Sodium in PDB 5t9x: Crystal Structure of BUGH16BWT

The structure of Crystal Structure of BUGH16BWT, PDB code: 5t9x was solved by B.Pluvinage, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	99.25 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	109.070, 109.070, 239.300, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 20.6

The binding sites of Sodium atom in the Crystal Structure of BUGH16BWT (pdb code 5t9x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of BUGH16BWT, PDB code: 5t9x:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of BUGH16BWT


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 BUGH16BWT within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:11.9 occ:1.00 OD1 A:ASP331 2.2 26.7 1.0 O A:GLY117 2.3 33.0 1.0 O A:ASP74 2.3 27.0 1.0 O A:ASP331 2.4 19.4 1.0 OD1 A:ASN76 2.6 38.6 1.0 OE1 A:GLU50 2.7 45.1 1.0 OE2 A:GLU50 2.8 52.9 1.0 CD A:GLU50 3.1 47.8 1.0 C A:ASP331 3.4 20.2 1.0 CG A:ASP331 3.4 25.6 1.0 C A:GLY117 3.4 33.9 1.0 C A:ASP74 3.5 26.2 1.0 CG A:ASN76 3.6 39.6 1.0 CA A:ASP331 3.9 21.9 1.0 CA A:GLY117 3.9 32.3 1.0 ND2 A:ASN76 4.0 40.7 1.0 CB A:ASP331 4.2 23.9 1.0 O A:HOH611 4.3 42.9 1.0 OD2 A:ASP331 4.3 28.5 1.0 CA A:ASP74 4.3 26.2 1.0 C A:PHE75 4.5 29.1 1.0 N A:TRP332 4.5 19.3 1.0 CB A:ASP74 4.5 28.9 1.0 N A:PHE75 4.5 26.2 1.0 CB A:PHE75 4.5 26.4 1.0 N A:CYS118 4.6 31.8 1.0 O A:PHE75 4.6 30.6 1.0 CG A:GLU50 4.6 45.5 1.0 N A:ASN76 4.6 31.4 1.0 CB A:TRP332 4.7 17.8 1.0 CD1 A:TRP332 4.7 17.6 1.0 CA A:PHE75 4.7 27.7 1.0 O A:HOH541 4.9 26.4 1.0 CA A:TRP332 4.9 18.4 1.0 CB A:ASN76 4.9 36.7 1.0 CA A:CYS118 5.0 32.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of BUGH16BWT


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 BUGH16BWT within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:19.3 occ:1.00 O B:GLY117 2.3 32.5 1.0 O B:ASP74 2.3 26.9 1.0 OD1 B:ASP331 2.3 26.2 1.0 O B:ASP331 2.6 23.1 1.0 OE1 B:GLU50 2.7 48.1 1.0 OD1 B:ASN76 2.8 53.4 1.0 OE2 B:GLU50 3.0 62.7 1.0 CD B:GLU50 3.2 56.1 1.0 C B:GLY117 3.3 36.5 1.0 C B:ASP74 3.5 27.2 1.0 CG B:ASP331 3.5 26.8 1.0 C B:ASP331 3.6 23.8 1.0 CA B:GLY117 3.7 38.0 1.0 CG B:ASN76 3.8 54.8 1.0 CA B:ASP331 4.0 24.0 1.0 C B:PHE75 4.2 34.1 1.0 ND2 B:ASN76 4.3 57.5 1.0 O B:PHE75 4.3 39.1 1.0 CB B:PHE75 4.3 29.5 1.0 CB B:ASP331 4.4 25.3 1.0 N B:PHE75 4.4 29.1 1.0 CA B:ASP74 4.5 28.4 1.0 OD2 B:ASP331 4.5 29.2 1.0 N B:CYS118 4.5 32.8 1.0 CA B:PHE75 4.5 30.4 1.0 N B:ASN76 4.5 37.8 1.0 N B:TRP332 4.6 23.7 1.0 CG B:GLU50 4.7 51.8 1.0 CB B:ASP74 4.7 30.0 1.0 CB B:TRP332 4.8 23.6 1.0 CD1 B:TRP332 4.8 23.3 1.0 O B:HOH566 4.9 35.6 1.0 CA B:CYS118 4.9 33.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of BUGH16BWT


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 BUGH16BWT within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:23.0 occ:1.00 OD1 C:ASP331 2.2 26.9 1.0 O C:GLY117 2.3 28.7 1.0 O C:ASP74 2.4 30.1 1.0 OE2 C:GLU50 2.5 74.5 1.0 O C:ASP331 2.5 23.4 1.0 OD1 C:ASN76 3.0 54.2 1.0 CD C:GLU50 3.3 75.1 1.0 C C:GLY117 3.4 32.8 1.0 OE1 C:GLU50 3.4 90.2 1.0 CG C:ASP331 3.4 28.1 1.0 C C:ASP331 3.5 25.1 1.0 C C:ASP74 3.5 31.4 1.0 CA C:GLY117 3.9 35.6 1.0 CG C:ASN76 3.9 52.2 1.0 CA C:ASP331 4.0 25.3 1.0 CA C:ASP74 4.2 32.9 1.0 OD2 C:ASP331 4.3 32.6 1.0 ND2 C:ASN76 4.3 54.2 1.0 CB C:ASP331 4.3 27.9 1.0 CB C:ASP74 4.3 37.4 1.0 C C:PHE75 4.4 35.1 1.0 O C:PHE75 4.4 36.6 1.0 N C:PHE75 4.5 30.9 1.0 CB C:PHE75 4.5 31.5 1.0 N C:CYS118 4.5 33.1 1.0 N C:TRP332 4.6 23.7 1.0 CA C:PHE75 4.7 32.5 1.0 N C:ASN76 4.7 39.4 1.0 CG C:GLU50 4.7 65.9 1.0 CB C:TRP332 4.8 24.8 1.0 CA C:CYS118 4.9 31.6 1.0 CA C:TRP332 5.0 24.8 1.0 CD1 C:TRP332 5.0 25.1 1.0

B.Pluvinage, J.M.Grondin, C.Amundsen, L.Klassen, P.E.Moote, Y.Xiao, D.Thomas, N.A.Pudlo, A.Anele, E.C.Martens, G.D.Inglis, R.E.R.Uwiera, A.B.Boraston, D.W.Abbott. Molecular Basis of An Agarose Metabolic Pathway Acquired By A Human Intestinal Symbiont. Nat Commun V. 9 1043 2018.
ISSN: ESSN 2041-1723
PubMed: 29535379
DOI: 10.1038/S41467-018-03366-X