Bromine in the structure of Crystal Structure of Triplex Dna (pdb 1d3r)

The binding sites of Bromine atom in the structure of Crystal Structure of Triplex Dna (pdb code 1d3r). This binding sites where shown with 5.0 Angstroms radius around Bromine atom. The 1d3r structure was solved by S.RHEE, Z.-J.HAN, K.LIU, H.T.TODD MILES, D.R.DAVIES, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.8 Space group P42 a (A) 53.800 b (A) 53.800 c (A) 43.100 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21 Rfree (%) 27.5 Bromine Binding Sites: Bromine binding site 1 out of 4 in 1d3r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Bromine in the PDB 1d3r. 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: Dc1, A: Bru2, A: Hoh100, A: Hoh112, A: Hoh118, A: Hoh130, A: Hoh137, A: Hoh180, C: Hoh105, C: Hoh123, C: Hoh175, conact list: Atom Atom Distance (A) Br N3 A:Dc1 4.88 Br C3' A:Dc1 4.10 Br C2 A:Dc1 4.71 Br C6 A:Dc1 3.48 Br N1 A:Dc1 4.00 Br C5 A:Dc1 3.70 Br C1' A:Dc1 4.41 Br C4 A:Dc1 4.44 Br C5' A:Dc1 4.72 Br C2' A:Dc1 3.37 Br C4' A:Dc1 4.94 Br O5' A:Dc1 3.69 Br N3 A:Bru2 3.88 Br C2 A:Bru2 4.44 Br C6 A:Bru2 2.54 Br N1 A:Bru2 3.85 Br C5 A:Bru2 1.54 Br P A:Bru2 4.87 Br C4 A:Bru2 2.65 Br OP2 A:Bru2 3.96 Br BR A:Bru2 0.00 Br O5' A:Bru2 4.83 Br O4 A:Bru2 3.04 Br O A:Hoh100 3.82 Br O A:Hoh112 3.96 Br O A:Hoh118 4.29 Br O A:Hoh130 4.10 Br O A:Hoh137 3.52 Br O A:Hoh180 3.96 Br O C:Hoh105 3.58 Br O C:Hoh123 3.81 Br O C:Hoh175 3.61 interactive model: Bromine binding site 2 out of 4 in 1d3r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Bromine in the PDB 1d3r. 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: Dc4, A: Bru5, A: Dc6, A: Hoh110, A: Hoh157, A: Hoh160, A: Hoh212, A: Hoh312, A: Hoh313, conact list: Atom Atom Distance (A) Br N3 A:Dc4 4.77 Br C2 A:Dc4 4.53 Br C6 A:Dc4 3.58 Br N1 A:Dc4 3.92 Br C5 A:Dc4 3.86 Br C1' A:Dc4 4.33 Br C4 A:Dc4 4.46 Br C2' A:Dc4 3.87 Br N3 A:Bru5 3.84 Br C2 A:Bru5 4.38 Br C6 A:Bru5 2.49 Br N1 A:Bru5 3.79 Br C5 A:Bru5 1.51 Br C1' A:Bru5 4.97 Br C4 A:Bru5 2.62 Br BR A:Bru5 0.00 Br O4 A:Bru5 3.01 Br N4 A:Dc6 4.90 Br O A:Hoh110 4.31 Br O A:Hoh157 4.39 Br O A:Hoh160 3.86 Br O A:Hoh212 3.35 Br O A:Hoh312 3.56 Br O A:Hoh313 4.32 interactive model: Bromine binding site 3 out of 4 in 1d3r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Bromine in the PDB 1d3r. 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: C: Dc31, C: Bru32, A: Hoh100, A: Hoh104, A: Hoh118, A: Hoh180, A: Hoh186, C: Hoh105, C: Hoh123, C: Hoh317, conact list: Atom Atom Distance (A) Br N3 C:Dc31 4.78 Br C3' C:Dc31 3.97 Br C2 C:Dc31 4.59 Br C6 C:Dc31 3.73 Br N1 C:Dc31 4.06 Br C5 C:Dc31 3.94 Br C1' C:Dc31 4.50 Br O3' C:Dc31 4.97 Br O4' C:Dc31 4.99 Br C4 C:Dc31 4.47 Br C5' C:Dc31 4.10 Br C2' C:Dc31 3.56 Br C4' C:Dc31 4.60 Br O5' C:Dc31 3.95 Br N3 C:Bru32 3.86 Br C2 C:Bru32 4.41 Br C6 C:Bru32 2.52 Br N1 C:Bru32 3.82 Br C5 C:Bru32 1.53 Br P C:Bru32 4.92 Br C4 C:Bru32 2.65 Br OP2 C:Bru32 3.93 Br BR C:Bru32 0.00 Br O5' C:Bru32 4.92 Br O4 C:Bru32 3.07 Br O A:Hoh100 3.93 Br O A:Hoh104 3.81 Br O A:Hoh118 4.09 Br O A:Hoh180 4.08 Br O A:Hoh186 4.04 Br O C:Hoh105 3.88 Br O C:Hoh123 4.17 Br O C:Hoh317 4.95 interactive model: Bromine binding site 4 out of 4 in 1d3r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Bromine in the PDB 1d3r. 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: C: Dc34, C: Bru35, C: Dc36, C: Hoh101, C: Hoh109, C: Hoh161, C: Hoh182, C: Hoh204, C: Hoh210, C: Hoh305, conact list: Atom Atom Distance (A) Br N3 C:Dc34 4.86 Br C2 C:Dc34 4.62 Br C6 C:Dc34 3.56 Br N1 C:Dc34 3.96 Br C5 C:Dc34 3.86 Br C1' C:Dc34 4.43 Br C4 C:Dc34 4.52 Br C2' C:Dc34 4.04 Br N3 C:Bru35 3.83 Br C2 C:Bru35 4.40 Br C6 C:Bru35 2.53 Br N1 C:Bru35 3.83 Br C5 C:Bru35 1.52 Br C4 C:Bru35 2.61 Br BR C:Bru35 0.00 Br O4 C:Bru35 3.00 Br N4 C:Dc36 4.73 Br O C:Hoh101 4.12 Br O C:Hoh109 3.82 Br O C:Hoh161 3.43 Br O C:Hoh182 4.13 Br O C:Hoh204 4.56 Br O C:Hoh210 3.57 Br O C:Hoh305 4.16 interactive model: