Atomistry » Sodium » PDB 6rca-6rmx » 6rjc
Atomistry »
  Sodium »
    PDB 6rca-6rmx »
      6rjc »

Sodium in PDB 6rjc: E.Coli Transketolase Apoenzyme

Enzymatic activity of E.Coli Transketolase Apoenzyme

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

Protein crystallography data

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

Other elements in 6rjc:

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

Calcium (Ca) 2 atoms

Sodium Binding Sites:

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 6rjc

Go back to Sodium Binding Sites List in 6rjc
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 6rjc

Go back to Sodium Binding Sites List in 6rjc
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

Reference:

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
Page generated: Tue Dec 15 12:54:39 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy