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Chlorine in PDB 1v3v: Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2

Enzymatic activity of Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2

All present enzymatic activity of Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2:
1.3.1.48;

Protein crystallography data

The structure of Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2, PDB code: 1v3v was solved by T.Hori, T.Yokomizo, H.Ago, M.Sugahara, G.Ueno, M.Yamamoto, T.Kumasaka, T.Shimizu, M.Miyano, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.10 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.553, 77.460, 79.095, 90.00, 102.29, 90.00
R / Rfree (%) 19.4 / 23.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2 (pdb code 1v3v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2, PDB code: 1v3v:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 1v3v

Go back to Chlorine Binding Sites List in 1v3v
Chlorine binding site 1 out of 6 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2


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 Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1003

b:41.9
occ:1.00
 O A:HOH1501 2.8 31.9 1.0
ND2 A:ASN318 3.1 24.9 1.0
O A:HOH1764 3.5 55.9 1.0
CB A:ASN318 3.7 24.0 1.0
CB A:ALA320 3.8 21.7 1.0
CG A:ASN318 3.9 24.5 1.0
CG A:GLU315 3.9 24.1 1.0
CA A:GLU315 4.0 23.4 1.0
CB A:GLU315 4.0 23.7 1.0
O A:GLU315 4.1 23.4 1.0
O A:HOH1601 4.1 42.8 1.0
C A:GLU315 4.6 23.3 1.0
N A:ALA320 4.6 22.1 1.0
CA A:ALA320 4.6 21.8 1.0
O A:HOH1463 4.8 39.9 1.0
O A:ASN318 4.9 23.4 1.0
C A:ASN318 4.9 23.3 1.0
CA A:ASN318 4.9 23.5 1.0
CD A:GLU315 5.0 24.5 1.0

Chlorine binding site 2 out of 6 in 1v3v

Go back to Chlorine Binding Sites List in 1v3v
Chlorine binding site 2 out of 6 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2


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 Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1004

b:39.6
occ:1.00
 ND1 A:HIS12 2.9 36.2 1.0
OG A:SER54 3.0 30.8 1.0
N A:PHE13 3.3 36.3 1.0
O A:SER54 3.5 32.0 1.0
C A:SER54 3.6 31.9 1.0
N A:LYS55 3.7 32.8 1.0
CG A:HIS12 3.7 36.3 1.0
CB A:HIS12 3.7 36.4 1.0
CD2 A:PHE13 3.8 36.0 1.0
CB A:SER54 3.8 30.8 1.0
CA A:HIS12 3.8 36.4 1.0
CA A:LYS55 3.8 33.8 1.0
CG A:LYS55 3.8 34.1 1.0
CE1 A:HIS12 3.9 36.2 1.0
C A:HIS12 4.0 36.5 1.0
CG A:PHE13 4.1 36.1 1.0
CB A:PHE13 4.2 36.1 1.0
CA A:PHE13 4.3 36.3 1.0
CA A:SER54 4.3 31.1 1.0
CB A:LYS55 4.4 33.9 1.0
CE2 A:PHE13 4.4 36.1 1.0
CD2 A:LEU9 4.5 33.8 1.0
NH1 A:ARG51 4.6 25.0 1.0
O A:PHE13 4.6 36.2 1.0
O A:ARG51 4.7 25.0 1.0
CD2 A:HIS12 4.9 36.3 1.0
C A:PHE13 5.0 36.3 1.0

Chlorine binding site 3 out of 6 in 1v3v

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Chlorine binding site 3 out of 6 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2


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 Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1005

b:49.4
occ:1.00
 O A:HOH1760 2.5 65.9 1.0
O A:HOH1418 2.9 29.4 1.0
NH2 A:ARG51 3.1 25.0 1.0
O A:ASN246 3.8 27.5 1.0
O A:PHE13 3.8 36.2 1.0
N A:GLY15 3.9 36.2 1.0
NZ A:LYS55 4.2 34.5 1.0
CZ A:ARG51 4.2 24.8 1.0
C A:ASN246 4.3 27.6 1.0
NH1 A:ARG51 4.5 25.0 1.0
CE A:LYS55 4.5 34.3 1.0
CA A:GLN14 4.6 36.6 1.0
CA A:GLY15 4.7 36.0 1.0
C A:PHE13 4.7 36.3 1.0
C A:GLN14 4.8 36.4 1.0
O A:GLY15 4.9 35.9 1.0
N A:ARG247 4.9 28.5 1.0
CA A:ASN246 4.9 26.9 1.0

Chlorine binding site 4 out of 6 in 1v3v

Go back to Chlorine Binding Sites List in 1v3v
Chlorine binding site 4 out of 6 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2


