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Ytterbium in PDB 5aen: Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine

Enzymatic activity of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine

All present enzymatic activity of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine:
3.3.2.6;

Protein crystallography data

The structure of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine, PDB code: 5aen was solved by D.Moser, S.K.Wittmann, J.Kramer, R.Blocher, J.Achenbach, D.Pogoryelov, E.Proschak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.715 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.996, 86.953, 98.223, 90.00, 90.00, 90.00
R / Rfree (%) 17.04 / 18.88

Other elements in 5aen:

The structure of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine (pdb code 5aen). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 4 binding sites of Ytterbium where determined in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine, PDB code: 5aen:
Jump to Ytterbium binding site number: 1; 2; 3; 4;

Ytterbium binding site 1 out of 4 in 5aen

Go back to Ytterbium Binding Sites List in 5aen
Ytterbium binding site 1 out of 4 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb613

b:27.0
occ:1.00
OD2 A:ASP481 2.8 7.4 1.0
O A:HOH2502 2.8 11.0 0.9
OD1 A:ASP481 2.8 7.4 1.0
CG A:ASP481 3.2 8.8 1.0
OD1 A:ASP482 4.3 10.5 1.0
OD2 A:ASP482 4.4 9.8 1.0
O A:HOH2498 4.6 11.0 0.9
CB A:ASP481 4.7 10.9 1.0
CG A:ASP482 4.8 11.1 1.0
CG A:LYS479 4.9 9.9 1.0
CB A:LYS479 4.9 9.6 1.0

Ytterbium binding site 2 out of 4 in 5aen

Go back to Ytterbium Binding Sites List in 5aen
Ytterbium binding site 2 out of 4 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb614

b:35.4
occ:1.00
OE2 A:GLU121 2.4 29.3 1.0
OE1 A:GLU121 2.6 26.2 1.0
CD A:GLU121 2.8 25.9 1.0
CG A:GLU121 4.3 25.8 1.0

Ytterbium binding site 3 out of 4 in 5aen

Go back to Ytterbium Binding Sites List in 5aen
Ytterbium binding site 3 out of 4 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb615

b:28.0
occ:1.00
OD2 A:ASP426 2.4 15.9 1.0
OD1 A:ASP422 2.5 16.0 1.0
O A:HOH2446 2.5 20.0 0.9
O A:HOH2444 2.5 18.4 1.0
OD2 A:ASP422 2.5 16.9 1.0
OD1 A:ASP426 2.5 17.4 1.0
O A:HOH2445 2.7 24.2 0.9
O A:HOH2454 2.7 22.1 1.0
CG A:ASP426 2.8 16.7 1.0
CG A:ASP422 2.8 16.2 1.0
CB A:ASP426 4.3 17.5 1.0
CB A:ASP422 4.3 16.0 1.0
O A:HOH2451 4.4 20.9 1.0
O A:ASP422 4.5 14.0 1.0
O A:HOH2198 4.6 30.8 0.9
C A:ASP422 4.9 14.1 1.0

Ytterbium binding site 4 out of 4 in 5aen

Go back to Ytterbium Binding Sites List in 5aen
Ytterbium binding site 4 out of 4 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Dimethyl(2-(4-Phenoxyphenoxy)Ethyl)Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb616

b:28.2
occ:1.00
OD2 A:ASP47 2.5 7.2 1.0
OD1 A:ASP47 2.6 8.9 1.0
O A:HOH2073 2.7 7.5 0.8
O A:HOH2607 2.7 4.8 0.9
CG A:ASP47 2.8 8.4 1.0
O A:HOH2072 2.9 7.9 0.9
CB A:ASP47 4.3 10.7 1.0
N A:ASN48 4.3 11.0 1.0
O A:HOH2075 4.4 9.2 1.0
CB A:ASN48 4.7 10.7 1.0
CA A:ASN48 4.8 11.2 1.0
O A:HOH2071 4.8 12.1 0.9
O A:HOH2074 4.8 16.3 0.9
O A:HOH2070 4.9 13.7 0.8
O A:HOH2030 4.9 17.7 0.8
CA A:ASP47 4.9 10.9 1.0
C A:ASP47 5.0 11.4 1.0

Reference:

D.Moser, S.K.Wittmann, J.Kramer, R.Blocher, J.Achenbach, D.Pogoryelov, E.Proschak. Peng: A Neural Gas-Based Approach For Pharmacophore Elucidation. Method Design, Validation and Virtual Screening For Novel Ligands of LTA4H. J.Chem.Inf.Model. 2015.
ISSN: ESSN 1549-960X
PubMed: 25625859
DOI: 10.1021/CI500618U
Page generated: Wed Dec 16 02:42:02 2020

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