Atomistry » Calcium » PDB 3v0a-3vl2 » 3vdr
Atomistry »
  Calcium »
    PDB 3v0a-3vl2 »
      3vdr »

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: Sat Jul 13 20:37:49 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy