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Calcium in PDB 3vdq: Crystal Structure of Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase in Complex with Nad(+) and Acetate

Enzymatic activity of Crystal Structure of Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase in Complex with Nad(+) and Acetate

All present enzymatic activity of Crystal Structure of Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase in Complex with Nad(+) and Acetate:
1.1.1.30;

Protein crystallography data

The structure of Crystal Structure of Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase in Complex with Nad(+) and Acetate, PDB code: 3vdq was solved by M.M.Hoque, S.Shimizu, M.T.Hossain, T.Yamamoto, K.Suzuki, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 91.400, 91.400, 262.090, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 24.3

Other elements in 3vdq:

The structure of Crystal Structure of Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase in Complex with Nad(+) and Acetate also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase in Complex with Nad(+) and Acetate (pdb code 3vdq). 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 Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase in Complex with Nad(+) and Acetate, PDB code: 3vdq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3vdq

Go back to Calcium Binding Sites List in 3vdq
Calcium binding site 1 out of 2 in the Crystal Structure of Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase in Complex with Nad(+) and Acetate


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 Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase in Complex with Nad(+) and Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:27.1
occ:1.00
 OXT B:ARG260 2.4 24.8 1.0
OXT D:ARG260 2.5 19.9 1.0
O B:HOH482 2.5 16.7 1.0
O B:HOH451 2.6 15.1 1.0
O D:HOH1053 2.6 14.8 1.0
O D:HOH1001 2.6 17.8 1.0
C B:ARG260 3.5 23.9 1.0
C D:ARG260 3.5 18.0 1.0
CG1 B:VAL147 3.7 16.3 1.0
O B:ARG260 3.8 24.6 1.0
CG1 D:VAL147 3.8 15.8 1.0
O D:ARG260 3.9 19.5 1.0
O D:THR258 4.3 19.7 1.0
O B:THR258 4.5 17.3 1.0
O B:HOH518 4.7 24.7 1.0
CB B:VAL147 4.7 16.2 1.0
O D:HOH1092 4.7 24.0 1.0
CB D:VAL147 4.8 16.6 1.0
C D:THR258 4.8 18.6 1.0
CA D:THR258 4.8 17.9 1.0
CA B:THR258 4.8 17.9 1.0
CA B:ARG260 4.8 23.2 1.0
O D:TRP257 4.8 19.3 1.0
CA D:ARG260 4.8 17.8 1.0
O B:TRP257 4.8 20.1 1.0
C B:THR258 4.9 18.9 1.0
N B:ARG260 5.0 21.5 1.0
N D:ARG260 5.0 16.3 1.0

Calcium binding site 2 out of 2 in 3vdq

Go back to Calcium Binding Sites List in 3vdq
Calcium binding site 2 out of 2 in the Crystal Structure of Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase in Complex with Nad(+) and Acetate


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 Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase in Complex with Nad(+) and Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:25.6
occ:1.00
 OXT A:ARG260 2.5 17.7 1.0
OXT C:ARG260 2.5 21.6 1.0
O C:HOH463 2.5 11.6 1.0
O A:HOH473 2.6 18.2 1.0
O C:HOH467 2.6 22.5 1.0
O C:HOH435 2.7 21.7 1.0
C C:ARG260 3.5 20.8 1.0
C A:ARG260 3.5 21.8 1.0
CG1 A:VAL147 3.7 9.5 1.0
O C:ARG260 3.8 20.9 1.0
CG1 C:VAL147 3.9 10.0 1.0
O A:ARG260 3.9 21.5 1.0
O A:THR258 4.4 19.2 1.0
O C:THR258 4.4 13.2 1.0
O C:HOH526 4.6 34.7 1.0
CB A:VAL147 4.7 14.8 1.0
O A:HOH504 4.8 33.2 1.0
O C:TRP257 4.8 13.8 1.0
O C:HOH418 4.8 33.7 1.0
C C:THR258 4.8 14.2 1.0
CA C:THR258 4.8 13.0 1.0
CA C:ARG260 4.8 19.8 1.0
CA A:ARG260 4.8 20.7 1.0
CB C:VAL147 4.9 15.7 1.0
C A:THR258 4.9 18.4 1.0
O A:TRP257 4.9 19.0 1.0
CA A:THR258 4.9 18.4 1.0
N C:ARG260 5.0 18.8 1.0
N A:ARG260 5.0 20.6 1.0

Reference:

M.M.Hoque, S.Shimizu, M.T.Hossain, T.Yamamoto, S.Imamura, K.Suzuki, M.Tsunoda, H.Amano, T.Sekiguchi, A.Takenaka. The Structures of Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase Before and After Nad+ and Acetate Binding Suggest A Dynamical Reaction Mechanism As A Member of the Sdr Family. Acta Crystallogr.,Sect.D V. 64 496 2008.
ISSN: ISSN 0907-4449
PubMed: 18453685
DOI: 10.1107/S0907444908004009
Page generated: Sat Dec 12 04:34:05 2020

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