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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

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