Sodium in PDB 5t3r: Crystal Structure of BT1762-1763

The structure of Crystal Structure of BT1762-1763, PDB code: 5t3r was solved by B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.89 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	151.770, 117.330, 119.890, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 25.9

The structure of Crystal Structure of BT1762-1763 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of BT1762-1763 (pdb code 5t3r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of BT1762-1763, PDB code: 5t3r:

Sodium binding site 1 out of 1 in the Crystal Structure of BT1762-1763


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 BT1762-1763 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:71.0 occ:1.00 OH A:TYR519 2.2 69.1 1.0 O A:SER55 2.3 76.4 1.0 O A:VAL53 2.4 75.3 1.0 O A:CYS58 3.1 65.7 1.0 CZ A:TYR519 3.3 77.0 1.0 C A:SER55 3.4 62.2 1.0 CE2 A:TYR508 3.4 79.6 1.0 C A:VAL53 3.6 65.0 1.0 O A:ARG54 3.6 72.4 1.0 C A:ARG54 3.7 57.2 1.0 CE1 A:TYR519 3.7 78.4 1.0 CG A:GLU75 3.8 66.2 1.0 N A:SER55 4.0 55.6 1.0 OH A:TYR508 4.0 71.7 1.0 CZ A:TYR508 4.1 78.1 1.0 OE2 A:GLU75 4.1 84.0 1.0 C A:CYS58 4.2 58.6 1.0 CA A:ARG54 4.2 54.2 1.0 O A:GLU75 4.3 68.5 1.0 CD2 A:TYR508 4.3 77.0 1.0 CA A:SER55 4.3 57.0 1.0 N A:ASP56 4.4 59.1 1.0 N A:ARG54 4.4 59.0 1.0 CA A:ASP56 4.4 66.9 1.0 CE2 A:TYR519 4.5 80.8 1.0 CD A:GLU75 4.5 78.5 1.0 N A:CYS58 4.6 59.6 1.0 CA A:VAL53 4.6 59.2 1.0 N A:ASP57 4.8 78.2 1.0 C A:ASP56 4.9 80.4 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