4.5 18.0 1.0 OD1 B:ASN195 4.6 16.6 1.0 CA B:GLY164 4.6 17.0 1.0 CA B:ASN195 4.6 15.3 1.0 O B:ALA194 4.7 16.0 1.0 OD1 B:ASP197 4.7 19.3 1.0 O B:ALA163 4.7 16.3 1.0 O B:ILE166 4.8 17.3 1.0 C B:ASN195 4.8 15.0 1.0 CG B:ASP197 4.9 16.1 1.0 C B:GLY164 4.9 17.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:20.4 occ:1.00 O C:HOH1099 2.3 19.4 1.0 O C:HOH1111 2.3 19.9 1.0 O C:HOH457 2.4 16.5 1.0 O C:HOH424 2.5 15.8 1.0 O C:HOH2157 2.5 26.2 1.0 O B:HOH532 3.3 20.0 1.0 CB B:ASN334 3.8 17.1 1.0 OD2 C:ASP197 3.9 15.2 1.0 O C:ASN195 4.1 15.2 1.0 CA C:ASN195 4.2 13.1 1.0 O B:HOH530 4.3 25.1 1.0 N B:ASN334 4.3 14.3 1.0 OD1 C:ASN195 4.4 17.3 1.0 OD1 C:ASP197 4.4 17.1 1.0 O C:HOH703 4.5 26.2 1.0 C C:ASN195 4.5 13.6 1.0 NE2 B:GLN382 4.5 17.7 1.0 O C:ALA194 4.5 13.6 1.0 O C:ALA163 4.5 16.6 1.0 CG C:ASP197 4.6 15.0 1.0 CA C:GLY164 4.6 18.1 1.0 O C:ILE166 4.7 16.2 1.0 CA B:ASN334 4.7 16.6 1.0 O C:ALA168 4.7 13.5 1.0 O C:GLY164 4.7 18.0 1.0 CG B:ASN334 4.7 22.2 1.0 CB C:ASN195 4.8 13.7 1.0 CG2 C:VAL170 4.8 14.1 1.0 ND2 B:ASN334 5.0 24.6 1.0 CG C:ASN195 5.0 17.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Glucuronoxylan Xylanohydrolase Xync From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Na403 b:34.9 occ:1.00 O D:HOH887 2.4 31.1 1.0 O D:HOH432 2.4 31.6 1.0 O D:HOH880 2.4 34.7 1.0 O D:HOH834 2.6 29.2 1.0 O D:HOH499 2.6 29.0 1.0 OD2 D:ASP197 4.2 24.1 1.0 O D:HOH2063 4.4 46.5 1.0 OD1 D:ASN195 4.5 29.3 1.0 O D:ASN195 4.5 27.3 1.0 O D:GLY164 4.5 30.9 1.0 CA D:ASN195 4.5 27.5 1.0 O D:ILE166 4.6 28.9 1.0 O D:ALA194 4.6 29.8 1.0 OD1 D:ASP197 4.6 28.8 1.0 CA D:GLY164 4.6 30.9 1.0 O D:ALA163 4.7 30.2 1.0 C D:ASN195 4.8 27.3 1.0 CG D:ASP197 4.8 26.1 1.0 O D:ALA168 4.9 25.1 1.0 C D:GLY164 5.0 31.1 1.0

F.J.St John, J.C.Hurlbert, J.D.Rice, J.F.Preston, E.Pozharski. Ligand Bound Structures of A Glycosyl Hydrolase Family 30 Glucuronoxylan Xylanohydrolase. J.Mol.Biol. V. 407 92 2011.
ISSN: ISSN 0022-2836
PubMed: 21256135
DOI: 10.1016/J.JMB.2011.01.010