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Chlorine 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:

Calcium (Ca) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 8 binding sites of Chlorine where determined in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis, PDB code: 2yz7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 2yz7

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Chlorine binding site 1 out of 8 in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl265

b:37.2
occ:0.50
 O C:HOH293 2.8 55.0 1.0
NZ A:LYS219 3.4 39.5 1.0
N A:VAL150 3.4 38.1 1.0
CG2 A:VAL150 3.7 38.4 1.0
CA A:SER149 3.7 37.8 1.0
C A:SER149 4.0 38.2 1.0
CB A:VAL150 4.1 39.1 1.0
CD1 D:LEU171 4.2 29.3 1.0
CB A:SER149 4.2 37.8 1.0
CA A:VAL150 4.3 38.2 1.0
CE A:LYS219 4.4 36.1 1.0
OG A:SER149 4.6 39.5 1.0
CD C:ARG260 4.7 39.2 1.0
OE2 A:GLU218 4.7 48.4 1.0
CB D:LEU171 4.7 29.8 1.0
O A:ALA148 4.8 35.7 1.0
NH1 C:ARG260 4.8 43.4 1.0
CG D:LEU171 4.8 31.1 1.0
CD2 D:LEU171 4.8 28.2 1.0
CB C:ARG260 4.9 35.1 1.0
N A:SER149 4.9 36.1 1.0

Chlorine binding site 2 out of 8 in 2yz7

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Chlorine binding site 2 out of 8 in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl266

b:40.4
occ:0.50
 O D:HOH350 2.7 41.8 1.0
NZ B:LYS219 3.1 40.1 1.0
N B:VAL150 3.3 34.9 1.0
CG2 B:VAL150 3.4 34.1 1.0
CA B:SER149 3.7 34.5 1.0
CE B:LYS219 3.7 42.2 1.0
C B:SER149 3.9 35.1 1.0
CB B:SER149 4.0 35.0 1.0
CB B:VAL150 4.0 34.5 1.0
OG B:SER149 4.2 39.1 1.0
CA B:VAL150 4.3 33.6 1.0
OE2 B:GLU218 4.3 52.2 1.0
O C:HOH342 4.5 24.6 1.0
CD B:GLU218 4.7 51.0 1.0
OE1 B:GLU218 4.9 48.5 1.0
N B:SER149 4.9 33.8 1.0
O B:ALA148 5.0 31.8 1.0

Chlorine binding site 3 out of 8 in 2yz7

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Chlorine binding site 3 out of 8 in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
C:Cl267

b:30.6
occ:0.50
 O A:HOH274 3.2 35.6 1.0
N C:VAL150 3.3 36.4 1.0
NZ C:LYS219 3.5 27.6 1.0
CG2 C:VAL150 3.7 38.9 1.0
CB C:VAL150 3.7 37.0 1.0
CA C:SER149 4.0 32.7 1.0
CA C:VAL150 4.1 37.1 1.0
C C:SER149 4.2 33.8 1.0
O C:HOH339 4.2 29.3 1.0
CE C:LYS219 4.3 29.4 1.0
OE2 C:GLU218 4.5 43.2 1.0
CB C:SER149 4.6 32.7 1.0
OG C:SER149 4.6 30.5 1.0
CD A:ARG260 4.7 34.7 1.0
CD1 B:LEU171 4.8 28.7 1.0
OE1 C:GLU218 4.9 41.5 1.0
NH1 A:ARG260 4.9 36.4 1.0
CD C:GLU218 5.0 41.1 1.0

Chlorine binding site 4 out of 8 in 2yz7

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Chlorine binding site 4 out of 8 in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
D:Cl268

b:33.9
occ:0.50
 N D:VAL150 3.1 39.2 1.0
NZ D:LYS219 3.3 32.2 1.0
CG2 D:VAL150 3.5 36.9 1.0
CA D:SER149 3.6 38.2 1.0
CB D:VAL150 3.8 36.9 1.0
C D:SER149 3.8 38.6 1.0
CB D:SER149 4.0 39.0 1.0
CA D:VAL150 4.1 38.7 1.0
CE D:LYS219 4.2 32.3 1.0
OG D:SER149 4.2 42.7 1.0
O A:HOH293 4.3 46.9 1.0
OE2 D:GLU218 4.5 49.3 1.0
CD B:ARG260 4.5 32.6 1.0
O D:ALA148 4.6 37.0 1.0
CD1 A:LEU171 4.8 30.6 1.0
NH1 B:ARG260 4.8 35.8 1.0
N D:SER149 4.8 36.8 1.0
CD D:GLU218 4.9 50.1 1.0
CB B:ARG260 5.0 34.3 1.0

Chlorine binding site 5 out of 8 in 2yz7

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Chlorine binding site 5 out of 8 in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl272

b:37.0
occ:0.50
 NZ E:LYS219 3.1 49.0 1.0
CG2 E:VAL150 3.5 50.7 1.0
N E:VAL150 3.5 46.1 1.0
CA E:SER149 3.9 44.1 1.0
OG E:SER149 4.0 44.1 1.0
CD G:ARG260 4.1 30.8 1.0
CE E:LYS219 4.2 48.1 1.0
C E:SER149 4.2 45.9 1.0
CB E:SER149 4.3 43.3 1.0
CB E:VAL150 4.3 50.2 1.0
CD1 H:LEU171 4.4 50.9 1.0
NH1 G:ARG260 4.5 30.1 1.0
CB G:ARG260 4.5 35.1 1.0
CA E:VAL150 4.5 48.8 1.0
O E:ALA148 4.7 38.9 1.0
CG G:ARG260 5.0 31.0 1.0
O E:HOH501 5.0 34.7 1.0

Chlorine binding site 6 out of 8 in 2yz7

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Chlorine binding site 6 out of 8 in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl271

b:30.7
occ:0.50
 N F:VAL150 2.9 41.9 1.0
NZ F:LYS219 3.0 37.1 1.0
O H:HOH814 3.1 33.0 1.0
CA F:SER149 3.3 38.2 1.0
CE F:LYS219 3.6 33.8 1.0
C F:SER149 3.6 40.3 1.0
CB F:VAL150 3.7 44.4 1.0
CA F:VAL150 3.9 43.4 1.0
CB F:SER149 3.9 35.2 1.0
CG2 F:VAL150 3.9 46.1 1.0
OE2 F:GLU218 4.3 45.0 1.0
OG F:SER149 4.3 36.8 1.0
O F:ALA148 4.5 34.9 1.0
N F:SER149 4.6 38.3 1.0
CD1 G:LEU171 4.7 31.8 1.0
O F:SER149 4.8 42.6 1.0
O G:HOH1127 4.9 28.1 1.0
C F:ALA148 4.9 35.9 1.0
CD F:GLU218 5.0 46.0 1.0
CD H:ARG260 5.0 35.3 1.0

Chlorine binding site 7 out of 8 in 2yz7

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Chlorine binding site 7 out of 8 in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl270

b:46.9
occ:0.50
 NZ G:LYS219 3.0 63.5 1.0
N G:VAL150 3.0 39.8 1.0
OG G:SER149 3.3 36.6 1.0
CE G:LYS219 3.5 63.5 1.0
O E:HOH514 3.6 41.0 1.0
CA G:SER149 3.6 38.3 1.0
CB G:VAL150 3.7 38.8 1.0
C G:SER149 3.8 39.9 1.0
CG2 G:VAL150 3.9 36.9 1.0
CA G:VAL150 3.9 39.2 1.0
CB G:SER149 4.0 37.7 1.0
OE2 G:GLU218 4.4 64.3 1.0
O G:VAL150 4.8 42.2 1.0
C G:VAL150 4.9 40.8 1.0
CD1 F:LEU171 4.9 36.8 1.0
N G:SER149 4.9 36.5 1.0
O G:SER149 4.9 40.0 1.0
O G:ALA148 5.0 33.0 1.0

Chlorine binding site 8 out of 8 in 2yz7

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Chlorine binding site 8 out of 8 in the X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of X-Ray Analyses of 3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl269

b:35.7
occ:0.50
 O F:HOH614 3.0 34.6 1.0
OG H:SER149 3.2 27.9 1.0
N H:VAL150 3.3 38.1 1.0
NZ H:LYS219 3.3 43.4 1.0
CA H:SER149 3.4 33.9 1.0
CG2 H:VAL150 3.5 36.2 1.0
CE H:LYS219 3.8 42.7 1.0
CB H:SER149 3.9 32.1 1.0
C H:SER149 3.9 35.9 1.0
CB H:VAL150 4.4 37.5 1.0
CA H:VAL150 4.4 38.7 1.0
CD1 E:LEU171 4.4 28.8 1.0
O H:ALA148 4.4 31.4 1.0
N H:SER149 4.6 32.2 1.0
CD F:ARG260 4.9 47.1 1.0
O E:HOH1063 4.9 41.2 1.0
O F:HOH801 4.9 47.5 1.0
CB F:ARG260 4.9 44.4 1.0
C H:ALA148 5.0 31.9 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: Sat Jul 20 15:18:11 2024

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