Terbium 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:

Yttrium	(Y)	2 atoms
Erbium	(Er)	1 atom

The binding sites of Terbium atom in the Engineered Nemo Minimal Ikk-Binding Domain (pdb code 8u7c). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 3 binding sites of Terbium where determined in the Engineered Nemo Minimal Ikk-Binding Domain, PDB code: 8u7c:
Jump to Terbium binding site number: 1; 2; 3;

Terbium binding site 1 out of 3 in the Engineered Nemo Minimal Ikk-Binding Domain


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 1 of Engineered Nemo Minimal Ikk-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Tb201 b:27.9 occ:1.00 O4 A:BTB204 2.3 26.1 1.0 O3 A:BTB204 2.3 29.1 1.0 OE1 A:GLU91 2.4 16.0 1.0 O8 A:BTB204 2.4 25.6 1.0 O6 A:BTB204 2.4 24.8 1.0 OE1 A:GLU88 2.4 19.4 1.0 OE2 A:GLU91 2.5 22.7 1.0 N A:BTB204 2.5 23.9 1.0 O A:HOH313 2.6 15.5 1.0 CD A:GLU91 2.8 16.6 1.0 C2 A:BTB204 3.1 29.1 1.0 C4 A:BTB204 3.2 26.7 1.0 C3 A:BTB204 3.3 30.0 1.0 C6 A:BTB204 3.3 25.2 1.0 C5 A:BTB204 3.4 27.0 1.0 CD A:GLU88 3.4 25.6 1.0 C8 A:BTB204 3.5 26.9 1.0 C7 A:BTB204 3.6 27.9 1.0 OE2 A:GLU88 3.7 33.7 1.0 O A:HOH304 4.2 37.5 1.0 CG A:GLU91 4.3 12.3 1.0 O A:PRO205 4.4 74.2 1.0 O A:HOH306 4.4 36.7 1.0 N A:PRO205 4.5 65.3 1.0 C A:PRO205 4.7 73.0 1.0 C1 A:BTB204 4.7 31.5 1.0 O A:HOH323 4.7 14.3 1.0 CG A:GLU88 4.8 17.1 1.0

Terbium binding site 2 out of 3 in the Engineered Nemo Minimal Ikk-Binding Domain


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 2 of Engineered Nemo Minimal Ikk-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Tb201 b:12.4 occ:1.00 O8 D:BTB209 2.2 11.3 1.0 O6 D:BTB209 2.3 13.8 1.0 OE1 D:GLU77 2.3 13.3 1.0 OE1 D:GLU74 2.4 11.8 1.0 O4 D:BTB209 2.4 10.1 1.0 O3 D:BTB209 2.5 12.8 1.0 OE2 D:GLU74 2.6 12.5 1.0 O D:HOH322 2.6 13.6 1.0 N D:BTB209 2.7 14.1 1.0 CD D:GLU74 2.8 11.5 1.0 C6 D:BTB209 3.1 12.8 1.0 C2 D:BTB209 3.3 12.3 1.0 C8 D:BTB209 3.3 14.1 1.0 CD D:GLU77 3.3 12.2 1.0 C4 D:BTB209 3.4 15.1 1.0 C5 D:BTB209 3.4 15.1 1.0 C7 D:BTB209 3.5 13.2 1.0 C3 D:BTB209 3.5 14.0 1.0 OE2 D:GLU77 3.7 12.1 1.0 CG D:GLU74 4.4 11.9 1.0 CG D:GLU77 4.6 9.5 1.0 NE D:ARG73 4.7 20.4 1.0 C1 D:BTB209 4.8 17.0 1.0 O D:HOH306 4.8 19.5 1.0 CB D:GLU77 4.8 7.4 1.0 NH2 D:ARG73 4.9 36.0 1.0

Terbium binding site 3 out of 3 in the Engineered Nemo Minimal Ikk-Binding Domain


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 3 of Engineered Nemo Minimal Ikk-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Tb202 b:11.2 occ:1.00 O8 D:BTB208 2.1 25.8 1.0 O4 D:BTB207 2.2 8.5 1.0 O4 D:BTB208 2.3 21.0 1.0 OE1 D:GLU56 2.4 10.9 1.0 O D:HOH311 2.4 14.2 1.0 O6 D:BTB208 2.5 16.1 1.0 O3 D:BTB208 2.5 12.5 1.0 N D:BTB208 2.6 12.9 1.0 C8 D:BTB208 3.1 14.2 1.0 C2 D:BTB208 3.2 15.0 1.0 C4 D:BTB208 3.3 15.0 1.0 C7 D:BTB208 3.3 12.9 1.0 CD D:GLU56 3.3 10.3 1.0 C4 D:BTB207 3.4 8.1 1.0 C3 D:BTB208 3.4 14.9 1.0 C6 D:BTB208 3.4 20.9 1.0 C5 D:BTB208 3.4 13.6 1.0 ER D:ER3203 3.7 13.8 1.0 OE2 D:GLU56 3.7 18.3 1.0 O D:HOH342 4.3 24.6 1.0 O D:HOH333 4.4 27.9 1.0 O8 D:BTB207 4.4 15.1 1.0 O D:HOH303 4.5 25.2 1.0 C2 D:BTB207 4.6 6.6 1.0 O3 D:BTB207 4.6 11.8 1.0 CG D:GLU56 4.7 8.0 1.0 C1 D:BTB208 4.7 17.4 1.0 C8 D:BTB207 4.7 14.3 1.0 O D:HOH304 4.9 13.2 1.0 CB D:GLU56 4.9 8.2 1.0 C3 D:BTB207 4.9 11.0 1.0 N D:BTB207 5.0 9.9 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