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Chlorine 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:

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase in Complex with Nad(+) and Acetate, PDB code: 3vdq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3vdq

Go back to Chlorine Binding Sites List in 3vdq
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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
A:Cl302

b:28.2
occ:1.00
 NZ A:LYS219 3.1 24.9 1.0
O C:HOH450 3.1 32.6 1.0
O A:HOH546 3.4 30.4 1.0
N A:VAL150 3.4 18.8 1.0
CA A:SER149 3.7 18.6 1.0
CG2 A:VAL150 3.8 19.6 1.0
CE A:LYS219 4.0 26.6 1.0
C A:SER149 4.1 18.4 1.0
CB A:SER149 4.1 18.6 1.0
OG A:SER149 4.1 20.9 1.0
CB A:VAL150 4.2 21.4 1.0
CA A:VAL150 4.4 20.2 1.0
OE2 A:GLU218 4.4 44.8 1.0
CD1 D:LEU171 4.4 9.2 1.0
O A:HOH447 4.5 29.3 1.0
CD C:ARG260 4.6 22.7 1.0
O A:ALA148 4.6 18.7 1.0
CB C:ARG260 4.8 19.6 1.0
N A:SER149 4.9 18.1 1.0
NH1 C:ARG260 5.0 25.1 1.0

Chlorine binding site 2 out of 4 in 3vdq

Go back to Chlorine Binding Sites List in 3vdq
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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
B:Cl302

b:27.4
occ:1.00
 NZ B:LYS219 3.1 23.2 1.0
O B:HOH520 3.1 35.4 1.0
O D:HOH1052 3.1 22.1 1.0
N B:VAL150 3.4 17.1 1.0
CA B:SER149 3.7 19.2 1.0
CE B:LYS219 3.9 24.2 1.0
CG1 B:VAL150 4.0 15.0 1.0
CG2 B:VAL150 4.0 15.8 1.0
C B:SER149 4.1 18.2 1.0
CB B:SER149 4.1 19.8 1.0
OG B:SER149 4.1 22.1 1.0
O B:HOH471 4.4 34.2 1.0
CB B:VAL150 4.4 17.3 1.0
CA B:VAL150 4.5 17.2 1.0
CD1 C:LEU171 4.6 15.4 1.0
O B:HOH480 4.6 32.4 1.0
O B:ALA148 4.6 18.9 1.0
CD D:ARG260 4.8 21.5 1.0
N B:SER149 4.9 17.9 1.0
NH1 D:ARG260 4.9 21.5 1.0
CB D:ARG260 5.0 16.7 1.0
OE2 B:GLU218 5.0 42.0 1.0

Chlorine binding site 3 out of 4 in 3vdq

Go back to Chlorine Binding Sites List in 3vdq
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl303

b:25.7
occ:1.00
 NZ C:LYS219 3.0 22.0 1.0
O A:HOH413 3.2 21.6 1.0
N C:VAL150 3.3 22.5 1.0
O C:HOH642 3.5 30.4 1.0
CA C:SER149 3.6 20.4 1.0
CG2 C:VAL150 3.8 26.6 1.0
CE C:LYS219 3.9 22.6 1.0
OG C:SER149 3.9 21.9 1.0
CB C:SER149 4.0 20.1 1.0
C C:SER149 4.0 20.9 1.0
CB C:VAL150 4.2 25.9 1.0
CA C:VAL150 4.3 23.7 1.0
CD1 B:LEU171 4.4 20.3 1.0
O C:HOH464 4.5 33.8 1.0
O C:HOH540 4.7 28.5 1.0
O C:ALA148 4.8 16.4 1.0
CD A:ARG260 4.9 23.9 1.0
N C:SER149 4.9 17.6 1.0
OE2 C:GLU218 5.0 41.2 1.0

Chlorine binding site 4 out of 4 in 3vdq

Go back to Chlorine Binding Sites List in 3vdq
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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
D:Cl302

b:30.5
occ:1.00
 O B:HOH439 3.1 15.1 1.0
NZ D:LYS219 3.2 24.4 1.0
N D:VAL150 3.3 20.5 1.0
O D:HOH1136 3.3 33.5 1.0
CA D:SER149 3.5 18.3 1.0
CG2 D:VAL150 3.8 21.9 1.0
C D:SER149 3.9 19.2 1.0
CB D:SER149 4.0 18.3 1.0
CE D:LYS219 4.0 25.3 1.0
OG D:SER149 4.1 18.6 1.0
CG1 D:VAL150 4.1 21.0 1.0
CB D:VAL150 4.3 24.6 1.0
CA D:VAL150 4.4 23.2 1.0
CD1 A:LEU171 4.6 17.7 1.0
O D:ALA148 4.7 12.6 1.0
N D:SER149 4.7 16.7 1.0
OE2 D:GLU218 4.8 45.5 1.0
CD B:ARG260 4.8 23.5 1.0
O D:HOH1138 5.0 34.3 1.0
CB B:ARG260 5.0 22.4 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: Sun Jul 21 06:50:32 2024

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