Sodium in PDB 5ngl: The Endo-BETA1,6-Glucanase BT3312

The structure of The Endo-BETA1,6-Glucanase BT3312, PDB code: 5ngl was solved by A.Basle, M.Temple, F.Cuskin, E.Lowe, H.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.79 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.379, 78.766, 145.526, 90.00, 94.94, 90.00
R / Rfree (%)	18.8 / 22.8

The binding sites of Sodium atom in the The Endo-BETA1,6-Glucanase BT3312 (pdb code 5ngl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Endo-BETA1,6-Glucanase BT3312, PDB code: 5ngl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Endo-BETA1,6-Glucanase BT3312


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Endo-BETA1,6-Glucanase BT3312 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:28.8 occ:1.00 OD1 B:ASP286 2.8 27.9 1.0 CG B:HIS281 3.2 16.2 1.0 ND1 B:HIS281 3.2 16.6 1.0 N B:ASP286 3.2 21.9 1.0 N B:ASN282 3.3 15.5 1.0 CG B:ASP286 3.3 26.5 1.0 C B:TYR285 3.5 18.9 1.0 CA B:TYR285 3.5 17.8 1.0 CD2 B:HIS281 3.5 15.2 1.0 CE1 B:HIS281 3.5 16.4 1.0 CB B:HIS281 3.6 16.1 1.0 CB B:ASN282 3.7 16.9 1.0 NE2 B:HIS281 3.7 16.1 1.0 O B:ASN282 3.8 17.7 1.0 CD1 B:LEU240 3.8 20.6 1.0 CZ B:PHE279 3.8 16.9 1.0 CB B:ASP286 3.8 25.2 1.0 CA B:ASN282 3.9 16.5 1.0 N B:TYR285 3.9 17.6 1.0 OD2 B:ASP286 4.0 30.9 1.0 ND2 B:ASN282 4.0 17.6 1.0 CA B:ASP286 4.1 23.1 1.0 CG B:ASN282 4.2 16.6 1.0 C B:HIS281 4.2 16.3 1.0 C B:ASN282 4.2 17.6 1.0 CE1 B:PHE279 4.2 17.0 1.0 O B:TYR285 4.2 19.2 1.0 CB B:LEU240 4.3 19.2 1.0 CG B:LEU240 4.4 20.2 1.0 OD1 B:ASN284 4.5 20.8 1.0 CA B:HIS281 4.5 16.2 1.0 CB B:TYR285 4.8 17.4 1.0 CE2 B:PHE279 4.9 16.8 1.0

Sodium binding site 2 out of 2 in the The Endo-BETA1,6-Glucanase BT3312


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Endo-BETA1,6-Glucanase BT3312 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:34.0 occ:1.00 OD2 B:ASP82 2.5 20.2 1.0 OH B:TYR277 2.7 23.6 1.0 OH B:TYR122 2.9 15.0 1.0 CE2 B:TYR122 3.5 16.7 1.0 CG B:ASP82 3.5 20.7 1.0 CZ B:TYR277 3.5 22.3 1.0 CZ B:TYR122 3.7 16.1 1.0 CE2 B:TYR231 3.7 23.9 1.0 CB B:ASP82 3.8 19.5 1.0 CD2 B:LEU336 3.9 16.9 1.0 CE1 B:TYR277 3.9 22.2 1.0 CD1 B:LEU336 4.0 17.9 1.0 CG B:LEU336 4.4 16.0 1.0 CD2 B:TYR231 4.4 21.6 1.0 OH B:TYR231 4.5 32.2 1.0 CE2 B:TYR277 4.5 22.5 1.0 CZ B:TYR231 4.6 26.2 1.0 OD1 B:ASP82 4.6 20.6 1.0 OE1 B:GLU334 4.6 20.4 1.0 CE B:LYS372 4.7 24.1 1.0 CB B:LYS372 4.7 19.4 1.0 CD2 B:TYR122 4.7 16.2 1.0 CB B:LEU336 4.8 15.1 1.0 CD B:LYS372 5.0 21.9 1.0

M.J.Temple, F.Cuskin, A.Basle, N.Hickey, G.Speciale, S.J.Williams, H.J.Gilbert, E.C.Lowe. A Bacteroidetes Locus Dedicated to Fungal 1,6-Beta-Glucan Degradation: Unique Substrate Conformation Drives Specificity of the Key Endo-1,6-Beta-Glucanase. J. Biol. Chem. V. 292 10639 2017.
ISSN: ESSN 1083-351X
PubMed: 28461332
DOI: 10.1074/JBC.M117.787606