Sodium in PDB 6t6h: Apo Structure of the Bottromycin Epimerase Both

The structure of Apo Structure of the Bottromycin Epimerase Both, PDB code: 6t6h was solved by J.Koehnke, A.Sikandar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.26 / 1.18
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	66.683, 80.133, 88.699, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 16.8

The binding sites of Sodium atom in the Apo Structure of the Bottromycin Epimerase Both (pdb code 6t6h). 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 Apo Structure of the Bottromycin Epimerase Both, PDB code: 6t6h:

Sodium binding site 1 out of 1 in the Apo Structure of the Bottromycin Epimerase Both


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Structure of the Bottromycin Epimerase Both within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:15.5 occ:1.00 HE1 A:TRP48 2.1 14.0 1.0 H A:HIS39 2.5 10.4 1.0 HD2 A:HIS39 2.6 12.6 1.0 O A:LEU37 2.7 9.3 1.0 O A:LEU65 2.8 10.9 1.0 HA A:VAL38 2.9 10.5 1.0 NE1 A:TRP48 2.9 11.7 1.0 HB3 A:HIS39 3.0 11.9 1.0 N A:HIS39 3.1 8.7 1.0 CD2 A:HIS39 3.3 10.5 1.0 H A:LEU65 3.4 13.9 1.0 C A:LEU37 3.4 8.6 1.0 HZ2 A:TRP48 3.5 13.1 1.0 HA A:ARG45 3.5 12.8 1.0 CA A:VAL38 3.5 8.8 1.0 CB A:HIS39 3.7 9.9 1.0 C A:VAL38 3.7 8.2 1.0 N A:VAL38 3.7 8.6 1.0 CE2 A:TRP48 3.8 9.6 1.0 CG A:HIS39 3.8 9.1 1.0 HD23 A:LEU65 3.8 28.7 1.0 N A:LEU65 3.8 11.6 1.0 C A:LEU65 3.9 9.2 1.0 CD1 A:TRP48 3.9 10.4 1.0 HB1 A:ALA64 3.9 16.2 1.0 CA A:HIS39 4.0 8.2 1.0 HD1 A:TRP48 4.0 12.5 1.0 CZ2 A:TRP48 4.0 10.9 1.0 HB2 A:LEU37 4.0 11.3 1.0 HB3 A:ARG45 4.1 14.2 1.0 HA A:ALA64 4.1 13.9 1.0 HG A:LEU65 4.2 22.4 1.0 HB2 A:ARG45 4.2 14.2 1.0 CA A:ARG45 4.4 10.7 1.0 HA A:HIS39 4.4 9.9 1.0 HB3 A:LEU37 4.4 11.3 1.0 H A:VAL38 4.4 10.2 1.0 CB A:ARG45 4.4 11.8 1.0 CA A:LEU65 4.4 11.1 1.0 C A:ALA64 4.5 10.5 1.0 CB A:LEU37 4.5 9.4 1.0 NE2 A:HIS39 4.5 11.9 1.0 HB2 A:HIS39 4.6 11.9 1.0 CA A:LEU37 4.6 8.8 1.0 CD2 A:LEU65 4.6 23.9 1.0 CA A:ALA64 4.6 11.6 1.0 CB A:ALA64 4.7 13.6 1.0 CG A:LEU65 4.8 18.6 1.0 HA A:ASP66 4.8 12.2 1.0 O A:VAL38 4.8 9.0 1.0 HD21 A:LEU65 4.8 28.7 1.0 HG13 A:VAL38 4.9 13.2 1.0 N A:ARG45 4.9 10.7 1.0 CB A:VAL38 5.0 10.0 1.0 N A:ASP66 5.0 10.4 1.0

A.Sikandar, L.Franz, S.Adam, J.Santos-Aberturas, L.Horbal, A.Luzhetskyy, A.W.Truman, O.V.Kalinina, J.Koehnke. The Bottromycin Epimerase Both Defines A Group of Atypical Alpha / Beta-Hydrolase-Fold Enzymes. Nat.Chem.Biol. V. 16 1013 2020.
ISSN: ESSN 1552-4469
PubMed: 32601484
DOI: 10.1038/S41589-020-0569-Y