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Ytterbium in PDB 3fhe: Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine.

Enzymatic activity of Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine.

All present enzymatic activity of Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine.:
3.3.2.6;

Protein crystallography data

The structure of Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine., PDB code: 3fhe was solved by B.Mamat, D.R.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.911, 86.844, 99.318, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 21.9

Other elements in 3fhe:

The structure of Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine. also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine. (pdb code 3fhe). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 3 binding sites of Ytterbium where determined in the Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine., PDB code: 3fhe:
Jump to Ytterbium binding site number: 1; 2; 3;

Ytterbium binding site 1 out of 3 in 3fhe

Go back to Ytterbium Binding Sites List in 3fhe
Ytterbium binding site 1 out of 3 in the Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine.


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb1002

b:33.4
occ:1.00
 O A:HOH920 2.3 29.5 1.0
O A:HOH642 2.3 30.3 1.0
OD1 A:ASP481 2.4 27.2 1.0
O A:HOH622 2.5 23.2 1.0
OXT A:ACT1005 2.5 27.2 1.0
OD2 A:ASP481 2.5 29.9 1.0
O A:ACT1005 2.6 28.4 1.0
CG A:ASP481 2.8 31.9 1.0
C A:ACT1005 3.0 28.2 1.0
CB A:ASP481 4.3 27.8 1.0
OD1 A:ASP482 4.3 29.9 1.0
OD2 A:ASP482 4.4 29.2 1.0
O A:HOH700 4.4 32.4 1.0
CH3 A:ACT1005 4.5 26.6 1.0
CG A:ASP482 4.7 30.1 1.0
CB A:LYS479 4.8 29.9 1.0
O A:HOH976 5.0 49.3 1.0

Ytterbium binding site 2 out of 3 in 3fhe

Go back to Ytterbium Binding Sites List in 3fhe
Ytterbium binding site 2 out of 3 in the Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine.


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb1003

b:60.2
occ:0.50
 O A:HOH984 2.2 54.9 1.0
OD1 A:ASP175 2.3 47.9 1.0
O A:HOH967 2.7 52.9 1.0
CG A:ASP175 3.2 39.2 1.0
OD2 A:ASP175 3.5 44.9 1.0
O A:HOH1043 4.3 57.5 1.0
CB A:ASP175 4.5 37.6 1.0
CA A:ASP175 4.8 36.4 1.0

Ytterbium binding site 3 out of 3 in 3fhe

Go back to Ytterbium Binding Sites List in 3fhe
Ytterbium binding site 3 out of 3 in the Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine.


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Leukotriene A4 Hydrolase Complexed with Inhibitor N-[3-(4- Benzylphenoxy)Propyl]-N-Methyl-Beta-Alanine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb611

b:59.8
occ:1.00
 O A:HOH1045 2.0 37.0 1.0
O A:HOH986 2.6 32.0 1.0
OD2 A:ASP426 2.8 47.2 1.0
CG A:ASP426 3.5 44.2 1.0
OD1 A:ASP426 3.6 53.7 1.0
O A:HOH624 3.7 21.2 1.0
O A:HOH997 4.0 58.8 1.0
O A:HOH812 4.0 38.6 1.0
O A:HOH780 4.2 39.1 1.0
O A:ASP426 4.5 32.1 1.0
CB A:ASP426 4.7 37.7 1.0
CA A:ASP426 4.7 34.2 1.0

Reference:

V.Sandanayaka, B.Mamat, R.K.Mishra, J.Winger, M.Krohn, L.M.Zhou, M.Keyvan, L.Enache, D.Sullins, E.Onua, J.Zhang, G.Halldorsdottir, H.Sigthorsdottir, A.Thorlaksdottir, G.Sigthorsson, M.Thorsteinnsdottir, D.R.Davies, L.J.Stewart, D.E.Zembower, T.Andresson, A.S.Kiselyov, J.Singh, M.E.Gurney. Discovery of 4-[(2S)-2-{[4-(4-Chlorophenoxy) Phenoxy]Methyl}-1-Pyrrolidinyl]Butanoic Acid (Dg-051) As A Novel Leukotriene A4 Hydrolase Inhibitor of Leukotriene B4 Biosynthesis. J.Med.Chem. V. 53 573 2010.
ISSN: ISSN 0022-2623
PubMed: 19950900
DOI: 10.1021/JM900838G
Page generated: Sat Oct 12 21:04:55 2024

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