Bromine in the structure of Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation (pdb 101d)

The binding sites of Bromine atom in the structure of Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation (pdb code 101d). This binding sites where shown with 5.0 Angstroms radius around Bromine atom. The 101d structure was solved by D.S.GOODSELL, M.L.KOPKA, R.E.DICKERSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.2 Space group P212121 a (A) 24.270 b (A) 39.620 c (A) 63.570 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Bromine Binding Sites: Bromine binding site 1 out of 2 in 101d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Bromine in the PDB 101d. 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: Dt8, A: Cbr9, A: Dg10, A: Hoh54, conact list: Atom Atom Distance (A) Br C3' A:Dt8 4.88 Br C2 A:Dt8 4.84 Br C6 A:Dt8 3.87 Br N1 A:Dt8 4.21 Br C5 A:Dt8 4.22 Br C1' A:Dt8 4.66 Br C7 A:Dt8 4.58 Br C4 A:Dt8 4.85 Br C2' A:Dt8 3.93 Br N3 A:Cbr9 4.06 Br C2 A:Cbr9 4.58 Br C6 A:Cbr9 2.72 Br N1 A:Cbr9 4.01 Br C5 A:Cbr9 1.81 Br C4 A:Cbr9 2.82 Br BR A:Cbr9 0.00 Br N4 A:Cbr9 3.12 Br O6 A:Dg10 4.64 Br O A:Hoh54 3.72 interactive model: Bromine binding site 2 out of 2 in 101d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Bromine in the PDB 101d. 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: B: Dt20, B: Cbr21, B: Dg22, B: Hoh36, B: Hoh43, B: Hoh49, B: Hoh62, conact list: Atom Atom Distance (A) Br N3 B:Dt20 4.92 Br C2 B:Dt20 4.65 Br C6 B:Dt20 3.77 Br N1 B:Dt20 4.01 Br C5 B:Dt20 4.13 Br C1' B:Dt20 4.43 Br C7 B:Dt20 4.57 Br C4 B:Dt20 4.70 Br C2' B:Dt20 3.69 Br N3 B:Cbr21 3.97 Br C2 B:Cbr21 4.48 Br C6 B:Cbr21 2.70 Br N1 B:Cbr21 3.96 Br C5 B:Cbr21 1.74 Br C4 B:Cbr21 2.73 Br BR B:Cbr21 0.00 Br N4 B:Cbr21 3.01 Br N7 B:Dg22 4.89 Br O6 B:Dg22 4.46 Br O B:Hoh36 4.06 Br O B:Hoh43 4.69 Br O B:Hoh49 4.28 Br O B:Hoh62 4.33 interactive model: