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Ytterbium in PDB 7av1: LTA4 Hydrolase in Complex with FRAGMENT2

Enzymatic activity of LTA4 Hydrolase in Complex with FRAGMENT2

All present enzymatic activity of LTA4 Hydrolase in Complex with FRAGMENT2:
3.3.2.6;

Protein crystallography data

The structure of LTA4 Hydrolase in Complex with FRAGMENT2, PDB code: 7av1 was solved by H.Srinivas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.18 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.873, 87.109, 98.962, 90, 90, 90
R / Rfree (%) 15.7 / 19.6

Other elements in 7av1:

The structure of LTA4 Hydrolase in Complex with FRAGMENT2 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the LTA4 Hydrolase in Complex with FRAGMENT2 (pdb code 7av1). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 2 binding sites of Ytterbium where determined in the LTA4 Hydrolase in Complex with FRAGMENT2, PDB code: 7av1:
Jump to Ytterbium binding site number: 1; 2;

Ytterbium binding site 1 out of 2 in 7av1

Go back to Ytterbium Binding Sites List in 7av1
Ytterbium binding site 1 out of 2 in the LTA4 Hydrolase in Complex with FRAGMENT2


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 FRAGMENT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb703

b:18.1
occ:1.00
OD2 A:ASP481 2.4 13.2 1.0
OXT A:ACT702 2.4 18.2 1.0
OD1 A:ASP481 2.4 13.4 1.0
O A:ACT702 2.5 18.2 1.0
CG A:ASP481 2.7 16.2 1.0
C A:ACT702 2.8 17.5 1.0
CB A:ASP481 4.2 15.7 1.0
CH3 A:ACT702 4.3 17.0 1.0
OD2 A:ASP482 4.4 22.9 1.0
OD1 A:ASP482 4.5 19.0 1.0
O A:HOH880 4.5 14.6 1.0
O A:HOH1290 4.7 26.1 1.0
CB A:LYS479 4.7 13.5 1.0
CG A:ASP482 4.8 20.3 1.0
CG A:LYS479 4.9 21.4 1.0

Ytterbium binding site 2 out of 2 in 7av1

Go back to Ytterbium Binding Sites List in 7av1
Ytterbium binding site 2 out of 2 in the LTA4 Hydrolase in Complex with FRAGMENT2


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 FRAGMENT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb704

b:46.1
occ:0.41
OD1 A:ASP175 2.4 34.2 1.0
CG A:ASP175 3.6 35.2 1.0
OD2 A:ASP175 4.1 44.3 1.0
CB A:ASP175 4.8 19.6 1.0
O A:ASP175 4.9 25.0 1.0
O A:HOH1390 4.9 51.6 1.0
CA A:ASP175 5.0 17.2 1.0

Reference:

C.Markert, G.Thoma, H.Srinivas, B.Bollbuck, R.M.Luond, W.Miltz, R.Wal̈Chli, R.Wolf, J.Hinrichs, C.Bergsdorf, K.Azzaoui, C.A.Penno, K.Klein, N.Wack, P.Jag̈Er, F.Hasler, C.Beerli, P.Loetscher, J.Dawson, G.Wieczorek, S.Numao, A.Littlewood-Evans, T.A.Rohn. Discovery of LYS006, A Potent and Highly Selective Inhibitor of Leukotriene A4 Hydrolase. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
Page generated: Wed Mar 3 15:46:53 2021

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