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

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

All present enzymatic activity of Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Selenazol- 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)-Selenazol- 2-Amine, PDB code: 8awh 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) 43.13 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.022, 87.519, 99.007, 90, 90, 90
R / Rfree (%) 15.6 / 18.7

Other elements in 8awh:

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

Ytterbium binding site 1 out of 4 in 8awh

Go back to Ytterbium Binding Sites List in 8awh
Ytterbium binding site 1 out of 4 in the Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Selenazol- 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)-Selenazol- 2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb702

b:13.4
occ:0.97
 O A:HOH995 2.2 11.3 1.0
O A:ACT706 2.4 14.2 1.0
OD1 A:ASP47 2.4 17.1 1.0
OD2 A:ASP47 2.5 18.0 1.0
OXT A:ACT706 2.5 13.4 1.0
C A:ACT706 2.8 13.9 1.0
CG A:ASP47 2.8 17.1 1.0
CB A:ASP47 4.3 17.7 1.0
CH3 A:ACT706 4.3 15.7 1.0
O A:HOH1266 4.4 37.1 1.0
N A:ASN48 4.5 14.3 1.0
O A:HOH839 4.5 11.4 1.0
OG A:SER95 4.5 15.4 0.5
O A:HOH1315 4.7 41.2 1.0
O A:HOH874 4.7 20.8 1.0
CB A:ASN48 4.7 15.6 1.0
O A:HOH979 4.8 23.4 1.0
CA A:ASP47 5.0 15.6 1.0

Ytterbium binding site 2 out of 4 in 8awh

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Ytterbium binding site 2 out of 4 in the Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Selenazol- 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)-Selenazol- 2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb703

b:60.8
occ:0.49
 OD1 A:ASP175 2.3 32.1 1.0
O A:HOH1199 3.0 45.9 1.0
O A:HOH1137 3.1 49.7 1.0
O A:HOH1365 3.3 49.0 1.0
CG A:ASP175 3.4 30.6 1.0
OD2 A:ASP175 4.0 40.3 1.0
CB A:ASP175 4.5 25.0 1.0
O A:ASP175 4.5 26.6 1.0
CA A:ASP175 4.6 22.5 1.0
O A:HOH1021 4.8 49.4 1.0
C A:ASP175 4.9 22.6 1.0

Ytterbium binding site 3 out of 4 in 8awh

Go back to Ytterbium Binding Sites List in 8awh
Ytterbium binding site 3 out of 4 in the Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Selenazol- 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)-Selenazol- 2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb704

b:28.6
occ:0.58
 YB A:YB704 0.0 28.6 0.6
O A:HOH810 2.1 38.3 1.0
OD1 A:ASP426 2.1 19.4 0.6
O A:HOH924 2.4 27.8 1.0
OXT A:ACT711 2.6 45.1 1.0
CG A:ASP426 3.3 21.2 0.6
O A:HOH809 3.5 32.1 1.0
OD1 A:ASP426 3.7 24.4 0.4
C A:ACT711 3.7 46.1 1.0
YB A:YB704 3.9 67.4 0.4
OD2 A:ASP426 4.0 26.1 0.6
CG A:ASP426 4.1 21.3 0.4
CB A:ASP426 4.4 19.9 0.4
CB A:ASP426 4.4 19.3 0.6
CH3 A:ACT711 4.5 42.8 1.0
CA A:ASP426 4.5 18.6 0.4
CA A:ASP426 4.5 18.3 0.6
O A:HOH816 4.5 57.6 1.0
O A:ACT711 4.6 46.2 1.0
O A:ASP426 4.6 17.6 0.4
O A:ASP426 4.6 17.1 0.6
OD2 A:ASP426 4.7 23.3 0.4

Ytterbium binding site 4 out of 4 in 8awh

Go back to Ytterbium Binding Sites List in 8awh
Ytterbium binding site 4 out of 4 in the Leukotriene A4 Hydrolase in Complex with 4-(4-Benzylphenyl)-Selenazol- 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)-Selenazol- 2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb704

b:67.4
occ:0.42
 YB A:YB704 0.0 67.4 0.4
O A:HOH816 2.4 57.6 1.0
OD2 A:ASP426 2.6 26.1 0.6
O A:HOH810 2.9 38.3 1.0
CG A:ASP426 3.1 21.2 0.6
OD1 A:ASP426 3.1 19.4 0.6
OD2 A:ASP426 3.7 23.3 0.4
YB A:YB704 3.9 28.6 0.6
CG A:ASP426 4.1 21.3 0.4
O A:HOH809 4.3 32.1 1.0
CB A:ASP426 4.4 19.9 0.4
CB A:ASP426 4.5 19.3 0.6
OD1 A:ASP426 4.8 24.4 0.4
O A:HOH808 4.9 32.2 1.0
O A:HOH924 4.9 27.8 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 21:28:17 2024

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