Sodium in PDB 5lx8: Crystal Structure of BT1762

The structure of Crystal Structure of BT1762, PDB code: 5lx8 was solved by A.Basle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.70 / 1.76
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	107.633, 129.380, 86.610, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.9

The binding sites of Sodium atom in the Crystal Structure of BT1762 (pdb code 5lx8). 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 BT1762, PDB code: 5lx8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of BT1762


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 BT1762 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:13.3 occ:1.00 O A:CYS76 2.3 13.2 1.0 O A:SER73 2.3 11.5 1.0 O A:VAL71 2.3 14.0 1.0 O A:HOH913 2.5 13.2 1.0 OH A:TYR537 2.6 15.0 1.0 C A:VAL71 3.4 12.6 1.0 C A:CYS76 3.5 12.9 1.0 C A:SER73 3.5 11.3 1.0 OH A:TYR526 3.6 13.5 1.0 OE2 A:GLU93 3.6 15.5 1.0 CE2 A:TYR526 3.8 11.9 1.0 CG A:GLU93 3.8 14.0 1.0 CZ A:TYR537 3.8 15.6 1.0 C A:ARG72 3.9 12.3 1.0 N A:SER73 4.0 11.5 1.0 CD A:GLU93 4.0 15.3 1.0 CZ A:TYR526 4.1 12.9 1.0 O A:ARG72 4.2 13.2 1.0 CA A:VAL71 4.3 13.8 1.0 N A:CYS76 4.3 12.4 1.0 N A:ARG72 4.3 12.3 1.0 CE1 A:TYR537 4.3 16.5 1.0 CA A:ARG72 4.3 12.5 1.0 CA A:SER73 4.4 10.8 1.0 CA A:CYS76 4.4 14.0 1.0 N A:TYR77 4.5 12.2 1.0 N A:ASP74 4.6 12.1 1.0 CA A:TYR77 4.6 12.5 1.0 O A:GLU93 4.7 12.9 1.0 CA A:ASP74 4.8 12.0 1.0 O A:ASP70 4.8 13.6 1.0 CD2 A:TYR526 4.8 12.8 1.0 CD1 A:TYR77 4.9 12.1 1.0 CB A:GLU93 4.9 14.0 1.0 CE2 A:TYR537 5.0 16.4 1.0 CB A:VAL71 5.0 14.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of BT1762


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 BT1762 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na607 b:28.1 occ:1.00 O A:HOH853 2.5 14.9 1.0 OH A:TYR372 2.7 13.7 1.0 O A:SER272 3.0 10.3 1.0 CB A:PHE275 3.5 10.8 1.0 CB A:SER272 3.6 12.7 1.0 CE2 A:TYR372 3.6 14.4 1.0 CZ A:TYR372 3.6 13.7 1.0 CA A:SER272 3.6 11.5 1.0 C A:SER272 3.7 10.9 1.0 NZ A:LYS371 3.7 13.3 1.0 O A:PHE275 4.0 10.9 1.0 CD2 A:PHE275 4.0 11.2 1.0 CG A:LEU276 4.0 13.2 1.0 CE A:LYS371 4.0 13.8 1.0 C A:PHE275 4.1 12.0 1.0 CG A:PHE275 4.2 10.6 1.0 CA A:PHE275 4.3 11.1 1.0 CD2 A:LEU276 4.3 14.1 1.0 O A:HIS361 4.4 10.9 1.0 CD1 A:LEU276 4.4 14.2 1.0 CB A:HIS361 4.5 10.8 1.0 ND1 A:HIS361 4.5 10.4 1.0 N A:PHE275 4.6 10.3 1.0 OG A:SER272 4.7 14.7 1.0 N A:LEU276 4.8 12.0 1.0 CA A:HIS361 4.9 10.8 1.0 CG A:HIS361 4.9 10.3 1.0 CD2 A:TYR372 4.9 14.4 1.0 CE1 A:TYR372 4.9 13.7 1.0 N A:SER272 5.0 11.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of BT1762


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 BT1762 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na608 b:37.0 occ:1.00 O A:TRP384 2.5 19.5 1.0 O A:HOH755 2.6 22.8 1.0 O A:TYR393 2.9 15.8 1.0 NZ A:LYS321 3.0 15.9 1.0 CG2 A:VAL395 3.3 18.3 1.0 C A:TYR393 3.4 14.8 1.0 C A:TRP384 3.4 19.7 1.0 O A:TYR394 3.5 14.3 1.0 CB A:TRP384 3.6 19.2 1.0 C A:TYR394 3.8 13.7 1.0 CA A:TRP384 3.8 20.1 1.0 CA A:TYR393 3.8 15.8 1.0 OD1 A:ASP318 3.8 17.1 1.0 N A:TYR394 4.0 13.7 1.0 CE3 A:TRP384 4.1 19.0 1.0 O A:HOH925 4.1 20.7 1.0 N A:VAL395 4.3 13.4 1.0 CA A:TYR394 4.4 14.0 1.0 CB A:VAL395 4.5 15.7 1.0 CE A:LYS321 4.5 16.2 1.0 CG A:TRP384 4.6 19.2 1.0 CA A:VAL395 4.6 13.6 1.0 N A:SER385 4.6 20.6 1.0 CD2 A:TRP384 4.6 19.8 1.0 O A:GLY392 4.7 16.3 1.0 CB A:TYR393 4.7 17.4 1.0 CG2 A:ILE378 4.8 18.4 1.0 CG A:ASP318 4.8 17.6 1.0 N A:TYR393 4.9 16.1 1.0 CB A:PRO311 5.0 19.9 1.0

A.J.Glenwright, K.R.Pothula, S.P.Bhamidimarri, D.S.Chorev, A.Basle, S.J.Firbank, H.Zheng, C.V.Robinson, M.Winterhalter, U.Kleinekathofer, D.N.Bolam, B.Van Den Berg. Structural Basis For Nutrient Acquisition By Dominant Members of the Human Gut Microbiota. Nature V. 541 407 2017.
ISSN: ESSN 1476-4687
PubMed: 28077872
DOI: 10.1038/NATURE20828