Bromine in the structure of Actinomycin D Binding to Cgatcgatcg (pdb 1i3w)

The binding sites of Bromine atom in the structure of Actinomycin D Binding to Cgatcgatcg (pdb code 1i3w). This binding sites where shown with 5.0 Angstroms radius around Bromine atom. The 1i3w structure was solved by H.ROBINSON, Y.-G.GAO, X.-L.YANG, R.SANISHVILI, A.JOACHIMIAK, A.H.-J.WANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.7 Space group P43212 a (A) 47.013 b (A) 47.013 c (A) 160.368 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.7 Rfree (%) 27.9 Bromine Binding Sites: Bromine binding site 1 out of 4 in 1i3w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Bromine in the PDB 1i3w. 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: Da7, A: Bru8, A: Dc9, D: Dt34, D: Dc35, A: Hoh2009, A: Hoh2012, A: Hoh2027, conact list: Atom Atom Distance (A) Br N9 A:Da7 4.17 Br C8 A:Da7 3.64 Br C5 A:Da7 4.45 Br C1' A:Da7 4.80 Br N7 A:Da7 3.81 Br C4 A:Da7 4.57 Br C2' A:Da7 4.43 Br N3 A:Bru8 4.09 Br C2 A:Bru8 4.66 Br C6 A:Bru8 2.83 Br N1 A:Bru8 4.12 Br C5 A:Bru8 1.87 Br C4 A:Bru8 2.83 Br BR A:Bru8 0.00 Br O4 A:Bru8 3.01 Br C4 A:Dc9 4.95 Br N4 A:Dc9 4.12 Br C2' D:Dt34 4.60 Br OP1 D:Dc35 4.97 Br O A:Hoh2009 2.93 Br O A:Hoh2012 4.23 Br O A:Hoh2027 3.75 interactive model: Bromine binding site 2 out of 4 in 1i3w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Bromine in the PDB 1i3w. 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: Da17, B: Bru18, B: Dc19, C: Dt24, B: Hoh2009, B: Hoh2029, B: Hoh2033, B: Hoh2035, B: Hoh2037, B: Hoh2039, C: Hoh2013, conact list: Atom Atom Distance (A) Br N9 B:Da17 3.82 Br N3 B:Da17 4.89 Br C3' B:Da17 4.83 Br C8 B:Da17 3.61 Br C5 B:Da17 4.14 Br C1' B:Da17 4.22 Br N7 B:Da17 3.89 Br C4 B:Da17 4.16 Br C2' B:Da17 3.52 Br N3 B:Bru18 4.07 Br C2 B:Bru18 4.64 Br C6 B:Bru18 2.80 Br N1 B:Bru18 4.10 Br C5 B:Bru18 1.87 Br C4 B:Bru18 2.83 Br OP2 B:Bru18 4.51 Br BR B:Bru18 0.00 Br O4 B:Bru18 2.99 Br C5 B:Dc19 4.91 Br C4 B:Dc19 4.65 Br N4 B:Dc19 3.86 Br C2' C:Dt24 4.81 Br O B:Hoh2009 3.05 Br O B:Hoh2029 3.61 Br O B:Hoh2033 3.88 Br O B:Hoh2035 4.43 Br O B:Hoh2037 3.68 Br O B:Hoh2039 3.71 Br O C:Hoh2013 3.57 interactive model: Bromine binding site 3 out of 4 in 1i3w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Bromine in the PDB 1i3w. 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: Dt14, B: Dc15, C: Da27, C: Bru28, C: Dc29, B: Hoh2001, B: Hoh2004, C: Hoh2025, C: Hoh2026, conact list: Atom Atom Distance (A) Br C3' B:Dt14 4.83 Br C2' B:Dt14 4.49 Br OP1 B:Dc15 4.56 Br N9 C:Da27 4.01 Br C8 C:Da27 3.53 Br C5 C:Da27 4.26 Br C1' C:Da27 4.59 Br N7 C:Da27 3.82 Br C4 C:Da27 4.46 Br C2' C:Da27 4.35 Br N3 C:Bru28 4.11 Br C2 C:Bru28 4.63 Br C6 C:Bru28 2.76 Br N1 C:Bru28 4.06 Br C5 C:Bru28 1.87 Br C4 C:Bru28 2.86 Br BR C:Bru28 0.00 Br O4 C:Bru28 3.19 Br N4 C:Dc29 4.25 Br O B:Hoh2001 4.40 Br O B:Hoh2004 2.31 Br O C:Hoh2025 3.77 Br O C:Hoh2026 3.56 interactive model: Bromine binding site 4 out of 4 in 1i3w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Bromine in the PDB 1i3w. 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: D: Da37, D: Bru38, D: Dc39, A: Hoh2018, D: Hoh2030, D: Hoh2031, D: Hoh2036, D: Hoh2038, conact list: Atom Atom Distance (A) Br N9 D:Da37 3.81 Br C8 D:Da37 3.51 Br C5 D:Da37 4.14 Br C1' D:Da37 4.42 Br N7 D:Da37 3.92 Br C4 D:Da37 4.22 Br C2' D:Da37 3.79 Br N3 D:Bru38 4.07 Br C2 D:Bru38 4.68 Br C6 D:Bru38 2.84 Br N1 D:Bru38 4.13 Br C5 D:Bru38 1.86 Br C4 D:Bru38 2.82 Br BR D:Bru38 0.00 Br O4 D:Bru38 3.00 Br C4 D:Dc39 4.99 Br N4 D:Dc39 4.38 Br O A:Hoh2018 3.48 Br O D:Hoh2030 3.78 Br O D:Hoh2031 4.51 Br O D:Hoh2036 3.61 Br O D:Hoh2038 3.98 interactive model: