Bromine in PDB 1r71: Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna

The structure of Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna, PDB code: 1r71 was solved by D.Khare, G.Ziegelin, E.Lanka, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.440, 110.440, 160.530, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 25

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna (pdb code 1r71). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 12 binding sites of Bromine where determined in the Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna, PDB code: 1r71:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 12 in the Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Br2 b:32.2 occ:0.25 BR E:BRU2 0.0 32.2 0.2 BR I:BRU2 1.1 31.3 0.2 C5 E:BRU2 1.9 13.6 0.5 O E:HOH33 2.5 45.4 1.0 C5 I:BRU2 2.7 26.6 0.5 C6 E:BRU2 2.8 21.1 0.5 C4 E:BRU2 3.0 14.5 0.5 O4 E:BRU2 3.2 14.8 0.5 C6 I:BRU2 3.3 28.6 0.5 C2' I:DC1 3.7 30.4 0.5 O E:HOH41 3.9 46.4 1.0 C8 E:DA1 3.9 23.6 0.5 O F:HOH189 4.0 62.2 1.0 N1 E:BRU2 4.0 20.2 0.5 O E:HOH24 4.0 37.3 1.0 C4 I:BRU2 4.0 25.5 0.5 C6 I:DC1 4.0 33.8 0.5 C2' E:DA1 4.1 26.1 0.5 CG A:PRO182 4.1 33.3 1.0 N7 E:DA1 4.1 27.7 0.5 N3 E:BRU2 4.2 12.3 0.5 N9 E:DA1 4.2 28.2 0.5 CB A:PRO182 4.4 29.2 1.0 O4 I:BRU2 4.4 27.1 0.5 N1 I:DC1 4.5 29.1 0.5 C2 E:BRU2 4.6 18.7 0.5 C5 I:DC1 4.6 28.7 0.5 O F:HOH94 4.6 14.4 0.5 C5 E:DA1 4.6 22.8 0.5 C1' I:DC1 4.6 32.2 0.5 C4 E:DA1 4.7 23.2 0.5 C1' E:DA1 4.7 31.7 0.5 N1 I:BRU2 4.7 28.8 0.5 O I:HOH35 4.7 54.3 1.0 O4 E:DT3 4.7 15.1 0.5 C3' I:DC1 4.9 32.1 0.5 O5' I:DC1 4.9 38.6 0.5

Bromine binding site 2 out of 12 in the Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Br2 b:31.3 occ:0.25 BR I:BRU2 0.0 31.3 0.2 BR E:BRU2 1.1 32.2 0.2 C5 E:BRU2 1.4 13.6 0.5 C5 I:BRU2 1.9 26.6 0.5 C4 E:BRU2 2.0 14.5 0.5 O4 E:BRU2 2.1 14.8 0.5 C6 E:BRU2 2.7 21.1 0.5 C6 I:BRU2 2.9 28.6 0.5 C4 I:BRU2 3.0 25.5 0.5 O E:HOH41 3.2 46.4 1.0 N3 E:BRU2 3.3 12.3 0.5 O4 I:BRU2 3.3 27.1 0.5 O E:HOH33 3.6 45.4 1.0 O F:HOH189 3.7 62.2 1.0 N1 E:BRU2 3.7 20.2 0.5 O4 E:DT3 3.8 15.1 0.5 C2 E:BRU2 3.9 18.7 0.5 C6 I:DC1 3.9 33.8 0.5 O F:HOH94 4.1 14.4 0.5 N7 E:DA1 4.1 27.7 0.5 C8 E:DA1 4.1 23.6 0.5 N1 I:BRU2 4.1 28.8 0.5 C5 I:DC1 4.2 28.7 0.5 N3 I:BRU2 4.2 27.0 0.5 C2' I:DC1 4.2 30.4 0.5 C5 E:DA1 4.3 22.8 0.5 N9 E:DA1 4.3 28.2 0.5 N1 I:DC1 4.4 29.1 0.5 C4 E:DA1 4.4 23.2 0.5 CG A:PRO182 4.6 33.3 1.0 O4 I:DT3 4.6 31.1 0.5 CB A:PRO182 4.6 29.2 1.0 O E:HOH24 4.6 37.3 1.0 C2 I:BRU2 4.7 24.6 0.5 N6 F:DA15 4.7 13.2 0.5 C2' E:DA1 4.7 26.1 0.5 C4 E:DT3 4.8 19.5 0.5 C7 I:DT3 4.8 23.0 0.5 C4 I:DC1 4.8 28.7 0.5 C1' I:DC1 4.9 32.2 0.5 C6 E:DA1 4.9 24.9 0.5 C7 E:DT3 5.0 26.7 0.5 C1' E:DA1 5.0 31.7 0.5

