Bromine in the structure of Rip-Radiation-Damage Induced Phasing (pdb 1n7a)

The binding sites of Bromine atom in the structure of Rip-Radiation-Damage Induced Phasing (pdb code 1n7a). This binding sites where shown with 5.0 Angstroms radius around Bromine atom. The 1n7a structure was solved by R.B.G.RAVELLI, H.-K.S.LEIROS, B.PAN, M.CAFFREY, S.MCSWEENEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.2 Space group P212121 a (A) 31.233 b (A) 51.102 c (A) 70.651 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 12.4 Rfree (%) 15.6 Bromine Binding Sites: Bromine binding site 1 out of 8 in 1n7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Bromine in the PDB 1n7a. 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: U1, A: Bgm2, A: A3, B: Bgm2, D: Bgm2, E: U1, E: Bgm2, A: Hoh253, B: Hoh285, D: Hoh292, E: Hoh381, conact list: Atom Atom Distance (A) Br O2' A:U1 4.48 Br N9 A:Bgm2 2.89 Br C3' A:Bgm2 4.30 Br C8 A:Bgm2 1.88 Br C5 A:Bgm2 3.93 Br C1' A:Bgm2 3.42 Br N7 A:Bgm2 2.79 Br O4' A:Bgm2 3.34 Br C4 A:Bgm2 4.01 Br C5' A:Bgm2 3.65 Br C2' A:Bgm2 3.50 Br C4' A:Bgm2 3.93 Br BR A:Bgm2 0.00 Br C8 A:A3 4.80 Br C5 A:A3 4.74 Br N6 A:A3 4.94 Br N7 A:A3 4.20 Br N3 B:Bgm2 4.59 Br N2 B:Bgm2 3.92 Br C2 B:Bgm2 4.53 Br N2 D:Bgm2 3.90 Br N3 E:U1 3.61 Br C2 E:U1 3.66 Br N1 E:U1 4.41 Br O2 E:U1 3.69 Br C4 E:U1 4.32 Br O2' E:U1 4.50 Br O4 E:U1 4.77 Br BR E:Bgm2 4.62 Br O A:Hoh253 4.54 Br O B:Hoh285 3.79 Br O D:Hoh292 4.75 Br O E:Hoh381 2.99 interactive model: Bromine binding site 2 out of 8 in 1n7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Bromine in the PDB 1n7a. 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: Bgm2, B: U1, B: Bgm2, B: A3, C: U1, C: Bgm2, G: Bgm2, A: Hoh311, B: Hoh257, C: Hoh382, G: Hoh296, conact list: Atom Atom Distance (A) Br N3 A:Bgm2 4.64 Br N2 A:Bgm2 3.97 Br C2 A:Bgm2 4.61 Br O2' B:U1 4.37 Br N9 B:Bgm2 2.91 Br C3' B:Bgm2 4.32 Br C8 B:Bgm2 1.89 Br C5 B:Bgm2 3.93 Br C1' B:Bgm2 3.40 Br N7 B:Bgm2 2.78 Br O4' B:Bgm2 3.35 Br C4 B:Bgm2 4.01 Br C5' B:Bgm2 3.59 Br C2' B:Bgm2 3.51 Br C4' B:Bgm2 3.98 Br BR B:Bgm2 0.00 Br O5' B:Bgm2 4.91 Br C8 B:A3 4.72 Br C5 B:A3 4.65 Br N6 B:A3 4.86 Br N7 B:A3 4.11 Br N3 C:U1 3.59 Br C2 C:U1 3.64 Br N1 C:U1 4.45 Br O2 C:U1 3.63 Br C4 C:U1 4.37 Br O2' C:U1 4.69 Br O4 C:U1 4.78 Br BR C:Bgm2 4.61 Br N2 G:Bgm2 3.89 Br O A:Hoh311 3.81 Br O B:Hoh257 4.59 Br O C:Hoh382 3.03 Br O G:Hoh296 4.80 interactive model: Bromine binding site 3 out of 8 in 1n7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Bromine in the PDB 1n7a. 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: Bgm2, B: U1, B: Bgm2, C: U1, C: Bgm2, C: A3, G: Bgm2, A: Hoh311, B: Hoh383, C: Hoh235, G: Hoh296, conact list: Atom Atom Distance (A) Br N2 A:Bgm2 3.95 Br N3 B:U1 3.58 Br C2 B:U1 3.63 Br C6 B:U1 4.99 Br N1 B:U1 4.36 Br O2 B:U1 3.62 Br C4 B:U1 4.35 Br O2' B:U1 4.39 Br O4 B:U1 4.80 Br BR B:Bgm2 4.61 Br O2' C:U1 4.46 Br N9 C:Bgm2 2.90 Br C3' C:Bgm2 4.29 Br C8 C:Bgm2 1.89 Br C5 C:Bgm2 3.94 Br C1' C:Bgm2 3.38 Br N7 C:Bgm2 2.79 Br O4' C:Bgm2 3.36 Br C4 C:Bgm2 4.02 Br C5' C:Bgm2 3.62 Br C2' C:Bgm2 3.50 Br C4' C:Bgm2 3.97 Br BR C:Bgm2 0.00 Br O5' C:Bgm2 4.99 Br C8 C:A3 4.83 Br C5 C:A3 4.81 Br N6 C:A3 4.93 Br N7 C:A3 4.23 Br N3 G:Bgm2 4.61 Br N2 G:Bgm2 3.91 Br C2 G:Bgm2 4.57 Br O A:Hoh311 4.78 Br O B:Hoh383 2.99 Br O C:Hoh235 4.73 Br O G:Hoh296 3.81 interactive model: Bromine binding site 4 out of 8 in 1n7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Bromine in the PDB 1n7a. 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: U1, D: Bgm2, D: A3, E: Bgm2, F: U1, F: Bgm2, H: Bgm2, D: Hoh384, E: Hoh371, H: Hoh308, conact list: Atom Atom Distance (A) Br O2' D:U1 4.22 Br N9 D:Bgm2 2.91 Br C3' D:Bgm2 4.32 Br C8 D:Bgm2 1.89 Br C5 D:Bgm2 3.93 Br C1' D:Bgm2 3.42 Br N7 D:Bgm2 2.77 Br O4' D:Bgm2 3.33 Br C4 D:Bgm2 4.01 Br C5' D:Bgm2 3.61 Br C2' D:Bgm2 3.53 Br C4' D:Bgm2 3.95 Br BR D:Bgm2 0.00 Br O5' D:Bgm2 4.95 Br C8 D:A3 4.76 Br C5 D:A3 4.67 Br N6 D:A3 4.82 Br N7 D:A3 4.14 Br N3 E:Bgm2 4.62 Br N2 E:Bgm2 3.95 Br C2 E:Bgm2 4.58 Br N3 F:U1 3.57 Br C2 F:U1 3.68 Br N1 F:U1 4.46 Br O2 F:U1 3.64 Br C4 F:U1 4.34 Br O2' F:U1 4.62 Br O4 F:U1 4.74 Br BR F:Bgm2 4.67 Br N2 H:Bgm2 3.91 Br O D:Hoh384 3.01 Br O E:Hoh371 3.75 Br O H:Hoh308 4.76 interactive model: Bromine binding site 5 out of 8 in 1n7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Bromine in the PDB 1n7a. 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: U1, A: Bgm2, B: Bgm2, D: Bgm2, E: U1, E: Bgm2, E: A3, A: Hoh385, B: Hoh285, D: Hoh292, E: Hoh266, conact list: Atom Atom Distance (A) Br N3 A:U1 3.55 Br C2 A:U1 3.66 Br N1 A:U1 4.44 Br O2 A:U1 3.68 Br C4 A:U1 4.29 Br O2' A:U1 4.68 Br O4 A:U1 4.69 Br BR A:Bgm2 4.62 Br N2 B:Bgm2 3.91 Br N3 D:Bgm2 4.61 Br N2 D:Bgm2 3.97 Br C2 D:Bgm2 4.58 Br O2' E:U1 4.27 Br N9 E:Bgm2 2.89 Br C3' E:Bgm2 4.30 Br C8 E:Bgm2 1.89 Br C5 E:Bgm2 3.93 Br C1' E:Bgm2 3.40 Br N7 E:Bgm2 2.79 Br O4' E:Bgm2 3.34 Br C4 E:Bgm2 4.01 Br C5' E:Bgm2 3.62 Br C2' E:Bgm2 3.55 Br C4' E:Bgm2 3.95 Br BR E:Bgm2 0.00 Br O5' E:Bgm2 4.95 Br C8 E:A3 4.73 Br C5 E:A3 4.74 Br N6 E:A3 4.89 Br N7 E:A3 4.13 Br O A:Hoh385 3.11 Br O B:Hoh285 4.75 Br O D:Hoh292 3.72 Br O E:Hoh266 4.70 interactive model: Bromine binding site 6 out of 8 in 1n7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Bromine in the PDB 1n7a. 