Bromine in the structure of Binding Of The Modified Daunorubicin WP401 Adjacent to A T- G Base Pair Induces The Reverse Watson-Crick Conformation: Crystal Structures of the WP401-Tggccg and WP401- Cgg[BR5C]Cg Complexes (pdb 380d)

The binding sites of Bromine atom in the structure of Binding Of The Modified Daunorubicin WP401 Adjacent to A T- G Base Pair Induces The Reverse Watson-Crick Conformation: Crystal Structures of the WP401-Tggccg and WP401- Cgg[BR5C]Cg Complexes (pdb code 380d). This binding sites where shown with 5.0 Angstroms radius around Bromine atom. The 380d structure was solved by R.DUTTA, Y.-G.GAO, W.PRIEBE, A.H.-J.WANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.0 Space group P43212 a (A) 37.230 b (A) 37.230 c (A) 61.960 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.9 Rfree (%) 24.2 Bromine Binding Sites: Bromine binding site 1 out of 4 in 380d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Bromine in the PDB 380d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G493, A: Cbr4, A: Dc5, B: Dg8, A: Hoh19, A: Hoh24, A: Hoh26, conact list: Atom Atom Distance (A) Br N9 A:G493 4.04 Br C8 A:G493 3.71 Br C5 A:G493 4.29 Br C1' A:G493 4.64 Br N7 A:G493 3.89 Br C4 A:G493 4.40 Br C2' A:G493 4.02 Br N3 A:Cbr4 4.11 Br C2 A:Cbr4 4.60 Br C6 A:Cbr4 2.77 Br N1 A:Cbr4 4.06 Br C5 A:Cbr4 1.84 Br C4 A:Cbr4 2.86 Br BR A:Cbr4 0.00 Br N4 A:Cbr4 3.10 Br N3 A:Dc5 4.88 Br C5 A:Dc5 4.66 Br C4 A:Dc5 4.15 Br N4 A:Dc5 3.44 Br O6 B:Dg8 4.97 Br O A:Hoh19 4.30 Br O A:Hoh24 3.89 Br O A:Hoh26 3.61 interactive model: Bromine binding site 2 out of 4 in 380d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Bromine in the PDB 380d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg2, B: G499, B: Cbr10, B: Dc11, B: Hoh20, B: Hoh37, B: Hoh39, B: Hoh48, conact list: Atom Atom Distance (A) Br O6 A:Dg2 4.94 Br N9 B:G499 3.99 Br C8 B:G499 3.71 Br C5 B:G499 4.31 Br C1' B:G499 4.53 Br N7 B:G499 3.93 Br C4 B:G499 4.37 Br C2' B:G499 3.90 Br N3 B:Cbr10 4.12 Br C2 B:Cbr10 4.60 Br C6 B:Cbr10 2.75 Br N1 B:Cbr10 4.04 Br C5 B:Cbr10 1.84 Br C4 B:Cbr10 2.88 Br BR B:Cbr10 0.00 Br N4 B:Cbr10 3.13 Br N3 B:Dc11 4.89 Br C5 B:Dc11 4.50 Br C4 B:Dc11 4.12 Br N4 B:Dc11 3.52 Br O B:Hoh20 4.04 Br O B:Hoh37 4.07 Br O B:Hoh39 3.50 Br O B:Hoh48 4.58 interactive model: Bromine binding site 3 out of 4 in 380d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Bromine in the PDB 380d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G493, B: Dc11, B: Dg12, A: Dm87, A: Hoh18, A: Hoh44, B: Hoh21, B: Hoh29, B: Hoh36, conact list: Atom Atom Distance (A) Br CM2 A:G493 4.61 Br O3' B:Dc11 4.72 Br O4' B:Dc11 4.89 Br C4' B:Dc11 4.68 Br O4' B:Dg12 4.51 Br C5' B:Dg12 3.52 Br C4' B:Dg12 4.09 Br O5' B:Dg12 4.77 Br N3' A:Dm87 3.22 Br C4' A:Dm87 3.55 Br O5' A:Dm87 3.26 Br O7 A:Dm87 3.99 Br C3' A:Dm87 2.90 Br C1' A:Dm87 2.74 Br O4' A:Dm87 4.85 Br C5' A:Dm87 4.06 Br C2' A:Dm87 1.86 Br BR A:Dm87 0.00 Br O A:Hoh18 3.94 Br O A:Hoh44 3.96 Br O B:Hoh21 4.25 Br O B:Hoh29 4.30 Br O B:Hoh36 4.90 interactive model: Bromine binding site 4 out of 4 in 380d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Bromine in the PDB 380d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dc5, A: Dg6, B: G499, B: Dm813, A: Hoh41, B: Hoh28, B: Hoh46, conact list: Atom Atom Distance (A) Br C1' A:Dc5 4.96 Br O2 A:Dc5 4.82 Br O3' A:Dc5 4.52 Br O4' A:Dc5 4.48 Br C4' A:Dc5 4.32 Br O4' A:Dg6 4.51 Br C5' A:Dg6 3.86 Br C4' A:Dg6 4.36 Br O5' A:Dg6 4.94 Br CM2 B:G499 4.39 Br N3' B:Dm813 2.98 Br C4' B:Dm813 3.38 Br O5' B:Dm813 3.31 Br O7 B:Dm813 4.07 Br C3' B:Dm813 2.75 Br C1' B:Dm813 2.84 Br O4' B:Dm813 4.68 Br C5' B:Dm813 3.98 Br C2' B:Dm813 1.83 Br BR B:Dm813 0.00 Br O6 B:Dm813 4.90 Br O A:Hoh41 3.79 Br O B:Hoh28 3.96 Br O B:Hoh46 4.33 interactive model: