Bromine in PDB 1n7b: Rip-Radiation-Damage Induced Phasing

The structure of Rip-Radiation-Damage Induced Phasing, PDB code: 1n7b was solved by R.B.G.Ravelli, H.-K.S.Leiros, B.Pan, M.Caffrey, S.Mcsweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.247, 51.154, 70.834, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 19.9

The structure of Rip-Radiation-Damage Induced Phasing also contains other interesting chemical elements:

Potassium

(K)

9 atoms

The binding sites of Bromine atom in the Rip-Radiation-Damage Induced Phasing (pdb code 1n7b). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Rip-Radiation-Damage Induced Phasing, PDB code: 1n7b:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Rip-Radiation-Damage Induced Phasing within 5.0Å range: probe atom residue distance (Å) B Occ A:Br2 b:12.8 occ:0.80 BR A:BGM2 0.0 12.8 0.8 C8 A:BGM2 1.8 4.0 1.0 O E:HOH381 2.2 18.7 1.0 N7 A:BGM2 2.8 3.6 1.0 N9 A:BGM2 2.9 3.6 1.0 O4' A:BGM2 3.3 6.0 1.0 C1' A:BGM2 3.4 4.4 1.0 C2' A:BGM2 3.5 6.3 1.0 N3 E:U1 3.6 7.3 1.0 C2 E:U1 3.7 5.6 1.0 C5' A:BGM2 3.7 8.3 1.0 O B:HOH285 3.7 18.7 1.0 O2 E:U1 3.7 8.2 1.0 N2 B:BGM2 3.9 6.0 1.0 N2 D:BGM2 3.9 4.5 1.0 C4' A:BGM2 3.9 6.1 1.0 C5 A:BGM2 3.9 4.3 1.0 C4 A:BGM2 4.0 3.6 1.0 N7 A:A3 4.2 4.6 1.0 C3' A:BGM2 4.3 5.6 1.0 C4 E:U1 4.3 8.7 1.0 N1 E:U1 4.4 8.3 1.0 O A:HOH253 4.5 24.4 1.0 O2' A:U1 4.5 15.4 1.0 C2 B:BGM2 4.5 3.8 1.0 N3 B:BGM2 4.6 4.3 1.0 O2' E:U1 4.6 15.4 1.0 BR E:BGM2 4.7 13.1 0.8 O4 E:U1 4.7 13.8 1.0 C5 A:A3 4.8 3.9 1.0 C8 A:A3 4.8 4.6 1.0 O A:HOH385 4.9 25.8 1.0 O D:HOH292 4.9 17.4 1.0 N6 A:A3 5.0 4.0 1.0 C6 E:U1 5.0 9.2 1.0 C5 E:U1 5.0 9.6 1.0

Bromine binding site 2 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Rip-Radiation-Damage Induced Phasing within 5.0Å range: probe atom residue distance (Å) B Occ B:Br2 b:11.9 occ:0.80 BR B:BGM2 0.0 11.9 0.8 C8 B:BGM2 1.9 4.4 1.0 O C:HOH382 2.3 14.6 1.0 N7 B:BGM2 2.7 4.1 1.0 N9 B:BGM2 2.9 4.4 1.0 O4' B:BGM2 3.3 5.7 1.0 C1' B:BGM2 3.4 4.8 1.0 C2' B:BGM2 3.5 5.3 1.0 N3 C:U1 3.6 5.3 1.0 C5' B:BGM2 3.6 8.1 1.0 O2 C:U1 3.7 7.3 1.0 C2 C:U1 3.7 5.4 1.0 O A:HOH311 3.7 19.0 1.0 N2 G:BGM2 3.9 4.9 1.0 C5 B:BGM2 3.9 3.3 1.0 N2 A:BGM2 4.0 4.8 1.0 C4' B:BGM2 4.0 7.1 1.0 C4 B:BGM2 4.0 3.5 1.0 N7 B:A3 4.1 4.0 1.0 C3' B:BGM2 4.3 6.2 1.0 C4 C:U1 4.4 7.2 1.0 O2' B:U1 4.4 18.3 1.0 N1 C:U1 4.5 6.0 1.0 C2 A:BGM2 4.6 3.1 1.0 N3 A:BGM2 4.6 4.1 1.0 BR C:BGM2 4.6 12.1 0.8 O B:HOH257 4.6 26.9 1.0 C5 B:A3 4.7 3.1 1.0 C8 B:A3 4.7 4.0 1.0 O2' C:U1 4.8 14.9 1.0 O4 C:U1 4.8 8.0 1.0 O G:HOH296 4.8 18.2 1.0 N6 B:A3 4.8 2.7 1.0 O B:HOH383 4.9 18.6 1.0 O5' B:BGM2 4.9 10.1 1.0

Bromine binding site 3 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Rip-Radiation-Damage Induced Phasing within 5.0Å range: probe atom residue distance (Å) B Occ C:Br2 b:12.1 occ:0.80 BR C:BGM2 0.0 12.1 0.8 C8 C:BGM2 1.9 3.8 1.0 O B:HOH383 2.4 18.6 1.0 N7 C:BGM2 2.8 3.2 1.0 N9 C:BGM2 2.9 4.0 1.0 O4' C:BGM2 3.3 4.8 1.0 C1' C:BGM2 3.4 4.3 1.0 C2' C:BGM2 3.5 5.4 1.0 N3 B:U1 3.6 7.0 1.0 C5' C:BGM2 3.6 7.5 1.0 O G:HOH296 3.6 18.2 1.0 C2 B:U1 3.6 7.5 1.0 O2 B:U1 3.7 8.5 1.0 C4' C:BGM2 3.9 4.5 1.0 C5 C:BGM2 3.9 3.1 1.0 N2 G:BGM2 3.9 4.9 1.0 N2 A:BGM2 3.9 4.8 1.0 C4 C:BGM2 4.0 3.0 1.0 N7 C:A3 4.2 3.6 1.0 C3' C:BGM2 4.3 5.2 1.0 C4 B:U1 4.3 9.3 1.0 N1 B:U1 4.4 8.1 1.0 O2' B:U1 4.5 18.3 1.0 O2' C:U1 4.5 14.9 1.0 C2 G:BGM2 4.6 3.4 1.0 N3 G:BGM2 4.6 4.3 1.0 BR B:BGM2 4.6 11.9 0.8 O C:HOH235 4.7 24.2 1.0 O C:HOH382 4.7 14.6 1.0 C5 C:A3 4.8 2.7 1.0 O4 B:U1 4.8 10.8 1.0 C8 C:A3 4.9 4.0 1.0 O A:HOH311 4.9 19.0 1.0 N6 C:A3 4.9 5.8 1.0 C6 B:U1 5.0 10.2 1.0 C5 B:U1 5.0 9.2 1.0 O5' C:BGM2 5.0 9.5 1.0

Bromine binding site 4 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Rip-Radiation-Damage Induced Phasing within 5.0Å range: probe atom residue distance (Å) B Occ D:Br2 b:12.1 occ:0.80 BR D:BGM2 0.0 12.1 0.8 C8 D:BGM2 1.9 3.5 1.0 O D:HOH384 2.5 19.4 1.0 N7 D:BGM2 2.8 3.4 1.0 N9 D:BGM2 2.9 4.0 1.0 O4' D:BGM2 3.3 5.1 1.0 C1' D:BGM2 3.4 3.8 1.0 C2' D:BGM2 3.5 5.9 1.0 C5' D:BGM2 3.5 7.8 1.0 N3 F:U1 3.6 8.0 1.0 O2 F:U1 3.7 7.6 1.0 C2 F:U1 3.7 8.0 1.0 O E:HOH371 3.7 20.2 1.0 C4' D:BGM2 3.9 5.5 1.0 C5 D:BGM2 3.9 3.5 1.0 N2 H:BGM2 4.0 3.8 1.0 N2 E:BGM2 4.0 4.0 1.0 C4 D:BGM2 4.0 3.7 1.0 N7 D:A3 4.2 4.1 1.0 O2' D:U1 4.2 17.2 1.0 C3' D:BGM2 4.3 6.7 1.0 C4 F:U1 4.3 10.6 1.0 N1 F:U1 4.5 9.1 1.0 C2 E:BGM2 4.6 3.5 1.0 N3 E:BGM2 4.6 4.0 1.0 C5 D:A3 4.7 3.6 1.0 O4 F:U1 4.7 13.6 1.0 O2' F:U1 4.7 17.8 1.0 BR F:BGM2 4.7 13.2 0.8 C8 D:A3 4.8 4.3 1.0 O D:HOH386 4.8 18.8 1.0 O H:HOH308 4.8 16.4 1.0 N6 D:A3 4.9 3.4 1.0 O5' D:BGM2 4.9 10.8 1.0

Bromine binding site 5 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Rip-Radiation-Damage Induced Phasing within 5.0Å range: probe atom residue distance (Å) B Occ E:Br2 b:13.1 occ:0.80 BR E:BGM2 0.0 13.1 0.8 C8 E:BGM2 1.9 4.1 1.0 O A:HOH385 2.4 25.8 1.0 N7 E:BGM2 2.8 4.0 1.0 N9 E:BGM2 2.9 4.2 1.0 O4' E:BGM2 3.3 5.6 1.0 C1' E:BGM2 3.4 4.2 1.0 C2' E:BGM2 3.5 5.9 1.0 N3 A:U1 3.6 6.6 1.0 C5' E:BGM2 3.6 7.0 1.0 O D:HOH292 3.7 17.4 1.0 C2 A:U1 3.7 5.0 1.0 O2 A:U1 3.7 6.8 1.0 C5 E:BGM2 3.9 3.7 1.0 N2 B:BGM2 3.9 6.0 1.0 C4' E:BGM2 4.0 5.5 1.0 C4 E:BGM2 4.0 3.6 1.0 N2 D:BGM2 4.0 4.5 1.0 N7 E:A3 4.2 4.3 1.0 C3' E:BGM2 4.3 5.8 1.0 O2' E:U1 4.3 15.4 1.0 C4 A:U1 4.3 8.3 1.0 N1 A:U1 4.5 7.2 1.0 C2 D:BGM2 4.6 3.9 1.0 N3 D:BGM2 4.6 3.7 1.0 BR A:BGM2 4.7 12.8 0.8 O E:HOH266 4.7 27.0 1.0 O B:HOH285 4.7 18.7 1.0 O E:HOH381 4.7 18.7 1.0 O2' A:U1 4.7 15.4 1.0 C5 E:A3 4.7 2.4 1.0 O4 A:U1 4.7 10.2 1.0 C8 E:A3 4.8 4.3 1.0 N6 E:A3 4.9 4.2 1.0 O5' E:BGM2 5.0 10.0 1.0

Bromine binding site 6 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Rip-Radiation-Damage Induced Phasing within 5.0Å range: probe atom residue distance (Å) B Occ F:Br2 b:13.2 occ:0.80 BR F:BGM2 0.0 13.2 0.8 C8 F:BGM2 1.9 4.5 1.0 O D:HOH386 2.2 18.8 1.0 N7 F:BGM2 2.8 4.0 1.0 N9 F:BGM2 2.9 4.2 1.0 O4' F:BGM2 3.3 4.9 1.0 C1' F:BGM2 3.4 4.0 1.0 C2' F:BGM2 3.5 4.8 1.0 N3 D:U1 3.6 4.6 1.0 C2 D:U1 3.6 5.2 1.0 C5' F:BGM2 3.6 8.3 1.0 O2 D:U1 3.7 5.9 1.0 O H:HOH308 3.7 16.4 1.0 C5 F:BGM2 3.9 4.2 1.0 C4' F:BGM2 3.9 5.9 1.0 N2 E:BGM2 4.0 4.0 1.0 C4 F:BGM2 4.0 3.8 1.0 N2 H:BGM2 4.0 3.8 1.0 N7 F:A3 4.3 3.2 1.0 C3' F:BGM2 4.3 5.2 1.0 C4 D:U1 4.3 6.7 1.0 O2' F:U1 4.3 17.8 1.0 N1 D:U1 4.4 6.0 1.0 O2' D:U1 4.5 17.2 1.0 C2 H:BGM2 4.6 3.3 1.0 N3 H:BGM2 4.6 3.4 1.0 O F:HOH247 4.6 26.5 1.0 O E:HOH371 4.7 20.2 1.0 BR D:BGM2 4.7 12.1 0.8 C5 F:A3 4.8 3.7 1.0 O4 D:U1 4.8 8.8 1.0 C8 F:A3 4.9 3.7 1.0 N6 F:A3 4.9 2.6 1.0 O D:HOH384 5.0 19.4 1.0 C6 D:U1 5.0 7.9 1.0

Bromine binding site 7 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Rip-Radiation-Damage Induced Phasing within 5.0Å range: probe atom residue distance (Å) B Occ G:Br2 b:12.1 occ:0.80 BR G:BGM2 0.0 12.1 0.8 C8 G:BGM2 1.8 4.6 1.0 O H:HOH387 2.3 15.1 1.0 N7 G:BGM2 2.8 4.2 1.0 N9 G:BGM2 2.9 4.4 1.0 O4' G:BGM2 3.3 5.7 1.0 C1' G:BGM2 3.4 5.4 1.0 C2' G:BGM2 3.5 5.7 1.0 N3 H:U1 3.6 4.3 1.0 C5' G:BGM2 3.6 9.7 1.0 O2 H:U1 3.7 7.6 1.0 C2 H:U1 3.7 4.8 1.0 O C:HOH315 3.9 21.9 1.0 C5 G:BGM2 3.9 3.3 1.0 C4' G:BGM2 3.9 6.6 1.0 N2 F:BGM2 4.0 4.5 1.0 C4 G:BGM2 4.0 3.6 1.0 N2 C:BGM2 4.0 4.8 1.0 N7 G:A3 4.2 4.1 1.0 C3' G:BGM2 4.3 6.7 1.0 C4 H:U1 4.4 6.5 1.0 N1 H:U1 4.5 7.0 1.0 O2' G:U1 4.5 15.8 1.0 O G:HOH229 4.6 20.9 1.0 C2 C:BGM2 4.6 3.5 1.0 C5 G:A3 4.6 3.3 1.0 N3 C:BGM2 4.7 4.2 1.0 O2' H:U1 4.7 14.8 1.0 C8 G:A3 4.7 4.0 1.0 O F:HOH228 4.7 14.4 1.0 BR H:BGM2 4.7 11.7 0.8 N6 G:A3 4.8 3.7 1.0 O G:HOH388 4.8 20.3 1.0 O4 H:U1 4.9 8.8 1.0 O5' G:BGM2 4.9 9.4 1.0 C6 G:A3 5.0 2.9 1.0

Bromine binding site 8 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Rip-Radiation-Damage Induced Phasing within 5.0Å range: probe atom residue distance (Å) B Occ H:Br2 b:11.7 occ:0.80 BR H:BGM2 0.0 11.7 0.8 C8 H:BGM2 1.8 3.5 1.0 O G:HOH388 2.4 20.3 1.0 N7 H:BGM2 2.8 3.3 1.0 N9 H:BGM2 2.9 3.5 1.0 O4' H:BGM2 3.3 5.4 1.0 C1' H:BGM2 3.4 3.4 1.0 C2' H:BGM2 3.5 6.3 1.0 C5' H:BGM2 3.6 8.2 1.0 O2 G:U1 3.6 7.3 1.0 N3 G:U1 3.6 7.0 1.0 C2 G:U1 3.6 6.0 1.0 O F:HOH228 3.9 14.4 1.0 C5 H:BGM2 3.9 4.0 1.0 N2 C:BGM2 3.9 4.8 1.0 C4' H:BGM2 4.0 6.1 1.0 N2 F:BGM2 4.0 4.5 1.0 C4 H:BGM2 4.0 3.6 1.0 N7 H:A3 4.2 4.5 1.0 C3' H:BGM2 4.3 4.1 1.0 N1 G:U1 4.4 7.1 1.0 C4 G:U1 4.4 7.8 1.0 O H:HOH219 4.4 20.8 1.0 O2' H:U1 4.5 14.8 1.0 N3 F:BGM2 4.6 3.9 1.0 C2 F:BGM2 4.6 4.4 1.0 O2' G:U1 4.6 15.8 1.0 BR G:BGM2 4.7 12.1 0.8 C5 H:A3 4.7 3.9 1.0 C8 H:A3 4.8 4.1 1.0 O H:HOH387 4.8 15.1 1.0 N6 H:A3 4.9 3.8 1.0 O4 G:U1 4.9 9.9 1.0 O C:HOH315 4.9 21.9 1.0 O5' H:BGM2 4.9 8.9 1.0 C6 G:U1 5.0 7.1 1.0

R.B.G.Ravelli, H.-K.S.Leiros, B.Pan, M.Caffrey, S.Mcsweeney. Specific Radiation-Damage Can Be Used to Solve Macromolecular Crystal Structures Structure V. 11 217 2003.
ISSN: ISSN 0969-2126
PubMed: 12575941
DOI: 10.1016/S0969-2126(03)00006-6