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: U1, D: Bgm2, E: Bgm2, F: U1, F: Bgm2, F: A3, H: Bgm2, E: Hoh371, F: Hoh247, F: Hoh386, H: Hoh308, conact list: Atom Atom Distance (A) Br N3 D:U1 3.60 Br C2 D:U1 3.62 Br C6 D:U1 5.00 Br N1 D:U1 4.37 Br O2 D:U1 3.64 Br C4 D:U1 4.34 Br O2' D:U1 4.48 Br O4 D:U1 4.79 Br BR D:Bgm2 4.67 Br N2 E:Bgm2 3.95 Br O2' F:U1 4.32 Br N9 F:Bgm2 2.91 Br C3' F:Bgm2 4.29 Br C8 F:Bgm2 1.89 Br C5 F:Bgm2 3.92 Br C1' F:Bgm2 3.41 Br N7 F:Bgm2 2.77 Br O4' F:Bgm2 3.33 Br C4 F:Bgm2 4.02 Br C5' F:Bgm2 3.65 Br C2' F:Bgm2 3.53 Br C4' F:Bgm2 3.94 Br BR F:Bgm2 0.00 Br O5' F:Bgm2 5.00 Br C8 F:A3 4.84 Br C5 F:A3 4.75 Br N6 F:A3 4.87 Br N7 F:A3 4.22 Br N3 H:Bgm2 4.61 Br N2 H:Bgm2 3.95 Br C2 H:Bgm2 4.57 Br O E:Hoh371 4.65 Br O F:Hoh247 4.68 Br O F:Hoh386 3.05 Br O H:Hoh308 3.78 interactive model: Bromine binding site 7 out of 8 in 1n7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Bromine in the PDB 1n7a. 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: Bgm2, F: Bgm2, G: U1, G: Bgm2, G: A3, H: U1, H: Bgm2, C: Hoh315, F: Hoh228, G: Hoh229, H: Hoh387, conact list: Atom Atom Distance (A) Br N3 C:Bgm2 4.63 Br N2 C:Bgm2 4.03 Br C2 C:Bgm2 4.60 Br N2 F:Bgm2 3.94 Br O2' G:U1 4.38 Br N9 G:Bgm2 2.88 Br C3' G:Bgm2 4.28 Br C8 G:Bgm2 1.87 Br C5 G:Bgm2 3.91 Br C1' G:Bgm2 3.40 Br N7 G:Bgm2 2.78 Br O4' G:Bgm2 3.36 Br C4 G:Bgm2 4.01 Br C5' G:Bgm2 3.60 Br C2' G:Bgm2 3.52 Br C4' G:Bgm2 3.95 Br BR G:Bgm2 0.00 Br O5' G:Bgm2 4.92 Br C8 G:A3 4.76 Br C6 G:A3 4.96 Br C5 G:A3 4.64 Br N6 G:A3 4.76 Br N7 G:A3 4.14 Br N3 H:U1 3.63 Br C2 H:U1 3.66 Br N1 H:U1 4.45 Br O2 H:U1 3.66 Br C4 H:U1 4.41 Br O2' H:U1 4.61 Br O4 H:U1 4.86 Br BR H:Bgm2 4.72 Br O C:Hoh315 3.83 Br O F:Hoh228 4.66 Br O G:Hoh229 4.63 Br O H:Hoh387 3.02 interactive model: Bromine binding site 8 out of 8 in 1n7a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Bromine in the PDB 1n7a. 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: Bgm2, F: Bgm2, G: U1, G: Bgm2, H: U1, H: Bgm2, H: A3, C: Hoh315, F: Hoh228, G: Hoh388, H: Hoh219, conact list: Atom Atom Distance (A) Br N2 C:Bgm2 3.93 Br N3 F:Bgm2 4.61 Br N2 F:Bgm2 3.99 Br C2 F:Bgm2 4.60 Br N3 G:U1 3.62 Br C2 G:U1 3.61 Br N1 G:U1 4.37 Br C1' G:U1 5.00 Br O2 G:U1 3.57 Br C4 G:U1 4.42 Br O2' G:U1 4.51 Br O4 G:U1 4.93 Br BR G:Bgm2 4.72 Br O2' H:U1 4.46 Br N9 H:Bgm2 2.91 Br C3' H:Bgm2 4.29 Br C8 H:Bgm2 1.88 Br C5 H:Bgm2 3.92 Br C1' H:Bgm2 3.39 Br N7 H:Bgm2 2.79 Br O4' H:Bgm2 3.35 Br C4 H:Bgm2 4.03 Br C5' H:Bgm2 3.57 Br C2' H:Bgm2 3.49 Br C4' H:Bgm2 3.94 Br BR H:Bgm2 0.00 Br O5' H:Bgm2 4.93 Br C8 H:A3 4.81 Br C5 H:A3 4.74 Br N6 H:A3 4.88 Br N7 H:A3 4.20 Br O C:Hoh315 4.85 Br O F:Hoh228 3.82 Br O G:Hoh388 3.06 Br O H:Hoh219 4.56 interactive model: