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Chlorine in PDB 1v3u: Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form

Enzymatic activity of Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form

All present enzymatic activity of Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form:
1.3.1.48;

Protein crystallography data

The structure of Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form, PDB code: 1v3u 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) 32.20 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.486, 74.591, 79.296, 90.00, 102.05, 90.00
R / Rfree (%) 21.4 / 25.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form (pdb code 1v3u). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form, PDB code: 1v3u:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 1v3u

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Chlorine binding site 1 out of 7 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form


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 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1001

b:29.7
occ:1.00
 O A:HOH1045 3.1 31.4 1.0
O A:HOH1057 3.1 33.2 1.0
N A:ALA325 3.3 31.5 1.0
NZ A:LYS324 3.3 30.3 1.0
CD A:LYS324 3.7 31.0 1.0
CE A:LYS324 3.8 30.8 1.0
O A:VAL46 3.8 30.6 1.0
CB A:ALA325 3.8 31.0 1.0
ND2 A:ASN321 3.9 43.9 1.0
CB A:ALA153 3.9 20.6 1.0
CA A:LYS324 4.0 32.6 1.0
CG A:MET316 4.1 46.0 1.0
O A:GLY323 4.1 35.0 1.0
C A:LYS324 4.1 32.1 1.0
CA A:ALA325 4.1 31.2 1.0
CG A:LYS324 4.5 31.4 1.0
CD A:PRO48 4.6 36.8 1.0
SD A:MET316 4.6 45.8 1.0
O A:ALA325 4.7 30.4 1.0
OD2 A:ASP47 4.7 32.5 1.0
CB A:LYS324 4.8 32.2 1.0
N A:ALA153 4.9 20.5 1.0
CA A:ASP47 4.9 33.7 1.0
C A:GLY323 4.9 35.0 1.0
N A:LYS324 4.9 33.9 1.0
C A:ALA325 4.9 30.9 1.0
C A:VAL46 4.9 30.8 1.0
CG A:ASN321 4.9 43.7 1.0
O A:HOH1022 5.0 35.2 1.0

Chlorine binding site 2 out of 7 in 1v3u

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Chlorine binding site 2 out of 7 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form


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 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1004

b:52.3
occ:1.00
 O A:VAL72 2.9 27.0 1.0
NH1 A:ARG70 3.2 28.6 1.0
NH2 A:ARG70 3.3 27.8 1.0
O A:HOH1324 3.4 54.2 1.0
CZ A:ARG70 3.7 27.9 1.0
C A:VAL72 3.7 26.9 1.0
CA A:VAL72 3.7 26.6 1.0
O A:HOH1156 3.9 47.8 1.0
CG1 A:VAL72 4.0 27.4 1.0
O A:HOH1158 4.2 43.4 1.0
O A:VAL71 4.3 25.2 1.0
CB A:VAL72 4.4 26.8 1.0
CB A:ALA81 4.8 22.5 1.0
N A:VAL72 4.9 25.7 1.0
NE A:ARG70 5.0 27.5 1.0
N A:GLU73 5.0 27.0 1.0

Chlorine binding site 3 out of 7 in 1v3u

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Chlorine binding site 3 out of 7 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form


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 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1006

b:35.0
occ:1.00
 O A:HOH1257 3.0 53.8 1.0
N A:ALA151 3.2 20.6 1.0
C A:ALA149 3.4 21.4 1.0
CB A:ALA151 3.4 21.1 1.0
CA A:ALA149 3.5 21.8 1.0
NZ A:LYS178 3.5 31.5 1.0
CB A:ALA173 3.7 26.3 1.0
CA A:ALA151 3.7 20.8 1.0
CA A:ALA173 3.7 26.2 1.0
CD A:LYS178 3.8 31.3 1.0
N A:ALA150 3.8 20.8 1.0
N A:GLY174 3.8 27.1 1.0
N A:GLY152 3.8 20.8 1.0
O A:ALA149 3.9 21.3 1.0
C A:ALA151 4.0 21.0 1.0
CE A:LYS178 4.0 31.5 1.0
C A:ALA173 4.3 26.6 1.0
CB A:ALA149 4.3 22.1 1.0
C A:ALA150 4.3 20.6 1.0
N A:ALA149 4.6 22.1 1.0
O A:ALA172 4.6 25.4 1.0
CA A:ALA150 4.6 20.6 1.0
CA A:GLY152 4.8 20.8 1.0
O A:ALA151 4.8 21.1 1.0
O A:HOH1063 4.9 39.6 1.0
CA A:GLY174 4.9 27.8 1.0
CG A:LYS178 4.9 31.3 1.0
N A:ALA173 5.0 25.6 1.0

Chlorine binding site 4 out of 7 in 1v3u

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Chlorine binding site 4 out of 7 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form


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 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1002

b:26.1
occ:1.00
 O B:HOH1106 2.9 37.1 1.0
O B:HOH1119 3.0 34.3 1.0
N B:ALA151 3.3 19.8 1.0
NZ B:LYS178 3.3 26.7 1.0
N B:GLY174 3.5 27.5 1.0
C B:ALA149 3.6 19.3 1.0
CA B:ALA173 3.6 26.8 1.0
CA B:ALA149 3.6 19.6 1.0
CD B:LYS178 3.7 27.0 1.0
CB B:ALA151 3.8 20.2 1.0
CB B:ALA173 3.8 26.5 1.0
N B:ALA150 3.8 19.3 1.0
CA B:ALA151 3.9 20.0 1.0
CE B:LYS178 4.0 27.0 1.0
O B:ALA149 4.0 19.1 1.0
N B:GLY152 4.1 20.0 1.0
C B:ALA173 4.1 27.2 1.0
C B:ALA151 4.2 20.2 1.0
O B:GLY319 4.3 26.7 1.0
C B:ALA150 4.4 19.6 1.0
CB B:ALA149 4.5 19.8 1.0
O B:ALA172 4.5 25.9 1.0
OH B:TYR193 4.6 36.1 1.0
CA B:ALA150 4.6 19.5 1.0
CA B:GLY174 4.6 28.3 1.0
N B:ALA149 4.7 19.8 1.0
CG B:LYS178 4.8 27.2 1.0
N B:ALA173 4.8 26.2 1.0
CA B:GLY152 5.0 19.6 1.0

Chlorine binding site 5 out of 7 in 1v3u

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Chlorine binding site 5 out of 7 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form


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 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1003

b:32.4
occ:1.00
 OG B:SER54 3.0 26.5 1.0
O B:HOH1126 3.1 28.4 1.0
ND1 B:HIS12 3.1 25.7 1.0
N B:PHE13 3.2 25.0 1.0
CD2 B:PHE13 3.5 24.2 1.0
CB B:SER54 3.6 26.7 1.0
C B:SER54 3.6 27.6 1.0
CA B:HIS12 3.7 25.1 1.0
N B:LYS55 3.7 28.6 1.0
CB B:HIS12 3.7 25.2 1.0
O B:SER54 3.7 27.6 1.0
CG B:HIS12 3.8 25.5 1.0
C B:HIS12 3.9 25.1 1.0
CA B:LYS55 3.9 30.0 1.0
CG B:PHE13 3.9 24.4 1.0
CB B:PHE13 4.0 24.4 1.0
CA B:PHE13 4.1 24.9 1.0
CE1 B:HIS12 4.1 25.5 1.0
CG B:LYS55 4.1 30.8 1.0
CD2 B:LEU9 4.2 21.2 1.0
CE2 B:PHE13 4.2 23.9 1.0
CA B:SER54 4.3 26.9 1.0
NH1 B:ARG51 4.4 22.1 1.0
O B:HOH1240 4.4 41.4 1.0
O B:PHE13 4.6 24.9 1.0
CB B:LYS55 4.6 30.3 1.0
O B:ARG51 4.7 24.1 1.0
CD1 B:LEU9 4.8 21.2 1.0
CD1 B:PHE13 4.9 24.1 1.0
C B:PHE13 4.9 24.9 1.0

Chlorine binding site 6 out of 7 in 1v3u

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Chlorine binding site 6 out of 7 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form


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 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1005

b:19.0
occ:1.00
 O B:HOH1027 2.8 24.5 1.0
NZ B:LYS324 3.2 15.8 1.0
O B:HOH1043 3.3 25.4 1.0
N B:ALA325 3.3 16.7 1.0
ND2 B:ASN321 3.6 24.0 1.0
CD B:LYS324 3.7 16.3 1.0
CG B:MET316 3.7 23.7 1.0
CB B:ALA325 3.8 16.7 1.0
CE B:LYS324 3.8 15.8 1.0
O B:VAL46 3.9 16.2 1.0
CB B:ALA153 3.9 18.9 1.0
CA B:LYS324 4.1 17.5 1.0
CA B:ALA325 4.2 16.8 1.0
C B:LYS324 4.2 17.2 1.0
CG B:ASN321 4.5 24.5 1.0
CG B:LYS324 4.5 16.7 1.0
O B:GLY323 4.6 19.4 1.0
O B:ALA325 4.6 16.8 1.0
O B:HOH1100 4.7 33.6 1.0
N B:ALA153 4.8 19.0 1.0
CD B:PRO48 4.8 19.3 1.0
SD B:MET316 4.8 23.3 1.0
O B:HOH1186 4.8 24.7 1.0
CB B:LYS324 4.8 17.1 1.0
CB B:MET316 4.9 23.7 1.0
OD2 B:ASP47 4.9 17.4 1.0
C B:ALA325 4.9 16.9 1.0
OD1 B:ASN321 4.9 24.4 1.0
CA B:ALA153 5.0 18.9 1.0
CA B:ASP47 5.0 17.4 1.0
C B:VAL46 5.0 16.2 1.0

Chlorine binding site 7 out of 7 in 1v3u

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Chlorine binding site 7 out of 7 in the Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Leukotriene B4 12- Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1007

b:53.2
occ:1.00
 NE2 B:HIS12 3.2 25.6 1.0
N B:GLU59 3.4 29.2 1.0
CD2 B:HIS12 3.7 25.4 1.0
CA B:LYS58 3.8 30.2 1.0
O B:LEU57 3.9 30.7 1.0
CG B:GLU59 3.9 29.8 1.0
C B:LYS58 4.1 29.8 1.0
CB B:GLU59 4.3 29.1 1.0
CA B:GLU59 4.4 28.7 1.0
CE1 B:HIS12 4.4 25.5 1.0
O B:HOH1207 4.5 55.3 1.0
CG B:LYS58 4.5 31.4 1.0
CD B:GLU59 4.5 30.6 1.0
O B:HOH1327 4.6 66.9 1.0
CB B:LYS58 4.7 30.6 1.0
C B:LEU57 4.7 30.7 1.0
N B:LYS58 4.8 30.5 1.0
OE1 B:GLU59 4.8 30.9 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 02:55:56 2024

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