Bromine in the structure of Structure of the Human G-Quadruplex Reveals A Novel Topology (pdb 1k8p)

The binding sites of Bromine atom in the structure of Structure of the Human G-Quadruplex Reveals A Novel Topology (pdb code 1k8p). This binding sites where shown with 5.0 Angstroms radius around Bromine atom. The 1k8p structure was solved by G.N.PARKINSON, M.P.H.LEE, S.NEIDLE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.4 Space group P3121 a (A) 56.607 b (A) 56.607 c (A) 40.546 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.3 Rfree (%) 28 Bromine Binding Sites: Bromine binding site 1 out of 4 in 1k8p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Bromine in the PDB 1k8p. 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: Bru1, B: Hoh2024, conact list: Atom Atom Distance (A) Br N3 A:Bru1 4.09 Br C2 A:Bru1 4.70 Br C6 A:Bru1 2.86 Br N1 A:Bru1 4.15 Br C5 A:Bru1 1.87 Br C4 A:Bru1 2.82 Br BR A:Bru1 0.00 Br O5' A:Bru1 4.66 Br O4 A:Bru1 3.02 Br O B:Hoh2024 4.88 interactive model: Bromine binding site 2 out of 4 in 1k8p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Bromine in the PDB 1k8p. 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: Dg4, A: Dg5, A: Bru6, A: Da8, A: Hoh2001, A: Hoh2003, A: Hoh2007, A: Hoh2013, A: Hoh2015, A: Hoh2029, A: Hoh2036, A: Hoh2042, conact list: Atom Atom Distance (A) Br C3' A:Dg4 4.94 Br C1' A:Dg4 4.61 Br O3' A:Dg4 4.59 Br O4' A:Dg4 4.76 Br C2' A:Dg4 4.67 Br C4' A:Dg4 4.63 Br O4' A:Dg5 4.96 Br C5' A:Dg5 4.39 Br C4' A:Dg5 4.99 Br N3 A:Bru6 4.10 Br C2 A:Bru6 4.68 Br C6 A:Bru6 2.83 Br N1 A:Bru6 4.12 Br C5 A:Bru6 1.87 Br C4 A:Bru6 2.84 Br BR A:Bru6 0.00 Br O4 A:Bru6 3.03 Br N9 A:Da8 3.94 Br N3 A:Da8 4.26 Br C8 A:Da8 4.29 Br C2 A:Da8 4.79 Br C6 A:Da8 4.92 Br C5 A:Da8 4.30 Br C1' A:Da8 4.29 Br N7 A:Da8 4.53 Br C4 A:Da8 3.95 Br C2' A:Da8 3.83 Br O A:Hoh2001 3.29 Br O A:Hoh2003 4.23 Br O A:Hoh2007 4.34 Br O A:Hoh2013 3.58 Br O A:Hoh2015 3.17 Br O A:Hoh2029 3.91 Br O A:Hoh2036 4.81 Br O A:Hoh2042 4.36 interactive model: Bromine binding site 3 out of 4 in 1k8p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Bromine in the PDB 1k8p. 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: Bru13, B: Hoh2024, conact list: Atom Atom Distance (A) Br N3 B:Bru13 4.11 Br C2 B:Bru13 4.71 Br C6 B:Bru13 2.88 Br N1 B:Bru13 4.16 Br C5 B:Bru13 1.88 Br C4 B:Bru13 2.83 Br BR B:Bru13 0.00 Br O5' B:Bru13 4.51 Br O4 B:Bru13 2.99 Br O B:Hoh2024 4.57 interactive model: Bromine binding site 4 out of 4 in 1k8p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Bromine in the PDB 1k8p. 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: Dg16, B: Dg17, B: Bru18, B: Da20, B: Hoh2044, conact list: Atom Atom Distance (A) Br C3' B:Dg16 4.07 Br O3' B:Dg16 3.07 Br O4' B:Dg16 4.59 Br C5' B:Dg16 4.82 Br C4' B:Dg16 3.88 Br OP1 B:Dg17 3.69 Br P B:Dg17 3.99 Br C5' B:Dg17 4.12 Br O5' B:Dg17 4.49 Br N3 B:Bru18 4.15 Br C2 B:Bru18 4.75 Br C6 B:Bru18 2.87 Br N1 B:Bru18 4.16 Br C5 B:Bru18 1.88 Br C4 B:Bru18 2.88 Br BR B:Bru18 0.00 Br O4 B:Bru18 3.12 Br N9 B:Da20 3.95 Br N3 B:Da20 3.84 Br C8 B:Da20 4.34 Br C2 B:Da20 4.18 Br C6 B:Da20 4.33 Br N1 B:Da20 4.43 Br C5 B:Da20 3.92 Br C1' B:Da20 4.48 Br N7 B:Da20 4.37 Br C4 B:Da20 3.65 Br C2' B:Da20 4.22 Br O B:Hoh2044 4.80 interactive model: