Sodium in the structure of Crystal Structure of DOT1L in Complex With 5-Iodotubercidin (pdb 3uwp)

The binding sites of Sodium atom in the structure of Crystal Structure of DOT1L in Complex With 5-Iodotubercidin (pdb code 3uwp). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3uwp structure 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, brief refinement statistics is given in the table below: Resolution (A) 40.0-2.0 Space group P65 a (A) 149.784 b (A) 149.784 c (A) 53.521 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.5 Rfree (%) 22.3 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3uwp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3uwp. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys52, A: Leu53, A: Ala54, A: Met55, A: Glu56, A: Asn57, A: Hoh480, A: Hoh481, A: Hoh482, conact list: Atom Atom Distance (A) Na O A:Lys52 2.57 Na C A:Lys52 3.67 Na CA A:Lys52 4.97 Na O A:Leu53 2.74 Na N A:Leu53 4.12 Na CB A:Leu53 4.99 Na C A:Leu53 3.36 Na CA A:Leu53 3.63 Na O A:Ala54 4.97 Na N A:Ala54 4.37 Na C A:Ala54 4.53 Na CA A:Ala54 4.99 Na O A:Met55 2.33 Na N A:Met55 4.16 Na C A:Met55 3.54 Na CA A:Met55 4.43 Na N A:Glu56 4.47 Na C A:Glu56 4.96 Na CA A:Glu56 4.59 Na N A:Asn57 4.28 Na CB A:Asn57 4.55 Na ND2 A:Asn57 3.64 Na OD1 A:Asn57 2.35 Na CG A:Asn57 3.27 Na O A:Hoh480 2.37 Na O A:Hoh481 2.34 Na O A:Hoh482 3.80 interactive model: