Yttrium in PDB 8u7c: Engineered Nemo Minimal Ikk-Binding Domain

The structure of Engineered Nemo Minimal Ikk-Binding Domain, PDB code: 8u7c was solved by A.E.Kennedy, M.Pellegrini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.23 / 1.44
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.514, 40.892, 50.15, 92.62, 106.14, 98.87
R / Rfree (%)	17.3 / 20.2

The structure of Engineered Nemo Minimal Ikk-Binding Domain also contains other interesting chemical elements:

Terbium	(Tb)	3 atoms
Erbium	(Er)	1 atom

The binding sites of Yttrium atom in the Engineered Nemo Minimal Ikk-Binding Domain (pdb code 8u7c). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 2 binding sites of Yttrium where determined in the Engineered Nemo Minimal Ikk-Binding Domain, PDB code: 8u7c:
Jump to Yttrium binding site number: 1; 2;

Yttrium binding site 1 out of 2 in the Engineered Nemo Minimal Ikk-Binding Domain


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Engineered Nemo Minimal Ikk-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Y201 b:70.0 occ:1.00 OE2 B:GLU88 2.5 65.8 1.0 OE1 B:GLU91 2.5 47.0 1.0 OE1 B:GLU88 2.8 69.7 1.0 CD B:GLU88 3.0 52.9 1.0 CD B:GLU91 3.6 59.0 1.0 OE2 B:GLU91 4.1 55.2 1.0 O B:HOH312 4.4 28.2 1.0 CG B:GLU88 4.5 33.4 1.0 CG B:GLU91 4.9 35.5 1.0 NH1 B:ARG87 4.9 41.9 1.0

Yttrium binding site 2 out of 2 in the Engineered Nemo Minimal Ikk-Binding Domain


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Engineered Nemo Minimal Ikk-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Y204 b:38.4 occ:1.00 OE2 D:GLU88 2.4 52.3 1.0 OE1 D:GLU91 2.6 32.3 1.0 N D:BTB210 2.6 58.7 1.0 O D:HOH301 2.6 35.3 1.0 O1 D:BTB210 2.6 64.8 1.0 OE1 D:GLU88 2.7 53.0 1.0 O6 D:BTB210 2.8 55.3 1.0 C2 D:BTB210 2.8 63.9 1.0 CD D:GLU88 2.9 48.8 1.0 C4 D:BTB210 3.0 60.6 1.0 O4 D:BTB210 3.0 59.8 1.0 C8 D:BTB210 3.1 60.8 1.0 C1 D:BTB210 3.1 64.8 1.0 C7 D:BTB210 3.2 57.9 1.0 O8 D:BTB210 3.2 62.8 1.0 C5 D:BTB210 3.6 57.5 1.0 CD D:GLU91 3.7 29.3 1.0 C6 D:BTB210 3.7 56.1 1.0 OE2 D:GLU91 4.1 33.7 1.0 C3 D:BTB210 4.3 70.3 1.0 CG D:GLU88 4.4 35.4 1.0 NE D:ARG87 4.6 38.9 1.0 O D:HOH307 4.6 23.9 1.0 NH2 D:ARG87 4.8 47.7 1.0 CG D:GLU91 4.9 18.6 1.0

A.E.Kennedy, A.H.Barczewski, C.R.Arnoldy, J.P.Pennington, K.A.Tiernan, M.B.Hidalgo, C.C.Reilly, T.Wongsri, M.J.Ragusa, G.Grigoryan, D.F.Mierke, M.Pellegrini. The Structure of A Nemo Construct Engineered For Screening Reveals Novel Determinants of Inhibition Structure 2025.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2025.01.010