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Calcium in PDB 3vdr: Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+)

Enzymatic activity of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+)

All present enzymatic activity of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+):
1.1.1.30;

Protein crystallography data

The structure of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+), PDB code: 3vdr was solved by M.M.Hoque, S.Shimizu, E.C.M.Juan, Y.Sato, M.T.Hossain, T.Yamamoto, S.Imamura, H.Amano, K.Suzuki, T.Sekiguchi, M.Tsunoda, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.00 / 3.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 91.100, 91.100, 262.000, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 24.1

Other elements in 3vdr:

The structure of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+) (pdb code 3vdr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+), PDB code: 3vdr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3vdr

Go back to Calcium Binding Sites List in 3vdr
Calcium binding site 1 out of 2 in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:51.7
occ:1.00
 O A:HOH466 2.4 29.1 1.0
O A:HOH446 2.7 39.0 1.0
OXT A:ARG260 3.0 42.4 1.0
OXT C:ARG260 3.1 36.3 1.0
CG1 C:VAL147 3.4 28.5 1.0
C A:ARG260 3.5 41.8 1.0
O A:ARG260 3.5 41.0 1.0
O A:THR258 3.7 34.4 1.0
CG1 A:VAL147 3.8 30.2 1.0
C C:ARG260 4.2 35.5 1.0
O C:THR258 4.3 37.8 1.0
CB C:VAL147 4.5 27.7 1.0
C A:THR258 4.5 34.8 1.0
O C:ARG260 4.6 35.8 1.0
CA A:THR258 4.6 33.8 1.0
CA A:ARG260 4.7 41.6 1.0
CB A:VAL147 4.9 31.7 1.0
N A:ARG260 4.9 40.6 1.0
C C:THR258 4.9 36.6 1.0
CA C:THR258 5.0 35.1 1.0

Calcium binding site 2 out of 2 in 3vdr

Go back to Calcium Binding Sites List in 3vdr
Calcium binding site 2 out of 2 in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:43.9
occ:1.00
 OXT B:ARG260 2.1 47.6 1.0
OXT D:ARG260 2.3 45.4 1.0
O D:HOH402 3.1 22.8 1.0
C B:ARG260 3.1 46.2 1.0
O B:HOH426 3.2 42.3 1.0
C D:ARG260 3.4 43.7 1.0
O B:ARG260 3.5 46.0 1.0
CG1 D:VAL147 3.8 31.4 1.0
CG1 B:VAL147 3.8 31.1 1.0
O D:ARG260 3.9 44.8 1.0
CA B:ARG260 4.4 45.3 1.0
O B:THR258 4.4 36.8 1.0
O D:THR258 4.4 33.9 1.0
N B:ARG260 4.6 43.0 1.0
O B:TRP257 4.6 32.6 1.0
CB B:VAL147 4.7 32.9 1.0
CA D:ARG260 4.7 41.6 1.0
C B:THR258 4.8 37.1 1.0
O D:TRP257 4.8 37.3 1.0
CA B:THR258 4.8 36.0 1.0
N D:ARG260 4.8 38.8 1.0
C D:THR258 4.8 34.4 1.0
CA D:THR258 4.9 34.1 1.0
CB D:VAL147 5.0 31.5 1.0

Reference:

M.M.Hoque, S.Shimizu, E.C.M.Juan, Y.Sato, M.T.Hossain, T.Yamamoto, S.Imamura, K.Suzuki, H.Amano, T.Sekiguchi, M.Tsunoda, A.Takenaka. Structure of D-3-Hydroxybutyrate Dehydrogenase Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad+. Acta Crystallogr.,Sect.F V. 65 331 2009.
ISSN: ESSN 1744-3091
PubMed: 19342772
DOI: 10.1107/S1744309109008537
Page generated: Tue Jul 8 17:34:05 2025

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