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 Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1001

b:20.3
occ:1.00
 ND1 B:HIS12 3.0 21.4 1.0
N B:PHE13 3.2 20.3 1.0
OG B:SER54 3.2 19.6 1.0
O B:HOH2386 3.4 22.9 1.0
CA B:HIS12 3.6 20.8 1.0
CD2 B:PHE13 3.6 19.1 1.0
N B:LYS55 3.6 21.1 1.0
C B:SER54 3.6 20.5 1.0
CB B:HIS12 3.7 21.0 1.0
CB B:SER54 3.7 19.5 1.0
CG B:HIS12 3.8 21.4 1.0
O B:SER54 3.8 20.5 1.0
CA B:LYS55 3.8 22.2 1.0
C B:HIS12 3.8 20.6 1.0
CG B:PHE13 4.0 19.2 1.0
O B:HOH2549 4.0 49.0 1.0
CB B:PHE13 4.1 19.5 1.0
CG B:LYS55 4.1 22.2 1.0
CE1 B:HIS12 4.1 21.7 1.0
CA B:PHE13 4.1 19.9 1.0
CE2 B:PHE13 4.3 18.6 1.0
CA B:SER54 4.3 19.8 1.0
CD2 B:LEU9 4.4 20.1 1.0
O B:PHE13 4.4 19.6 1.0
CB B:LYS55 4.5 22.0 1.0
NH1 B:ARG51 4.5 14.6 1.0
CD1 B:LEU9 4.8 20.3 1.0
C B:PHE13 4.8 19.8 1.0
CD1 B:PHE13 4.8 19.1 1.0
N B:HIS12 4.9 20.9 1.0
O B:ARG51 5.0 16.0 1.0

Chlorine binding site 5 out of 6 in 1v3v

Go back to Chlorine Binding Sites List in 1v3v
Chlorine binding site 5 out of 6 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1002

b:26.3
occ:1.00
 O B:HOH2552 2.9 34.5 1.0
O B:HOH2533 2.9 35.3 1.0
O B:HOH2556 3.0 20.9 1.0
OD1 B:ASN318 3.0 18.3 1.0
CG B:GLU315 3.7 17.2 1.0
CB B:ASN318 3.7 17.0 1.0
CG B:ASN318 3.7 17.8 1.0
CA B:GLU315 3.9 15.7 1.0
CB B:GLU315 3.9 16.4 1.0
CB B:ALA320 3.9 16.8 1.0
O B:GLU315 4.2 15.6 1.0
O B:HOH2786 4.2 49.4 1.0
C B:GLU315 4.5 15.8 1.0
N B:ALA320 4.7 16.7 1.0
CA B:ALA320 4.8 16.7 1.0
O B:HOH2521 4.9 22.1 1.0
CD B:GLU315 4.9 17.7 1.0
CA B:ASN318 4.9 16.6 1.0
C B:ASN318 4.9 16.6 1.0
O B:ASN318 4.9 16.4 1.0
O B:HOH2456 5.0 28.5 1.0

Chlorine binding site 6 out of 6 in 1v3v

Go back to Chlorine Binding Sites List in 1v3v
Chlorine binding site 6 out of 6 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complexed with Nadp and 15-Oxo-PGE2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1006

b:25.0
occ:1.00
 O B:HOH2410 3.0 17.0 1.0
O B:HOH2765 3.2 49.0 1.0
O B:HOH2696 3.3 32.3 1.0
NH2 B:ARG51 3.3 15.0 1.0
O B:HOH2502 3.3 26.7 1.0
N B:GLY15 3.4 19.7 1.0
O B:ASN246 3.5 19.4 1.0
O B:HOH2386 3.6 22.9 1.0
O B:PHE13 3.7 19.6 1.0
CA B:GLN14 3.9 19.9 1.0
NZ B:LYS55 4.0 21.8 1.0
O B:HOH2576 4.0 38.2 1.0
C B:GLN14 4.1 19.8 1.0
C B:ASN246 4.2 19.5 1.0
O B:HOH2401 4.3 20.5 1.0
CA B:GLY15 4.3 19.8 1.0
CZ B:ARG51 4.4 14.6 1.0
C B:PHE13 4.4 19.8 1.0
N B:GLN14 4.5 20.0 1.0
NH1 B:ARG51 4.6 14.6 1.0
O B:GLY15 4.8 19.6 1.0
O B:HOH2697 4.8 35.3 1.0
CA B:ASN246 4.9 18.8 1.0
N B:ARG247 4.9 20.1 1.0
O B:HOH2776 4.9 60.4 1.0
OD2 B:ASP249 5.0 26.5 1.0
CB B:GLN14 5.0 20.6 1.0

Reference:

T.Hori, T.Yokomizo, H.Ago, M.Sugahara, G.Ueno, M.Yamamoto, T.Kumasaka, T.Shimizu, M.Miyano. Structural Basis of Leukotriene B4 12-Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Catalytic Mechanism and A Possible Src Homology 3 Domain Binding Loop J.Biol.Chem. V. 279 22615 2004.
ISSN: ISSN 0021-9258
PubMed: 15007077
DOI: 10.1074/JBC.M312655200
Page generated: Sat Jul 20 02:56:30 2024

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