Atomistry » Sodium » PDB 2ekb-2fm1 » 2ez9
Atomistry »
  Sodium »
    PDB 2ekb-2fm1 »
      2ez9 »

Sodium in PDB 2ez9: Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate

Enzymatic activity of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate

All present enzymatic activity of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate:
1.2.3.3;

Protein crystallography data

The structure of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate, PDB code: 2ez9 was solved by G.Wille, D.Meyer, A.Steinmetz, E.Hinze, R.Golbik, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.62 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 118.661, 154.517, 165.640, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18

Other elements in 2ez9:

The structure of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate (pdb code 2ez9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate, PDB code: 2ez9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2ez9

Go back to Sodium Binding Sites List in 2ez9
Sodium binding site 1 out of 2 in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1513

b:6.5
occ:0.50
 O A:MET452 2.7 9.7 1.0
OE1 A:GLN455 2.8 10.5 1.0
O A:HOH1685 3.1 10.7 1.0
CD A:GLN455 3.7 11.6 1.0
C A:MET452 3.8 9.6 1.0
NE2 A:GLN455 4.1 11.1 1.0
CD2 A:HIS58 4.3 6.8 1.0
O A:SER451 4.6 10.2 1.0
CA A:MET452 4.6 9.4 1.0
N A:THR453 4.6 9.2 1.0
CA A:THR453 4.7 9.6 1.0
CG A:GLN455 4.9 10.9 1.0
NE2 A:HIS58 4.9 7.9 1.0

Sodium binding site 2 out of 2 in 2ez9

Go back to Sodium Binding Sites List in 2ez9
Sodium binding site 2 out of 2 in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1511

b:6.7
occ:0.50
 OE1 B:GLN455 2.7 9.3 1.0
O B:MET452 2.8 9.5 1.0
O B:HOH1684 3.0 11.1 1.0
CD B:GLN455 3.6 9.4 1.0
C B:MET452 3.8 9.6 1.0
NE2 B:GLN455 4.0 11.0 1.0
CD2 B:HIS58 4.1 7.3 1.0
N B:THR453 4.6 9.0 1.0
CA B:THR453 4.6 9.4 1.0
O B:SER451 4.7 10.7 1.0
CA B:MET452 4.7 9.4 1.0
CG B:GLN455 4.8 8.7 1.0
NE2 B:HIS58 4.8 6.5 1.0
CG B:HIS58 4.9 7.6 1.0

Reference:

G.Wille, D.Meyer, A.Steinmetz, E.Hinze, R.Golbik, K.Tittmann. The Catalytic Cycle of A Thiamin Diphosphate Enzyme Examined By Cryocrystallography. Nat.Chem.Biol. V. 2 324 2006.
ISSN: ISSN 1552-4450
PubMed: 16680160
DOI: 10.1038/NCHEMBIO788
Page generated: Sun Aug 17 10:29:00 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy