Atomistry » Chlorine » PDB 2yjb-2yzr » 2yz7
Atomistry »
  Chlorine »
    PDB 2yjb-2yzr »
      2yz7 »

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

Go back to Chlorine Binding Sites List in 2yz7
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

Go back to Chlorine Binding Sites List in 2yz7
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

Go back to Chlorine Binding Sites List in 2yz7
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

Go back to Chlorine Binding Sites List in 2yz7
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

Go back to Chlorine Binding Sites List in 2yz7
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

Go back to Chlorine Binding Sites List in 2yz7
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

Go back to Chlorine Binding Sites List in 2yz7
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

Go back to Chlorine Binding Sites List in 2yz7
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy