Magnesium in PDB 2ztv: The Binary Complex of D-3-Hydroxybutyrate Dehydrogenase with Nad+

All present enzymatic activity of The Binary Complex of D-3-Hydroxybutyrate Dehydrogenase with Nad+:
1.1.1.30;

The structure of The Binary Complex of D-3-Hydroxybutyrate Dehydrogenase with Nad+, PDB code: 2ztv 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 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.230, 106.793, 163.164, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.6

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

Magnesium binding site 1 out of 2 in the The Binary Complex of D-3-Hydroxybutyrate Dehydrogenase with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Binary Complex of D-3-Hydroxybutyrate Dehydrogenase with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:15.2 occ:1.00 O D:HOH1007 2.3 27.8 1.0 O A:HOH1006 2.3 21.4 1.0 OXT D:ARG260 2.4 22.3 1.0 OXT A:ARG260 2.4 29.5 1.0 O A:HOH1008 2.4 24.6 1.0 O D:HOH1005 2.4 23.8 1.0 C A:ARG260 3.4 28.4 1.0 C D:ARG260 3.4 22.7 1.0 O A:ARG260 3.7 29.0 1.0 O D:ARG260 3.7 23.1 1.0 CG1 A:VAL147 3.7 21.8 1.0 CG1 D:VAL147 3.8 24.6 1.0 O D:THR258 4.4 23.0 1.0 O A:THR258 4.5 27.5 1.0 O A:TRP257 4.7 26.2 1.0 O A:HOH1142 4.7 32.0 1.0 CB D:VAL147 4.7 23.7 1.0 CB A:VAL147 4.7 19.2 1.0 O D:TRP257 4.7 21.0 1.0 CA A:ARG260 4.7 27.5 1.0 CA D:ARG260 4.8 22.8 1.0 C D:THR258 4.8 22.4 1.0 CA D:THR258 4.8 21.4 1.0 CA A:THR258 4.9 25.4 1.0 C A:THR258 4.9 25.6 1.0 N A:ARG260 5.0 27.0 1.0 O D:HOH1239 5.0 37.3 1.0

Magnesium binding site 2 out of 2 in the The Binary Complex of D-3-Hydroxybutyrate Dehydrogenase with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Binary Complex of D-3-Hydroxybutyrate Dehydrogenase with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:17.1 occ:1.00 O B:HOH1003 1.9 30.6 1.0 O B:HOH1001 2.3 23.0 1.0 O C:HOH1004 2.3 23.9 1.0 OXT B:ARG260 2.3 27.6 1.0 O C:HOH1002 2.4 24.4 1.0 OXT C:ARG260 2.4 30.6 1.0 C B:ARG260 3.4 26.5 1.0 C C:ARG260 3.5 31.0 1.0 O B:ARG260 3.6 27.8 1.0 CG1 C:VAL147 3.7 24.7 1.0 O C:ARG260 3.8 31.3 1.0 CG1 B:VAL147 3.8 25.1 1.0 O B:THR258 4.4 27.4 1.0 O C:THR258 4.4 26.9 1.0 O C:HOH1132 4.6 31.2 1.0 O B:HOH1209 4.7 35.9 1.0 CA B:ARG260 4.7 26.0 1.0 CB C:VAL147 4.8 20.5 1.0 O C:TRP257 4.8 26.6 1.0 O B:TRP257 4.8 27.8 1.0 CB B:VAL147 4.8 27.0 1.0 CA B:THR258 4.8 28.7 1.0 C B:THR258 4.8 28.2 1.0 C C:THR258 4.8 25.7 1.0 CA C:THR258 4.8 24.1 1.0 CA C:ARG260 4.9 29.5 1.0 N B:ARG260 4.9 26.1 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