Bromine binding site 3 out of 12 in the Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Br17 b:45.1 occ:0.50 BR I:BRU17 0.0 45.1 0.5 C5 I:BRU17 1.9 35.8 0.5 N7 E:DG17 2.2 22.1 0.5 C8 E:DG17 2.6 21.0 0.5 C4 I:BRU17 2.8 33.3 0.5 O4 I:BRU17 2.9 30.5 0.5 C6 I:BRU17 2.9 35.1 0.5 C8 I:DA16 3.4 20.5 0.5 C5 E:DG17 3.5 17.9 0.5 N7 I:DA16 3.5 19.4 0.5 O I:HOH37 3.6 27.9 0.5 C8 E:DA16 3.7 21.3 0.5 N9 I:DA16 3.8 22.3 0.5 C2' E:DA16 3.9 34.1 0.5 C5 I:DA16 3.9 20.3 0.5 N9 E:DG17 3.9 21.9 0.5 N9 E:DA16 4.0 25.6 0.5 N7 E:DA16 4.1 19.7 0.5 C4 I:DA16 4.1 21.5 0.5 N3 I:BRU17 4.1 30.0 0.5 N1 I:BRU17 4.2 31.4 0.5 C2' I:DA16 4.2 28.5 0.5 C6 E:DG17 4.4 21.3 0.5 C4 E:DG17 4.4 16.8 0.5 C1' E:DA16 4.4 30.8 0.5 O6 E:DG17 4.4 27.6 0.5 C1' I:DA16 4.4 31.2 0.5 C4 E:DA16 4.5 17.6 0.5 C5 E:DA16 4.5 19.8 0.5 C2 I:BRU17 4.6 29.6 0.5 O I:HOH27 4.7 56.4 1.0 C6 I:DA16 4.7 18.8 0.5 N3 I:DA16 4.9 18.9 0.5 OP2 I:BRU17 5.0 26.8 0.5 O4' E:DG17 5.0 21.8 0.5

Bromine binding site 4 out of 12 in the Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Br2 b:44.3 occ:0.25 BR F:BRU2 0.0 44.3 0.2 BR J:BRU2 1.2 31.4 0.2 C5 F:BRU2 1.9 27.2 0.5 O J:HOH31 2.5 54.5 1.0 C5 J:BRU2 2.7 20.4 0.5 C6 F:BRU2 2.8 31.7 0.5 C4 F:BRU2 3.0 24.9 0.5 O4 F:BRU2 3.2 27.2 0.5 C6 J:BRU2 3.4 24.0 0.5 C8 J:DA1 3.6 21.0 0.5 O F:HOH160 3.7 53.7 1.0 C2' J:DA1 3.7 31.3 0.5 O J:HOH26 3.9 40.4 1.0 C4 J:BRU2 4.0 18.5 0.5 N9 J:DA1 4.0 23.6 0.5 N1 F:BRU2 4.1 30.3 0.5 C6 F:DC1 4.1 35.9 0.5 N3 F:BRU2 4.2 19.4 0.5 N7 J:DA1 4.2 18.7 0.5 CG B:PRO182 4.2 37.1 1.0 C2' F:DC1 4.3 37.7 0.5 O F:HOH211 4.3 59.2 1.0 O4 J:BRU2 4.3 19.9 0.5 C1' J:DA1 4.3 31.9 0.5 C5 F:DC1 4.4 34.3 0.5 CB B:PRO182 4.4 34.4 1.0 N1 F:DC1 4.5 34.1 0.5 C2 F:BRU2 4.6 27.4 0.5 N1 J:BRU2 4.7 26.9 0.5 O4 F:DT3 4.8 20.4 0.5 C4 J:DA1 4.8 19.3 0.5 O F:HOH91 4.8 30.9 1.0 C1' F:DC1 4.9 38.5 0.5 C5 J:DA1 4.9 16.5 0.5 C4 F:DC1 5.0 28.4 0.5

Bromine binding site 5 out of 12 in the Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Br17 b:49.1 occ:0.50 BR F:BRU17 0.0 49.1 0.5 C5 F:BRU17 1.9 38.5 0.5 N7 J:DG17 2.1 26.8 0.5 C8 J:DG17 2.6 22.5 0.5 O F:HOH188 2.8 69.3 1.0 C6 F:BRU17 3.0 36.8 0.5 C4 F:BRU17 3.0 32.7 0.5 O4 F:BRU17 3.1 29.5 0.5 C2' F:DA16 3.2 33.8 0.5 C5 J:DG17 3.4 19.0 0.5 N9 F:DA16 3.5 35.7 0.5 O F:HOH157 3.5 33.7 0.5 C8 F:DA16 3.7 35.7 0.5 C8 J:DA16 3.7 23.2 0.5 C1' F:DA16 3.7 36.5 0.5 N7 J:DA16 3.8 20.4 0.5 N9 J:DG17 3.9 20.6 0.5 C4 F:DA16 3.9 36.9 0.5 N9 J:DA16 4.1 22.7 0.5 C5 J:DA16 4.2 20.4 0.5 N7 F:DA16 4.2 37.3 0.5 N1 F:BRU17 4.2 34.1 0.5 N3 F:BRU17 4.2 32.3 0.5 C6 J:DG17 4.3 21.5 0.5 O6 J:DG17 4.3 29.8 0.5 C5 F:DA16 4.3 33.4 0.5 C4 J:DG17 4.3 22.2 0.5 C2' J:DA16 4.3 24.6 0.5 C4 J:DA16 4.4 17.7 0.5 N3 F:DA16 4.6 37.1 0.5 C3' F:DA16 4.6 35.7 0.5 O F:HOH150 4.7 26.4 0.5 C2 F:BRU17 4.7 33.5 0.5 C1' J:DA16 4.8 23.5 0.5 O4' J:DG17 4.8 26.6 0.5 C6 J:DA16 4.9 17.4 0.5 O4' F:DA16 5.0 38.9 0.5 C1' J:DG17 5.0 30.5 0.5

Bromine binding site 6 out of 12 in the Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Br2 b:31.4 occ:0.25 BR J:BRU2 0.0 31.4 0.2 BR F:BRU2 1.2 44.3 0.2 C5 F:BRU2 1.4 27.2 0.5 C5 J:BRU2 1.9 20.4 0.5 C4 F:BRU2 2.0 24.9 0.5 O4 F:BRU2 2.2 27.2 0.5 C6 F:BRU2 2.7 31.7 0.5 C6 J:BRU2 2.9 24.0 0.5 C4 J:BRU2 2.9 18.5 0.5 O F:HOH160 3.1 53.7 1.0 O4 J:BRU2 3.2 19.9 0.5 N3 F:BRU2 3.3 19.4 0.5 O J:HOH31 3.6 54.5 1.0 C8 J:DA1 3.7 21.0 0.5 N1 F:BRU2 3.7 30.3 0.5 O4 F:DT3 3.9 20.4 0.5 O F:HOH211 3.9 59.2 1.0 N7 J:DA1 3.9 18.7 0.5 C2 F:BRU2 4.0 27.4 0.5 N9 J:DA1 4.1 23.6 0.5 N1 J:BRU2 4.1 26.9 0.5 N3 J:BRU2 4.1 18.2 0.5 O F:HOH91 4.2 30.9 1.0 C5 F:DC1 4.3 34.3 0.5 C6 F:DC1 4.3 35.9 0.5 C2' J:DA1 4.4 31.3 0.5 C5 J:DA1 4.5 16.5 0.5 CG B:PRO182 4.5 37.1 1.0 O J:HOH26 4.5 40.4 1.0 CB B:PRO182 4.5 34.4 1.0 N1 F:DC1 4.6 34.1 0.5 C4 J:DA1 4.6 19.3 0.5 C4 F:DC1 4.6 28.4 0.5 C2 J:BRU2 4.6 18.9 0.5 O4 J:DT3 4.6 30.9 0.5 C7 J:DT3 4.7 35.5 0.5 C1' J:DA1 4.7 31.9 0.5 C4 F:DT3 4.7 14.2 0.5 C2' F:DC1 4.8 37.7 0.5 N6 I:DA15 4.8 23.7 0.5 N3 F:DC1 4.9 27.7 0.5 C2 F:DC1 4.9 30.5 0.5 C7 F:DT3 5.0 17.4 0.5

