Sodium in PDB 6tj9: Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate

Enzymatic activity of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate

All present enzymatic activity of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate:
2.2.1.1;

Protein crystallography data

The structure of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate, PDB code: 6tj9 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) 47.66 / 0.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.760, 102.080, 133.130, 90.00, 90.00, 90.00
R / Rfree (%) 9.9 / 11

Other elements in 6tj9:

The structure of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate (pdb code 6tj9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate, PDB code: 6tj9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6tj9

Go back to Sodium Binding Sites List in 6tj9
Sodium binding site 1 out of 2 in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na717

b:7.4
occ:0.29
 O A:HOH820 1.8 9.7 0.7
O A:VAL234 2.1 12.1 1.0
O A:HOH820 2.1 6.5 0.3
O A:GLY176 2.2 9.0 1.0
O A:HOH1104 2.3 16.8 1.0
O A:ALA231 2.4 8.8 1.0
HA A:ARG232 3.3 11.2 0.4
HA A:ARG232 3.3 10.5 0.6
C A:VAL234 3.3 9.2 1.0
C A:GLY176 3.4 6.7 1.0
HE2 A:TYR148 3.5 13.1 1.0
HA A:THR235 3.5 12.3 1.0
HD11 A:ILE179 3.5 10.4 1.0
C A:ALA231 3.6 7.6 1.0
HB A:VAL234 3.7 11.3 1.0
H A:VAL234 3.8 11.3 1.0
HA2 A:GLY176 3.8 8.3 1.0
O A:ARG232 3.8 11.1 0.6
CA A:ARG232 4.0 8.8 0.6
CA A:ARG232 4.0 9.3 0.4
HA A:LYS177 4.0 7.7 1.0
C A:ARG232 4.0 9.4 0.6
CA A:GLY176 4.1 6.9 1.0
O A:LYS237 4.1 7.0 0.5
HG12 A:ILE179 4.1 8.7 1.0
HA3 A:GLY176 4.1 8.3 1.0
O A:LYS237 4.1 6.4 0.5
HG A:SER239 4.1 8.7 1.0
N A:VAL234 4.1 9.4 1.0
CA A:VAL234 4.2 8.9 1.0
C A:ARG232 4.2 9.8 0.4
HG13 A:ILE179 4.2 8.7 1.0
N A:ARG232 4.2 7.4 0.6
N A:ARG232 4.2 8.1 0.4
OG A:SER239 4.2 7.3 1.0
HG12 A:VAL234 4.3 12.9 1.0
O A:ARG232 4.3 11.1 0.4
N A:THR235 4.3 9.1 1.0
CA A:THR235 4.3 10.3 1.0
CB A:VAL234 4.4 9.4 1.0
CD1 A:ILE179 4.4 8.7 1.0
CE2 A:TYR148 4.4 10.9 1.0
CG1 A:ILE179 4.4 7.3 1.0
N A:LYS177 4.5 6.1 1.0
HB1 A:ALA231 4.6 9.3 1.0
HA A:ALA231 4.6 9.0 1.0
CA A:ALA231 4.7 7.5 1.0
CA A:LYS177 4.7 6.4 1.0
OH A:TYR148 4.7 17.7 1.0
HG22 A:THR235 4.8 21.2 1.0
O A:HOH1418 4.8 29.6 1.0
HD13 A:ILE179 4.9 10.4 1.0
CG1 A:VAL234 4.9 10.7 1.0
N A:ALA233 4.9 9.9 1.0
H A:LYS237 5.0 9.1 0.5
HB2 A:SER239 5.0 7.4 1.0
H A:LYS237 5.0 9.3 0.5

Sodium binding site 2 out of 2 in 6tj9

Go back to Sodium Binding Sites List in 6tj9
Sodium binding site 2 out of 2 in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na717

b:7.3
occ:0.52
 O B:HOH1084 1.8 6.0 0.5
O B:VAL234 2.2 10.9 1.0
O B:GLY176 2.3 9.0 1.0
O B:ALA231 2.3 9.2 1.0
O B:HOH820 2.4 15.2 1.0
O B:HOH1084 2.4 7.3 0.5
HA B:ARG232 3.3 12.2 0.5
C B:VAL234 3.3 8.8 1.0
HA B:ARG232 3.4 12.1 0.6
C B:GLY176 3.4 7.0 1.0
C B:ALA231 3.5 8.3 1.0
HE2 B:TYR148 3.6 14.1 1.0
HD11 B:ILE179 3.6 11.1 1.0
HB B:VAL234 3.6 11.4 1.0
HA B:THR235 3.7 10.8 1.0
H B:VAL234 3.7 11.6 1.0
HA2 B:GLY176 3.8 8.3 1.0
O B:ARG232 3.9 12.7 0.6
CA B:ARG232 4.0 10.1 0.6
CA B:ARG232 4.0 10.2 0.5
HA B:LYS177 4.0 7.6 1.0
HG B:SER239 4.0 9.9 1.0
O B:LYS237 4.1 6.7 1.0
C B:ARG232 4.1 10.8 0.6
CA B:GLY176 4.1 6.9 1.0
N B:VAL234 4.1 9.6 1.0
HG12 B:ILE179 4.1 9.5 1.0
HA3 B:GLY176 4.1 8.3 1.0
CA B:VAL234 4.1 9.0 1.0
N B:ARG232 4.2 9.0 0.6
N B:ARG232 4.2 9.0 0.5
C B:ARG232 4.2 11.0 0.5
OG B:SER239 4.2 8.3 1.0
HG13 B:ILE179 4.3 9.5 1.0
CB B:VAL234 4.3 9.5 1.0
N B:THR235 4.3 8.7 1.0
HG12 B:VAL234 4.3 13.3 1.0
O B:ARG232 4.4 11.7 0.5
CA B:THR235 4.4 9.0 1.0
CD1 B:ILE179 4.4 9.2 1.0
HA B:ALA231 4.5 10.1 1.0
HB1 B:ALA231 4.5 10.2 1.0
O B:HOH1449 4.5 19.5 1.0
CE2 B:TYR148 4.5 11.8 1.0
CG1 B:ILE179 4.5 7.9 1.0
N B:LYS177 4.5 6.3 1.0
CA B:ALA231 4.6 8.4 1.0
CA B:LYS177 4.7 6.3 1.0
N B:ALA233 4.8 11.5 1.0
CG1 B:VAL234 4.9 11.1 1.0
OH B:TYR148 4.9 17.4 1.0
H B:LYS237 4.9 8.3 1.0
HD13 B:ILE179 4.9 11.1 1.0
HB2 B:SER239 5.0 9.0 1.0

Reference:

F.Rabe Von Pappenheim, M.Aldeghi, B.Shome, T.Begley, B.L.De Groot, K.Tittmann. Structural Basis For Antibiotic Action of the B 1 Antivitamin 2'-Methoxy-Thiamine. Nat.Chem.Biol. V. 16 1237 2020.
ISSN: ESSN 1552-4469
PubMed: 32839604
DOI: 10.1038/S41589-020-0628-4
Page generated: Tue Dec 15 14:22:16 2020

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