Ytterbium in PDB 8qpn: LTA4 Hydrolase in Complex with Compound 6(S)

All present enzymatic activity of LTA4 Hydrolase in Complex with Compound 6(S):
3.3.2.6;

The structure of LTA4 Hydrolase in Complex with Compound 6(S), PDB code: 8qpn was solved by H.Srinivas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.79, 86.869, 99.022, 90, 90, 90
R / Rfree (%)	18.9 / 22.3

The structure of LTA4 Hydrolase in Complex with Compound 6(S) also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Ytterbium atom in the LTA4 Hydrolase in Complex with Compound 6(S) (pdb code 8qpn). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 3 binding sites of Ytterbium where determined in the LTA4 Hydrolase in Complex with Compound 6(S), PDB code: 8qpn:
Jump to Ytterbium binding site number: 1; 2; 3;

Ytterbium binding site 1 out of 3 in the LTA4 Hydrolase in Complex with Compound 6(S)


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of LTA4 Hydrolase in Complex with Compound 6(S) within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb703 b:28.9 occ:1.00 O A:ACT702 2.5 29.3 1.0 OD1 A:ASP482 2.5 27.6 1.0 OD2 A:ASP482 2.6 23.1 1.0 OXT A:ACT702 2.6 29.2 1.0 C A:ACT702 2.9 29.1 1.0 CG A:ASP482 2.9 25.4 1.0 OD1 A:ASP483 4.3 24.9 1.0 OD2 A:ASP483 4.4 26.3 1.0 CH3 A:ACT702 4.4 28.4 1.0 CB A:ASP482 4.4 23.6 1.0 O A:HOH812 4.5 18.9 1.0 CG A:ASP483 4.7 25.4 1.0 CB A:LYS480 4.7 23.3 1.0 O A:HOH1186 4.8 50.4 1.0 CG A:LYS480 4.9 27.8 1.0

Ytterbium binding site 2 out of 3 in the LTA4 Hydrolase in Complex with Compound 6(S)


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of LTA4 Hydrolase in Complex with Compound 6(S) within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb704 b:46.2 occ:0.26 OD1 A:ASP176 2.4 41.0 1.0 CG A:ASP176 3.6 40.3 1.0 O A:HOH1317 4.2 46.4 1.0 OD2 A:ASP176 4.2 42.8 1.0 O A:ASP176 4.7 33.4 1.0 CB A:ASP176 4.7 34.2 1.0 CA A:ASP176 4.7 31.5 1.0 O A:HOH1207 4.9 48.8 1.0 C A:ASP176 4.9 33.0 1.0

Ytterbium binding site 3 out of 3 in the LTA4 Hydrolase in Complex with Compound 6(S)


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of LTA4 Hydrolase in Complex with Compound 6(S) within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb705 b:70.8 occ:1.00 OD1 A:ASP427 2.4 48.4 1.0 CG A:ASP427 3.7 45.6 1.0 O A:HOH943 3.7 26.6 1.0 CB A:ASP427 4.4 34.5 1.0 CA A:ASP427 4.5 30.4 1.0 O A:HOH1296 4.6 44.9 1.0 OD2 A:ASP427 4.6 50.1 1.0 O A:ASP427 4.6 29.9 1.0

G.Thoma, C.Markert, R.Lueoend, W.Miltz, C.Spanka, B.Bollbuck, R.M.Wolf, H.Srinivas, C.A.Penno, M.Kiffe, M.Gajewska, D.Bednarczyk, G.Wieczorek, A.Evans, C.Beerli, T.A.Rohn. Discovery of Amino Alcohols As Highly Potent, Selective, and Orally Efficacious Inhibitors of Leukotriene A4 Hydrolase. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 38015154
DOI: 10.1021/ACS.JMEDCHEM.3C01866