Magnesium in PDB 2ztl: Closed Conformation of D-3-Hydroxybutyrate Dehydrogenase Complexed with Nad+ and L-3-Hydroxybutyrate

All present enzymatic activity of Closed Conformation of D-3-Hydroxybutyrate Dehydrogenase Complexed with Nad+ and L-3-Hydroxybutyrate:
1.1.1.30;

The structure of Closed Conformation of D-3-Hydroxybutyrate Dehydrogenase Complexed with Nad+ and L-3-Hydroxybutyrate, PDB code: 2ztl was solved by K.Nakashima, Y.Nakajima, K.Ito, T.Yoshimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.018, 106.384, 165.168, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 22.9

The binding sites of Magnesium atom in the Closed Conformation of D-3-Hydroxybutyrate Dehydrogenase Complexed with Nad+ and L-3-Hydroxybutyrate (pdb code 2ztl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Closed Conformation of D-3-Hydroxybutyrate Dehydrogenase Complexed with Nad+ and L-3-Hydroxybutyrate, PDB code: 2ztl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Closed Conformation of D-3-Hydroxybutyrate Dehydrogenase Complexed with Nad+ and L-3-Hydroxybutyrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Closed Conformation of D-3-Hydroxybutyrate Dehydrogenase Complexed with Nad+ and L-3-Hydroxybutyrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:21.5 occ:1.00 O D:HOH409 1.8 25.5 1.0 OXT D:ARG260 2.0 19.4 1.0 O A:HOH410 2.0 20.0 1.0 O D:HOH407 2.1 19.3 1.0 OXT A:ARG260 2.1 22.0 1.0 O D:HOH408 2.1 25.6 1.0 C A:ARG260 3.0 22.2 1.0 C D:ARG260 3.0 19.6 1.0 O A:ARG260 3.2 22.7 1.0 O D:ARG260 3.3 20.1 1.0 O A:TRP257 4.3 19.5 1.0 O D:TRP257 4.4 17.0 1.0 CA A:ARG260 4.4 21.6 1.0 CA D:ARG260 4.4 18.7 1.0 O D:HOH1208 4.4 26.6 1.0 CG1 D:VAL147 4.5 17.9 1.0 CG1 A:VAL147 4.5 20.0 1.0 O A:HOH1205 4.6 27.4 1.0 O D:THR258 4.6 18.2 1.0 N D:ARG260 4.7 18.1 1.0 N A:ARG260 4.7 20.8 1.0 CG A:ARG260 4.9 22.1 1.0 O A:THR258 4.9 21.1 1.0 C D:THR258 4.9 16.5 1.0 CA D:THR258 5.0 15.8 1.0 CG D:ARG260 5.0 18.9 1.0 CA A:THR258 5.0 20.0 1.0

Magnesium binding site 2 out of 2 in the Closed Conformation of D-3-Hydroxybutyrate Dehydrogenase Complexed with Nad+ and L-3-Hydroxybutyrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Closed Conformation of D-3-Hydroxybutyrate Dehydrogenase Complexed with Nad+ and L-3-Hydroxybutyrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:24.0 occ:1.00 O B:HOH402 1.9 19.9 1.0 O C:HOH404 2.0 35.1 1.0 OXT C:ARG260 2.0 23.3 1.0 O C:HOH403 2.1 23.1 1.0 OXT B:ARG260 2.1 21.8 1.0 O B:HOH405 2.1 30.6 1.0 C C:ARG260 3.0 24.0 1.0 C B:ARG260 3.1 22.8 1.0 O C:ARG260 3.4 24.1 1.0 O B:ARG260 3.4 22.8 1.0 O C:HOH1668 4.2 33.4 1.0 O C:TRP257 4.3 19.6 1.0 CA C:ARG260 4.4 22.6 1.0 O B:TRP257 4.4 22.9 1.0 O C:HOH1314 4.4 28.9 1.0 CA B:ARG260 4.4 22.4 1.0 CG1 B:VAL147 4.5 20.1 1.0 CG1 C:VAL147 4.6 17.3 1.0 N C:ARG260 4.6 22.3 1.0 N B:ARG260 4.7 22.6 1.0 O C:THR258 4.7 21.1 1.0 O B:THR258 4.8 22.2 1.0 CG C:ARG260 4.8 22.6 1.0 CA C:THR258 5.0 19.4 1.0

K.Nakashima, K.Ito, Y.Nakajima, R.Yamazawa, S.Miyakawa, T.Yoshimoto. Closed Complex of the D-3-Hydroxybutyrate Dehydrogenase Induced By An Enantiomeric Competitive Inhibitor. J.Biochem. V. 145 467 2009.
ISSN: ISSN 0021-924X
PubMed: 19122202
DOI: 10.1093/JB/MVN186