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Sodium in PDB 5b4t: Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and A Substrate D-3- Hydroxybutyrate

Enzymatic activity of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and A Substrate D-3- Hydroxybutyrate

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

Protein crystallography data

The structure of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and A Substrate D-3- Hydroxybutyrate, PDB code: 5b4t 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) 24.67 / 1.19
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.780, 62.780, 119.490, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 17.3

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 A Substrate D-3- Hydroxybutyrate (pdb code 5b4t). 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 A Substrate D-3- Hydroxybutyrate, PDB code: 5b4t:

Sodium binding site 1 out of 1 in 5b4t

Go back to Sodium Binding Sites List in 5b4t
Sodium binding site 1 out of 1 in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and A Substrate D-3- Hydroxybutyrate


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 A Substrate D-3- Hydroxybutyrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:4.7
occ:0.50
 O A:HOH429 2.3 10.5 1.0
OXT A:ARG260 2.3 9.8 1.0
O A:HOH437 2.4 9.4 1.0
C A:ARG260 3.4 8.1 1.0
CG1 A:VAL147 3.8 7.8 1.0
O A:ARG260 3.8 9.5 1.0
O A:THR258 4.3 7.9 1.0
CB A:VAL147 4.7 6.2 1.0
CA A:ARG260 4.7 8.2 1.0
O A:TRP257 4.7 6.4 1.0
O A:HOH616 4.8 24.1 1.0
C A:THR258 4.8 6.6 1.0
CA A:THR258 4.8 6.5 1.0
O A:HOH496 4.9 17.7 1.0
N A:ARG260 4.9 7.8 1.0

Reference:

H.Kanazawa, M.M.Hoque, M.Tsunoda, K.Suzuki, T.Yamamoto, G.Kawai, J.Kondo, A.Takenaka. Structural Insights Into the Catalytic Reaction Trigger and Inhibition of D-3-Hydroxybutyrate Dehydrogenase Acta Crystallogr.,Sect.F V. 72 507 2016.
ISSN: ESSN 2053-230X
PubMed: 27380367
DOI: 10.1107/S2053230X16007767
Page generated: Tue Dec 15 10:26:41 2020

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