Sodium in PDB 9fjx: Crystal Structure of Human Crbn-DDB1 in Complex with Lenalidomide

The structure of Crystal Structure of Human Crbn-DDB1 in Complex with Lenalidomide, PDB code: 9fjx was solved by Y.-V.Le Bihan, R.L.M.Van Montfort, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.15 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.673, 129.068, 198.446, 90, 90, 90
R / Rfree (%)	19.6 / 23.2

The structure of Crystal Structure of Human Crbn-DDB1 in Complex with Lenalidomide also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human Crbn-DDB1 in Complex with Lenalidomide (pdb code 9fjx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human Crbn-DDB1 in Complex with Lenalidomide, PDB code: 9fjx:

Sodium binding site 1 out of 1 in the Crystal Structure of Human Crbn-DDB1 in Complex with Lenalidomide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Crbn-DDB1 in Complex with Lenalidomide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:72.8 occ:1.00 O B:HOH887 3.3 58.4 1.0 OD1 B:ASP279 3.8 54.5 1.0 CG2 B:ILE278 4.0 41.1 1.0 OD2 B:ASP279 4.2 56.7 1.0 CD1 B:ILE278 4.2 43.1 1.0 CG B:ASP279 4.3 53.1 1.0 CB B:ILE278 4.4 41.0 1.0 O B:HOH872 4.4 58.0 1.0 ND2 B:ASN276 4.4 57.1 1.0 CG B:ASN276 4.9 56.0 1.0 CG1 B:ILE278 5.0 41.9 1.0

Y.Chrisochoidou, A.Scarpino Dr, S.Morales, S.Martin, S.A.Bird, Y.Li Dr, B.A.Walker, J.Caldwell, Y.V.Le Bihan Dr, C.Pawlyn Dr. Evaluating the Impact of Crbn Mutations on Response to Immunomodulatory Drugs and Novel Crbn-Binding Agents in Myeloma. Blood 2025.
ISSN: ESSN 1528-0020
PubMed: 39841463
DOI: 10.1182/BLOOD.2024025861