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Calcium in PDB 2yz7: X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis

Enzymatic activity of X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis

All present enzymatic activity of X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis:
1.1.1.30;

Protein crystallography data

The structure of X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis, PDB code: 2yz7 was solved by M.M.Hoque, E.C.M.Juan, S.Shimizu, M.T.Hossain, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.302, 118.827, 118.726, 90.00, 93.90, 90.00
R / Rfree (%) 19.7 / 27

Other elements in 2yz7:

The structure of X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis (pdb code 2yz7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis, PDB code: 2yz7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2yz7

Go back to Calcium Binding Sites List in 2yz7
Calcium binding site 1 out of 4 in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca261

b:19.7
occ:0.50
 O C:HOH298 2.3 34.3 1.0
O A:HOH278 2.4 25.2 1.0
OXT C:ARG260 2.6 36.6 1.0
OXT A:ARG260 2.7 37.9 1.0
O C:HOH282 2.7 22.6 1.0
O C:HOH304 2.8 32.6 1.0
C A:ARG260 3.6 36.4 1.0
C C:ARG260 3.7 34.5 1.0
CG1 C:VAL147 3.9 28.7 1.0
O A:ARG260 3.9 36.5 1.0
CG1 A:VAL147 3.9 28.5 1.0
O A:THR258 4.1 28.5 1.0
O C:ARG260 4.2 33.7 1.0
O C:THR258 4.5 28.7 1.0
O A:TRP257 4.7 31.1 1.0
C A:THR258 4.7 30.0 1.0
CA C:THR258 4.8 27.9 1.0
O C:TRP257 4.8 28.3 1.0
CB C:VAL147 4.8 28.7 1.0
CA A:THR258 4.8 29.5 1.0
C C:THR258 4.9 29.2 1.0
CA A:ARG260 4.9 35.2 1.0
CB A:VAL147 4.9 29.7 1.0
N A:ARG260 5.0 32.7 1.0

Calcium binding site 2 out of 4 in 2yz7

Go back to Calcium Binding Sites List in 2yz7
Calcium binding site 2 out of 4 in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca262

b:20.6
occ:0.50
 OXT D:ARG260 2.5 26.8 1.0
O B:HOH282 2.5 37.8 1.0
O B:HOH286 2.6 23.4 1.0
O B:HOH287 2.7 25.6 1.0
OXT B:ARG260 2.8 31.8 1.0
O D:THR258 3.6 32.7 1.0
C D:ARG260 3.6 25.6 1.0
CG1 B:VAL147 3.7 30.7 1.0
C B:ARG260 3.8 34.5 1.0
CG1 D:VAL147 3.9 18.2 1.0
O B:ARG260 4.0 36.9 1.0
O D:ARG260 4.1 25.6 1.0
C D:THR258 4.3 31.6 1.0
CA D:THR258 4.5 29.7 1.0
O B:THR258 4.7 34.9 1.0
O B:TRP257 4.8 28.4 1.0
CB B:VAL147 4.8 29.6 1.0
CA D:ARG260 4.8 27.0 1.0
N D:ARG260 4.9 27.6 1.0
CA B:THR258 4.9 32.5 1.0
CB D:VAL147 4.9 23.9 1.0
O D:TRP257 4.9 28.1 1.0
O B:HOH289 4.9 32.1 1.0

Calcium binding site 3 out of 4 in 2yz7

Go back to Calcium Binding Sites List in 2yz7
Calcium binding site 3 out of 4 in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca263

b:20.9
occ:0.50
 OXT E:ARG260 2.5 47.5 1.0
OXT G:ARG260 2.5 31.2 1.0
O G:HOH1086 2.5 23.8 1.0
O E:HOH523 2.7 39.8 1.0
O E:HOH521 2.7 26.1 1.0
C E:ARG260 3.3 47.3 1.0
O E:ARG260 3.4 48.2 1.0
C G:ARG260 3.5 35.9 1.0
CG1 G:VAL147 3.9 32.2 1.0
O G:ARG260 3.9 34.0 1.0
CG1 E:VAL147 4.1 39.2 1.0
O G:THR258 4.2 38.2 1.0
O G:TRP257 4.5 40.9 1.0
O E:THR258 4.6 41.5 1.0
C G:THR258 4.7 37.8 1.0
CA E:ARG260 4.7 45.4 1.0
CA G:THR258 4.8 39.8 1.0
CB G:VAL147 4.8 31.7 1.0
CA G:ARG260 4.8 35.3 1.0
O E:TRP257 4.9 41.6 1.0
N G:ARG260 4.9 36.1 1.0
N E:ARG260 5.0 43.2 1.0
CA E:THR258 5.0 40.4 1.0
C E:THR258 5.0 41.8 1.0

Calcium binding site 4 out of 4 in 2yz7

Go back to Calcium Binding Sites List in 2yz7
Calcium binding site 4 out of 4 in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca264

b:24.5
occ:0.50
 O F:HOH821 2.3 25.9 1.0
OXT F:ARG260 2.4 46.0 1.0
O H:HOH1146 2.4 30.4 1.0
OXT H:ARG260 2.5 30.0 1.0
O F:HOH823 2.5 38.8 1.0
O H:HOH623 2.6 29.8 1.0
C H:ARG260 3.4 28.9 1.0
C F:ARG260 3.4 45.0 1.0
O H:ARG260 3.6 27.4 1.0
O F:ARG260 3.8 45.3 1.0
CG1 F:VAL147 4.0 32.1 1.0
CG1 H:VAL147 4.0 33.2 1.0
O F:THR258 4.3 29.2 1.0
O H:THR258 4.3 36.2 1.0
O H:HOH1050 4.4 44.5 1.0
O F:TRP257 4.5 28.7 1.0
C F:THR258 4.7 30.8 1.0
CA F:THR258 4.7 27.4 1.0
CA F:ARG260 4.8 44.0 1.0
O H:HOH1201 4.8 28.6 1.0
CA H:ARG260 4.8 29.7 1.0
C H:THR258 4.9 35.0 1.0
N F:ARG260 4.9 42.1 1.0
CA H:THR258 4.9 34.6 1.0
O H:TRP257 4.9 35.6 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 Faecalisd-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: Tue Jul 8 09:45:09 2025

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