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Sodium in PDB 3w8f: Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Malonate

Enzymatic activity of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Malonate

All present enzymatic activity of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Malonate:
1.1.1.30;

Protein crystallography data

The structure of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Malonate, PDB code: 3w8f was solved by H.Kanazawa, M.Tsunoda, M.M.Hoque, K.Suzuki, T.Yamamoto, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.82 / 1.45
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.830, 62.830, 119.290, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 16.7

Other elements in 3w8f:

The structure of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Malonate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Malonate (pdb code 3w8f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Malonate, PDB code: 3w8f:

Sodium binding site 1 out of 1 in 3w8f

Go back to Sodium Binding Sites List in 3w8f
Sodium binding site 1 out of 1 in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Malonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:5.2
occ:0.50
 O A:HOH434 2.3 10.7 1.0
OXT A:ARG260 2.3 9.6 1.0
O A:HOH454 2.4 10.5 1.0
C A:ARG260 3.4 7.9 1.0
CG1 A:VAL147 3.7 6.1 1.0
O A:ARG260 3.7 9.1 1.0
O A:THR258 4.3 7.1 1.0
CB A:VAL147 4.7 4.8 1.0
O A:TRP257 4.7 4.6 1.0
CA A:ARG260 4.8 6.2 1.0
CA A:THR258 4.8 4.4 1.0
C A:THR258 4.8 4.6 1.0
O A:HOH559 4.9 22.4 1.0
N A:ARG260 4.9 5.4 1.0
O A:HOH520 5.0 21.5 1.0

Reference:

H.Kanazawa, M.Tsunoda, M.M.Hoque, K.Suzuki, T.Yamamoto, A.Takenaka. X-Ray Diffraction of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and Malonate To Be Published.
Page generated: Sun Aug 17 18:08:59 2025

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