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Ytterbium in PDB 8ava: Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine

Enzymatic activity of Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine

All present enzymatic activity of Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine:
3.3.2.6; 3.4.11.4;

Protein crystallography data

The structure of Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine, PDB code: 8ava was solved by T.Teder, J.Z.Haeggstrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.64 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.072, 87.094, 99.271, 90, 90, 90
R / Rfree (%) 14.6 / 16.9

Other elements in 8ava:

The structure of Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine (pdb code 8ava). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 5 binding sites of Ytterbium where determined in the Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine, PDB code: 8ava:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5;

Ytterbium binding site 1 out of 5 in 8ava

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Ytterbium binding site 1 out of 5 in the Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine


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 in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb702

b:15.3
occ:1.00
 O A:HOH1080 2.2 17.7 1.0
O A:ACT707 2.3 13.8 1.0
OD1 A:ASP47 2.5 17.8 1.0
OD2 A:ASP47 2.5 17.8 1.0
OXT A:ACT707 2.5 15.5 1.0
C A:ACT707 2.7 13.3 1.0
CG A:ASP47 2.8 17.5 1.0
O A:HOH1270 4.3 40.3 1.0
CH3 A:ACT707 4.3 15.9 1.0
CB A:ASP47 4.3 17.9 1.0
N A:ASN48 4.5 17.0 1.0
OG A:SER95 4.5 17.9 0.4
O A:HOH948 4.5 14.3 1.0
O A:HOH1365 4.6 34.6 1.0
O A:HOH912 4.7 24.8 1.0
O A:HOH877 4.8 22.1 1.0
CB A:ASN48 4.8 18.2 1.0
CA A:ASP47 4.9 16.9 1.0

Ytterbium binding site 2 out of 5 in 8ava

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Ytterbium binding site 2 out of 5 in the Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine


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 in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb703

b:46.6
occ:0.48
 O A:HOH1413 2.1 35.4 1.0
O A:HOH932 2.2 44.5 1.0
OD1 A:ASP175 2.3 32.0 1.0
O A:HOH1241 2.5 54.8 1.0
O A:HOH1223 3.1 44.8 1.0
CG A:ASP175 3.4 29.7 1.0
O A:HOH1425 3.5 53.3 1.0
OD2 A:ASP175 4.0 35.2 1.0
O A:HOH1336 4.1 63.5 1.0
O A:HOH1131 4.2 48.2 1.0
CB A:ASP175 4.6 24.9 1.0
CA A:ASP175 4.7 22.0 1.0
O A:ASP175 4.7 26.4 1.0

Ytterbium binding site 3 out of 5 in 8ava

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Ytterbium binding site 3 out of 5 in the Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine


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 in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb704

b:29.8
occ:0.58
 YB A:YB704 0.0 29.8 0.6
O A:HOH811 1.4 12.7 1.0
OD1 A:ASP426 2.0 19.6 0.6
O A:HOH819 2.2 38.3 1.0
O A:HOH876 2.3 35.2 1.0
O A:HOH873 2.5 31.2 1.0
OXT A:ACT712 2.6 40.4 1.0
CG A:ASP426 3.3 20.1 0.6
O A:HOH814 3.5 29.2 1.0
OD1 A:ASP426 3.7 23.4 0.4
C A:ACT712 3.8 48.8 1.0
O A:HOH840 3.8 49.1 1.0
YB A:YB704 3.9 42.8 0.4
CG A:ASP426 4.1 21.5 0.4
OD2 A:ASP426 4.1 22.3 0.6
CB A:ASP426 4.3 18.8 0.6
CB A:ASP426 4.3 19.9 0.4
CA A:ASP426 4.4 18.7 0.4
CA A:ASP426 4.4 18.0 0.6
O A:ASP426 4.5 18.6 0.4
O A:HOH806 4.5 49.3 1.0
O A:ASP426 4.5 18.1 0.6
CH3 A:ACT712 4.6 46.3 1.0
O A:HOH830 4.7 46.0 1.0
O A:ACT712 4.7 44.7 1.0
OD2 A:ASP426 4.8 23.6 0.4
C A:ASP426 5.0 18.1 0.4
CB A:TYR429 5.0 20.2 1.0
C A:ASP426 5.0 17.6 0.6

Ytterbium binding site 4 out of 5 in 8ava

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Ytterbium binding site 4 out of 5 in the Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb704

b:42.8
occ:0.42
 YB A:YB704 0.0 42.8 0.4
O A:HOH925 2.0 40.0 1.0
O A:HOH819 2.1 38.3 1.0
O A:HOH1440 2.3 47.4 1.0
O A:HOH830 2.4 46.0 1.0
O A:HOH876 2.5 35.2 1.0
O A:HOH840 3.0 49.1 1.0
OD1 A:ASP426 3.3 19.6 0.6
OD2 A:ASP426 3.3 22.3 0.6
CG A:ASP426 3.4 20.1 0.6
O A:HOH811 3.4 12.7 1.0
OD2 A:ASP426 3.8 23.6 0.4
YB A:YB704 3.9 29.8 0.6
O A:HOH814 4.1 29.2 1.0
CG A:ASP426 4.1 21.5 0.4
CB A:ASP426 4.5 19.9 0.4
CB A:ASP426 4.6 18.8 0.6
O A:HOH804 4.7 29.7 1.0
OD1 A:ASP426 4.7 23.4 0.4

Ytterbium binding site 5 out of 5 in 8ava

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Ytterbium binding site 5 out of 5 in the Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 5 of Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Oxazol-2- Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb705

b:49.0
occ:0.37
 O A:HOH839 2.4 36.6 1.0
O A:HOH856 2.5 44.8 1.0
OE1 A:GLU182 2.5 56.9 1.0
O A:HOH1359 2.7 43.5 1.0
CD A:GLU182 3.3 55.1 1.0
O A:HOH1283 3.4 31.8 1.0
O A:HOH809 3.7 55.7 1.0
OD1 A:ASP180 4.1 31.0 1.0
OE2 A:GLU182 4.1 57.7 1.0
CG A:GLU182 4.1 49.9 1.0
CB A:GLU182 4.1 43.6 1.0
OD2 A:ASP180 4.2 28.0 1.0
NH2 A:ARG24 4.5 52.6 1.0
O A:HOH1287 4.5 34.6 1.0
CG A:ASP180 4.6 29.0 1.0
O A:HOH1319 4.7 35.6 1.0
O A:HOH1422 4.9 46.5 1.0

Reference:

T.Teder, S.Konig, R.Singh, B.Samuelsson, O.Werz, U.Garscha, J.Z.Haeggstrom. Modulation of the 5-Lipoxygenase Pathway By Chalcogen-Containing Inhibitors of Leukotriene A4 Hydrolase Int J Mol Sci 2023.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS24087539
Page generated: Sat Oct 12 21:28:14 2024

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