Sodium in PDB 5mj3: Interleukin-23 Complex with An Antagonistic Alphabody, Crystal Form 1

The structure of Interleukin-23 Complex with An Antagonistic Alphabody, Crystal Form 1, PDB code: 5mj3 was solved by J.Desmet, K.Verstraete, Y.Bloch, E.Lorent, Y.Wen, B.Devreese, K.Vandenbroucke, S.Loverix, T.Hettmann, S.Deroo, K.Somers, P.Hendrikx, I.Lasters, S.N.Savvides, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.61 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.960, 56.740, 100.070, 90.00, 99.73, 90.00
R / Rfree (%)	16.5 / 19.8

The binding sites of Sodium atom in the Interleukin-23 Complex with An Antagonistic Alphabody, Crystal Form 1 (pdb code 5mj3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Interleukin-23 Complex with An Antagonistic Alphabody, Crystal Form 1, PDB code: 5mj3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Interleukin-23 Complex with An Antagonistic Alphabody, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Interleukin-23 Complex with An Antagonistic Alphabody, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:39.4 occ:1.00 O A:HOH674 2.2 41.3 1.0 O A:THR114 2.2 34.0 1.0 O A:LEU117 2.3 35.8 1.0 O A:HOH540 2.5 42.6 1.0 O A:HOH650 2.6 44.4 1.0 HE1 A:PHE128 2.9 34.5 1.0 HA A:LYS118 3.4 38.9 1.0 C A:THR114 3.5 32.8 1.0 C A:LEU117 3.5 36.9 1.0 H A:ASP119 3.7 34.6 1.0 HA A:ASP115 3.7 33.8 1.0 CE1 A:PHE128 3.8 34.5 1.0 HB A:THR114 3.8 35.0 1.0 O A:HOH735 3.9 52.6 1.0 O A:ASP115 4.1 34.5 1.0 O A:HOH740 4.1 52.2 1.0 OG1 A:THR114 4.1 36.3 1.0 CA A:LYS118 4.1 38.9 1.0 C A:ASP115 4.2 34.2 1.0 N A:ASP119 4.2 34.6 1.0 CA A:ASP115 4.2 33.8 1.0 N A:LYS118 4.2 34.3 1.0 H A:LEU117 4.3 32.5 1.0 N A:ASP115 4.3 31.7 1.0 CB A:THR114 4.3 35.0 1.0 HG1 A:THR114 4.4 36.3 1.0 HB2 A:ASP119 4.4 38.9 1.0 HD1 A:PHE128 4.4 34.1 1.0 N A:LEU117 4.5 32.5 1.0 HZ A:PHE128 4.5 38.1 1.0 CA A:THR114 4.5 32.6 1.0 C A:LYS118 4.6 37.4 1.0 CA A:LEU117 4.6 31.5 1.0 CD1 A:PHE128 4.6 34.1 1.0 CZ A:PHE128 4.6 38.1 1.0 N A:ILE116 4.8 34.2 1.0 HB2 A:LEU117 5.0 31.9 1.0

Sodium binding site 2 out of 2 in the Interleukin-23 Complex with An Antagonistic Alphabody, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Interleukin-23 Complex with An Antagonistic Alphabody, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:36.8 occ:1.00 O A:SER249 2.2 42.0 1.0 O A:HOH658 2.5 37.5 1.0 O A:LEU246 2.5 39.8 1.0 O A:HOH732 2.9 58.9 1.0 HB2 A:PRO245 3.2 41.4 1.0 H A:SER249 3.2 33.9 1.0 C A:SER249 3.4 36.9 1.0 C A:LEU246 3.6 43.5 1.0 H A:LEU246 3.7 38.0 1.0 HA A:ARG250 3.8 33.2 1.0 N A:SER249 3.9 33.9 1.0 CB A:PRO245 4.0 41.4 1.0 N A:LEU246 4.0 38.0 1.0 HB3 A:PRO245 4.0 41.4 1.0 HA A:LYS247 4.0 45.6 1.0 H A:ASN248 4.2 35.0 1.0 CA A:SER249 4.3 34.4 1.0 N A:ARG250 4.4 34.8 1.0 CA A:LEU246 4.4 43.7 1.0 CA A:ARG250 4.5 33.2 1.0 C A:PRO245 4.5 43.0 1.0 N A:ASN248 4.5 35.0 1.0 N A:LYS247 4.5 43.0 1.0 CA A:LYS247 4.6 45.6 1.0 HA A:PRO245 4.6 39.0 1.0 CA A:PRO245 4.6 39.0 1.0 O A:GLN251 4.6 37.4 1.0 HB3 A:LEU246 4.7 50.1 1.0 C A:LYS247 4.7 41.0 1.0 HB3 A:SER249 4.7 36.4 1.0 HG12 A:VAL252 4.9 37.6 0.6

J.Desmet, K.Verstraete, Y.Bloch, E.Lorent, Y.Wen, B.Devreese, K.Vandenbroucke, S.Loverix, T.Hettmann, S.Deroo, K.Somers, P.Henderikx, I.Lasters, S.N.Savvides. Structural Basis of Il-23 Antagonism By An Alphabody Protein Scaffold. Nat Commun V. 5 5237 2014.
ISSN: ESSN 2041-1723
PubMed: 25354530
DOI: 10.1038/NCOMMS6237