Bromine binding site 7 out of 12 in the Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna within 5.0Å range: probe atom residue distance (Å) B Occ G:Br2 b:31.5 occ:0.25 BR G:BRU2 0.0 31.5 0.2 BR L:BRU2 1.2 42.0 0.2 C5 L:BRU2 1.7 20.2 0.5 C5 G:BRU2 1.9 24.6 0.5 O4 L:BRU2 2.1 24.4 0.5 C4 L:BRU2 2.1 18.9 0.5 C6 G:BRU2 2.8 24.7 0.5 C6 L:BRU2 2.9 25.7 0.5 C4 G:BRU2 2.9 27.0 0.5 O4 G:BRU2 3.2 28.1 0.5 N3 L:BRU2 3.4 18.1 0.5 N1 L:BRU2 3.9 26.3 0.5 O4 L:DT3 3.9 15.1 0.5 C8 G:DA1 4.0 26.4 0.5 N1 G:BRU2 4.0 28.5 0.5 O L:HOH205 4.1 38.0 1.0 C2 L:BRU2 4.1 24.9 0.5 C2' G:DA1 4.2 28.7 0.5 N3 G:BRU2 4.2 25.6 0.5 N9 G:DA1 4.2 26.9 0.5 N7 G:DA1 4.2 30.4 0.5 C5 L:DC1 4.3 35.7 0.5 C6 L:DC1 4.3 34.0 0.5 C7 G:DT3 4.4 33.7 0.5 N6 K:DA15 4.5 16.2 0.5 C4 G:DA1 4.5 23.0 0.5 C5 G:DA1 4.5 24.2 0.5 C2 G:BRU2 4.6 21.8 0.5 C1' G:DA1 4.6 30.9 0.5 CG D:PRO182 4.7 35.4 1.0 O G:HOH22 4.7 44.0 1.0 CB D:PRO182 4.7 32.4 1.0 N1 L:DC1 4.7 31.2 0.5 C4 L:DC1 4.7 32.5 0.5 C2' L:DC1 4.8 38.5 0.5 C4 L:DT3 4.8 21.5 0.5 O4 G:DT3 4.9 26.8 0.5

Bromine binding site 8 out of 12 in the Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna within 5.0Å range: probe atom residue distance (Å) B Occ L:Br2 b:42.0 occ:0.25 BR L:BRU2 0.0 42.0 0.2 BR G:BRU2 1.2 31.5 0.2 C5 L:BRU2 1.9 20.2 0.5 C5 G:BRU2 2.7 24.6 0.5 C6 L:BRU2 2.8 25.7 0.5 C4 L:BRU2 3.0 18.9 0.5 C6 G:BRU2 3.1 24.7 0.5 O4 L:BRU2 3.2 24.4 0.5 C2' G:DA1 3.4 28.7 0.5 O G:HOH22 3.8 44.0 1.0 C4 G:BRU2 4.0 27.0 0.5 N1 L:BRU2 4.0 26.3 0.5 C8 G:DA1 4.0 26.4 0.5 C2' L:DC1 4.0 38.5 0.5 N9 G:DA1 4.1 26.9 0.5 N3 L:BRU2 4.2 18.1 0.5 C6 L:DC1 4.2 34.0 0.5 C1' G:DA1 4.2 30.9 0.5 CG D:PRO182 4.3 35.4 1.0 O4 G:BRU2 4.4 28.1 0.5 CB D:PRO182 4.4 32.4 1.0 N1 G:BRU2 4.5 28.5 0.5 C5 L:DC1 4.5 35.7 0.5 C2 L:BRU2 4.6 24.9 0.5 N7 G:DA1 4.6 30.4 0.5 N1 L:DC1 4.6 31.2 0.5 O L:HOH205 4.7 38.0 1.0 C3' G:DA1 4.7 34.1 0.5 O4 L:DT3 4.7 15.1 0.5 C4 G:DA1 4.8 23.0 0.5 C7 G:DT3 4.8 33.7 0.5 OP2 G:BRU2 4.8 33.1 0.5 C1' L:DC1 4.9 38.9 0.5 C5' G:BRU2 5.0 32.3 0.5

