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Sodium in PDB 5b4u: 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: 5b4u 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) 20.83 / 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 (%) 13.4 / 15.1

Other elements in 5b4u:

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 5b4u). 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: 5b4u:

Sodium binding site 1 out of 1 in 5b4u

Go back to Sodium Binding Sites List in 5b4u
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:5.1
occ:0.50
 O A:HOH426 2.3 10.4 1.0
OXT A:ARG260 2.4 9.4 1.0
O A:HOH468 2.4 9.9 1.0
C A:ARG260 3.4 7.7 1.0
O A:ARG260 3.7 9.5 1.0
CG1 A:VAL147 3.8 5.8 1.0
O A:THR258 4.3 6.5 1.0
CB A:VAL147 4.7 4.4 1.0
O A:TRP257 4.7 3.9 1.0
CA A:ARG260 4.8 6.5 1.0
C A:THR258 4.8 4.8 1.0
CA A:THR258 4.8 4.3 1.0
O A:HOH686 4.9 20.1 1.0
O A:HOH507 4.9 22.0 1.0
N A:ARG260 4.9 5.9 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 10:27:19 2020

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