Iodine 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:

Sodium

(Na)

1 atom

The binding sites of Iodine 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 Iodine atom.
In total 3 binding sites of Iodine where determined in the Crystal Structure of DOT1L in Complex with 5-Iodotubercidin, PDB code: 3uwp:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Crystal Structure of DOT1L in Complex with 5-Iodotubercidin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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:I421 b:61.7 occ:0.30 IAE A:5ID421 0.0 61.7 0.3 C7 A:5ID421 2.1 42.8 1.0 C8 A:5ID421 3.0 39.8 1.0 I A:IOD422 3.0 57.0 0.5 C5 A:5ID421 3.3 39.9 1.0 N6 A:5ID421 3.8 44.6 1.0 C6 A:5ID421 4.0 41.4 1.0 CG2 A:VAL249 4.0 42.6 1.0 N9 A:5ID421 4.2 40.6 1.0 CG1 A:VAL249 4.2 40.3 1.0 C4 A:5ID421 4.3 38.6 1.0 I A:IOD423 4.4 54.9 0.2 CZ A:PHE223 4.6 36.3 1.0 CE1 A:PHE245 4.7 34.3 1.0 CB A:VAL249 4.7 41.6 1.0 CZ A:PHE245 4.9 34.4 1.0 CD1 A:PHE245 4.9 35.9 1.0

Iodine binding site 2 out of 3 in the Crystal Structure of DOT1L in Complex with 5-Iodotubercidin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of DOT1L in Complex with 5-Iodotubercidin within 5.0Å range: probe atom residue distance (Å) B Occ A:I422 b:57.0 occ:0.45 IAE A:5ID421 3.0 61.7 0.3 N6 A:5ID421 3.4 44.6 1.0 CD1 A:LEU224 4.0 45.3 1.0 CG2 A:VAL249 4.1 42.6 1.0 C7 A:5ID421 4.3 42.8 1.0 C6 A:5ID421 4.4 41.4 1.0 C5 A:5ID421 4.6 39.9 1.0 CD A:LYS187 4.7 46.7 1.0 CG A:LEU224 4.9 43.3 1.0

Iodine binding site 3 out of 3 in the Crystal Structure of DOT1L in Complex with 5-Iodotubercidin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of DOT1L in Complex with 5-Iodotubercidin within 5.0Å range: probe atom residue distance (Å) B Occ A:I423 b:54.9 occ:0.25 N A:GLY246 3.2 40.9 1.0 CG2 A:VAL249 3.5 42.6 1.0 CA A:PHE245 4.0 36.0 1.0 CA A:GLY246 4.1 43.1 1.0 C A:PHE245 4.1 38.0 1.0 CB A:VAL249 4.3 41.6 1.0 IAE A:5ID421 4.4 61.7 0.3 CB A:PHE245 4.6 34.6 1.0 O A:ALA244 4.8 37.2 1.0 CD1 A:PHE245 4.9 35.9 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