Sodium in PDB 3uwp: Crystal Structure of DOT1L in Complex with 5-Iodotubercidin

All present enzymatic activity of Crystal Structure of DOT1L in Complex with 5-Iodotubercidin:
2.1.1.43;

The structure of Crystal Structure of DOT1L in Complex with 5-Iodotubercidin, PDB code: 3uwp was solved by W.Yu, W.Tempel, D.Smil, M.Schapira, Y.Li, M.Vedadi, K.T.Nguyen, A.K.Wernimont, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, P.J.Brown, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.05
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	149.784, 149.784, 53.521, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 22.3

The structure of Crystal Structure of DOT1L in Complex with 5-Iodotubercidin also contains other interesting chemical elements:

Iodine

(I)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of DOT1L in Complex with 5-Iodotubercidin (pdb code 3uwp). 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 DOT1L in Complex with 5-Iodotubercidin, PDB code: 3uwp:

Sodium binding site 1 out of 1 in the Crystal Structure of DOT1L in Complex with 5-Iodotubercidin


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 DOT1L in Complex with 5-Iodotubercidin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na424 b:39.1 occ:1.00 O A:MET55 2.3 45.8 1.0 O A:HOH481 2.3 39.5 1.0 OD1 A:ASN57 2.3 40.1 1.0 O A:HOH480 2.4 36.6 1.0 O A:LYS52 2.6 39.5 1.0 O A:LEU53 2.7 44.4 1.0 CG A:ASN57 3.3 43.7 1.0 C A:LEU53 3.4 43.2 1.0 C A:MET55 3.5 46.2 1.0 CA A:LEU53 3.6 42.2 1.0 ND2 A:ASN57 3.6 39.4 1.0 C A:LYS52 3.7 38.9 1.0 O A:HOH482 3.8 57.6 1.0 N A:LEU53 4.1 38.9 1.0 N A:MET55 4.2 43.3 1.0 N A:ASN57 4.3 47.9 1.0 N A:ALA54 4.4 43.1 1.0 CA A:MET55 4.4 44.4 1.0 N A:GLU56 4.5 47.0 1.0 C A:ALA54 4.5 44.5 1.0 CB A:ASN57 4.6 46.2 1.0 CA A:GLU56 4.6 49.5 1.0 C A:GLU56 5.0 49.2 1.0 O A:ALA54 5.0 48.9 1.0 CA A:LYS52 5.0 37.5 1.0 CB A:LEU53 5.0 43.4 1.0 CA A:ALA54 5.0 44.0 1.0

W.Yu, E.J.Chory, A.K.Wernimont, W.Tempel, A.Scopton, A.Federation, J.J.Marineau, J.Qi, D.Barsyte-Lovejoy, J.Yi, R.Marcellus, R.E.Iacob, J.R.Engen, C.Griffin, A.Aman, E.Wienholds, F.Li, J.Pineda, G.Estiu, T.Shatseva, T.Hajian, R.Al-Awar, J.E.Dick, M.Vedadi, P.J.Brown, C.H.Arrowsmith, J.E.Bradner, M.Schapira. Catalytic Site Remodelling of the DOT1L Methyltransferase By Selective Inhibitors. Nat Commun V. 3 1288 2012.
ISSN: ESSN 2041-1723
PubMed: 23250418
DOI: 10.1038/NCOMMS2304