Bromine binding site 9 out of 12 in the Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna within 5.0Å range: probe atom residue distance (Å) B Occ L:Br17 b:51.0 occ:0.50 BR L:BRU17 0.0 51.0 0.5 C5 L:BRU17 1.9 34.2 0.5 N7 G:DG17 2.5 16.9 0.5 C4 L:BRU17 2.8 32.6 0.5 O4 L:BRU17 2.9 24.2 0.5 C6 L:BRU17 2.9 37.7 0.5 C8 G:DG17 3.0 17.5 0.5 O L:HOH335 3.5 53.8 1.0 N7 L:DA16 3.6 27.4 0.5 C8 G:DA16 3.6 34.8 0.5 C8 L:DA16 3.7 25.4 0.5 N9 G:DA16 3.7 31.6 0.5 C2' G:DA16 3.7 28.0 0.5 C5 G:DG17 3.8 16.2 0.5 N7 G:DA16 4.0 33.5 0.5 N3 L:BRU17 4.1 26.5 0.5 N1 L:BRU17 4.1 36.0 0.5 C5 L:DA16 4.2 24.3 0.5 C1' G:DA16 4.2 33.0 0.5 C4 G:DA16 4.2 30.3 0.5 N9 G:DG17 4.3 18.6 0.5 N9 L:DA16 4.3 26.4 0.5 O6 G:DG17 4.4 25.3 0.5 C5 G:DA16 4.4 25.8 0.5 C6 G:DG17 4.5 17.6 0.5 C2' L:DA16 4.6 30.0 0.5 C2 L:BRU17 4.6 34.9 0.5 C4 L:DA16 4.6 22.3 0.5 O G:HOH34 4.6 38.6 0.5 C4 G:DG17 4.7 22.7 0.5 C6 L:DA16 4.9 25.3 0.5

Bromine binding site 10 out of 12 in the Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of the Dna Binding Domain of Korb in Complex with the Operator Dna within 5.0Å range: probe atom residue distance (Å) B Occ H:Br2 b:47.2 occ:0.25 BR H:BRU2 0.0 47.2 0.2 BR K:BRU2 1.2 30.2 0.2 C5 H:BRU2 1.9 33.9 0.5 O K:HOH37 2.6 43.7 1.0 C6 H:BRU2 2.8 30.3 0.5 C5 K:BRU2 3.0 23.2 0.5 C4 H:BRU2 3.0 28.7 0.5 O4 H:BRU2 3.2 29.8 0.5 C8 K:DA1 3.7 31.6 0.5 C6 K:BRU2 3.7 28.4 0.5 C2' H:DC1 3.8 36.0 0.5 C6 H:DC1 3.9 40.5 0.5 C2' K:DA1 4.0 31.3 0.5 N1 H:BRU2 4.1 25.6 0.5 C4 K:BRU2 4.1 24.9 0.5 N7 K:DA1 4.2 27.7 0.5 N3 H:BRU2 4.2 24.1 0.5 O K:HOH26 4.2 38.9 1.0 O4 K:BRU2 4.2 25.6 0.5 N1 H:DC1 4.2 37.9 0.5 C5 H:DC1 4.3 36.8 0.5 N9 K:DA1 4.3 28.2 0.5 CG C:PRO182 4.4 40.1 1.0 C1' H:DC1 4.5 38.5 0.5 C2 H:BRU2 4.6 26.2 0.5 C1' K:DA1 4.7 30.5 0.5 CB C:PRO182 4.8 38.0 1.0 O4 H:DT3 4.8 25.8 0.5 O G:HOH28 4.9 11.7 0.5 O5' H:DC1 4.9 44.0 0.5 C2 H:DC1 4.9 37.0 0.5 O H:HOH38 4.9 62.4 1.0 C5 K:DA1 4.9 25.0 0.5 C4 H:DC1 5.0 34.3 0.5

D.Khare, G.Ziegelin, E.Lanka, U.Heinemann. Sequence-Specific Dna Binding Determined By Contacts Outside the Helix-Turn-Helix Motif of the Parb Homolog Korb. Nat.Struct.Mol.Biol. V. 11 656 2004.
ISSN: ISSN 1545-9993
PubMed: 15170177
DOI: 10.1038/NSMB773