Bromine in the structure of 5'-R(*Cp*Ap*Cp*Cp*Gp*Gp*Ap*Up*Gp*Gp*Up*(Bro) Up*Cp*Gp*Gp*Up*G)-3' (pdb 406d)

The binding sites of Bromine atom in the structure of 5'-R(*Cp*Ap*Cp*Cp*Gp*Gp*Ap*Up*Gp*Gp*Up*(Bro) Up*Cp*Gp*Gp*Up*G)-3' (pdb code 406d). This binding sites where shown with 5.0 Angstroms radius around Bromine atom. The 406d structure was solved by S.A.SHAH, A.T.BRUNGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-1.8 Space group P3 a (A) 39.627 b (A) 39.627 c (A) 91.018 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 26.2 Rfree (%) 29.4 Bromine Binding Sites: Bromine binding site 1 out of 2 in 406d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Bromine in the PDB 406d. 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: U11, A: 5bu12, A: G15, A: U16, conact list: Atom Atom Distance (A) Br N3 A:U11 4.47 Br C3' A:U11 4.37 Br C2 A:U11 4.68 Br C6 A:U11 3.61 Br N1 A:U11 4.24 Br C5 A:U11 3.43 Br P A:U11 4.99 Br C4 A:U11 3.93 Br OP2 A:U11 4.21 Br C2' A:U11 4.81 Br O5' A:U11 4.41 Br O4 A:U11 4.37 Br N3 A:5bu12 4.08 Br C2 A:5bu12 4.67 Br C6 A:5bu12 2.83 Br N1 A:5bu12 4.12 Br C5 A:5bu12 1.86 Br P A:5bu12 4.64 Br C4 A:5bu12 2.82 Br OP2 A:5bu12 3.74 Br BR A:5bu12 0.00 Br O5' A:5bu12 4.38 Br O4 A:5bu12 3.09 interactive model: Bromine binding site 2 out of 2 in 406d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Bromine in the PDB 406d. 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: E: U28, E: 5bu29, E: Hoh49, E: A24, E: U25, E: 59, conact list: Atom Atom Distance (A) Br N3 E:U28 4.73 Br C3' E:U28 4.30 Br C2 E:U28 4.88 Br C6 E:U28 3.65 Br N1 E:U28 4.35 Br C5 E:U28 3.51 Br O3' E:U28 4.87 Br C4 E:U28 4.14 Br OP2 E:U28 4.54 Br C2' E:U28 4.78 Br O5' E:U28 4.51 Br O4 E:U28 4.60 Br N3 E:5bu29 4.15 Br C2 E:5bu29 4.72 Br C6 E:5bu29 2.82 Br N1 E:5bu29 4.13 Br C5 E:5bu29 1.89 Br P E:5bu29 4.33 Br C4 E:5bu29 2.91 Br OP2 E:5bu29 3.24 Br BR E:5bu29 0.00 Br O5' E:5bu29 4.27 Br O4 E:5bu29 3.22 Br O E:Hoh49 4.56 interactive model: