Sodium in PDB 6rjc: E.Coli Transketolase Apoenzyme

All present enzymatic activity of E.Coli Transketolase Apoenzyme:
2.2.1.1;

The structure of E.Coli Transketolase Apoenzyme, PDB code: 6rjc was solved by F.Rabe Von Pappenheim, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.95 / 1.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.905, 102.048, 132.933, 90.00, 90.00, 90.00
R / Rfree (%)	10.4 / 12.3

The structure of E.Coli Transketolase Apoenzyme also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the E.Coli Transketolase Apoenzyme (pdb code 6rjc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the E.Coli Transketolase Apoenzyme, PDB code: 6rjc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the E.Coli Transketolase Apoenzyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E.Coli Transketolase Apoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na725 b:10.3 occ:0.64 O A:HOH1217 2.3 6.1 0.3 O A:VAL234 2.3 17.2 1.0 O A:GLY176 2.3 10.8 1.0 O A:HOH1217 2.4 11.0 0.7 O A:HOH1013 2.4 15.4 1.0 O A:ALA231 2.4 11.6 1.0 HA A:ARG232 3.3 13.9 1.0 C A:VAL234 3.4 12.7 1.0 C A:GLY176 3.4 8.9 1.0 HA A:THR235 3.5 16.3 1.0 C A:ALA231 3.5 10.2 1.0 HE2 A:TYR148 3.5 16.8 1.0 HD11 A:ILE179 3.6 12.5 1.0 HA2 A:GLY176 3.8 11.5 1.0 H A:VAL234 3.8 13.8 1.0 HB A:VAL234 3.8 16.5 1.0 CA A:ARG232 4.0 11.6 1.0 HA A:LYS177 4.0 10.4 1.0 O A:ARG232 4.0 15.6 1.0 O A:LYS237 4.0 9.1 1.0 CA A:GLY176 4.1 9.6 1.0 HG12 A:ILE179 4.1 10.7 1.0 C A:ARG232 4.1 12.0 1.0 HA3 A:GLY176 4.2 11.5 1.0 N A:VAL234 4.2 11.5 1.0 N A:ARG232 4.2 10.4 1.0 CA A:VAL234 4.2 11.7 1.0 HG13 A:ILE179 4.3 10.7 1.0 OG A:SER239 4.3 9.5 1.0 N A:THR235 4.3 12.3 1.0 CA A:THR235 4.3 13.6 1.0 HG12 A:VAL234 4.4 19.0 1.0 CD1 A:ILE179 4.5 10.4 1.0 CE2 A:TYR148 4.5 14.0 1.0 CB A:VAL234 4.5 13.7 1.0 HB1 A:ALA231 4.5 12.3 1.0 CG1 A:ILE179 4.5 8.9 1.0 N A:LYS177 4.5 8.1 1.0 O A:HOH1428 4.5 22.6 0.9 HA A:ALA231 4.6 12.4 1.0 CA A:ALA231 4.6 10.4 1.0 HG22 A:THR235 4.7 23.9 1.0 CA A:LYS177 4.7 8.6 1.0 HG A:SER239 4.7 11.4 1.0 OH A:TYR148 4.8 22.1 1.0 HB2 A:SER239 4.9 10.1 1.0 N A:ALA233 4.9 11.3 1.0 H A:LYS237 4.9 11.8 0.3 H A:LYS237 4.9 11.8 0.7 HD13 A:ILE179 5.0 12.5 1.0 CG1 A:VAL234 5.0 15.8 1.0

Sodium binding site 2 out of 2 in the E.Coli Transketolase Apoenzyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E.Coli Transketolase Apoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Na723 b:8.7 occ:0.80 O B:VAL234 2.2 12.2 1.0 O B:GLY176 2.3 10.1 1.0 O B:ALA231 2.3 10.3 1.0 O B:HOH1033 2.4 10.5 1.0 O B:HOH998 2.4 12.5 1.0 HA B:ARG232 3.4 12.8 1.0 C B:VAL234 3.4 10.3 1.0 C B:GLY176 3.4 8.4 1.0 C B:ALA231 3.5 10.3 1.0 HA B:THR235 3.6 12.6 1.0 HD11 B:ILE179 3.6 11.9 1.0 HE2 B:TYR148 3.7 16.2 1.0 HB B:VAL234 3.7 13.5 1.0 HA2 B:GLY176 3.8 10.2 1.0 H B:VAL234 3.8 12.9 1.0 O B:LYS237 4.0 8.0 1.0 CA B:ARG232 4.0 10.7 1.0 CA B:GLY176 4.1 8.5 1.0 HA B:LYS177 4.1 9.8 1.0 HG12 B:ILE179 4.1 10.7 1.0 HA3 B:GLY176 4.2 10.2 1.0 N B:VAL234 4.2 10.8 1.0 CA B:VAL234 4.2 10.7 1.0 O B:ARG232 4.2 13.1 1.0 N B:ARG232 4.2 10.2 1.0 C B:ARG232 4.2 11.2 1.0 OG B:SER239 4.2 9.5 1.0 HG13 B:ILE179 4.3 10.7 1.0 N B:THR235 4.3 9.8 1.0 CA B:THR235 4.4 10.5 1.0 HG12 B:VAL234 4.4 15.4 1.0 CB B:VAL234 4.4 11.2 1.0 O B:HOH1437 4.4 16.4 0.9 HB1 B:ALA231 4.4 11.5 1.0 HA B:ALA231 4.4 11.3 1.0 CD1 B:ILE179 4.5 9.9 1.0 CG1 B:ILE179 4.5 8.9 1.0 N B:LYS177 4.5 8.1 1.0 CA B:ALA231 4.6 9.4 1.0 CE2 B:TYR148 4.6 13.5 1.0 HG B:SER239 4.7 11.4 1.0 CA B:LYS177 4.8 8.2 1.0 H B:LYS237 4.8 10.3 1.0 HD13 B:ILE179 4.9 11.9 1.0 HB2 B:SER239 4.9 10.6 1.0 N B:ALA233 4.9 11.6 1.0 CG1 B:VAL234 5.0 12.8 1.0 OH B:TYR148 5.0 18.7 1.0

S.Dai, L.M.Funk, F.R.Von Pappenheim, V.Sautner, M.Paulikat, B.Schroder, J.Uranga, R.A.Mata, K.Tittmann. Low-Barrier Hydrogen Bonds in Enzyme Cooperativity. Nature V. 573 609 2019.
ISSN: ESSN 1476-4687
PubMed: 31534226
DOI: 10.1038/S41586-019-1581-9