Bromine in PDB 1qbp: Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs

The structure of Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs, PDB code: 1qbp was solved by A.C.Anderson, R.H.O'neil, D.J.Filman, C.A.Frederick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	999.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.450, 24.270, 104.450, 90.00, 118.76, 90.00
R / Rfree (%)	21.7 / 25.3

Pages:

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

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs (pdb code 1qbp). 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 A Brominated Rna Helix with Four Mismatched Base Pairs, PDB code: 1qbp:
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 A Brominated Rna Helix with Four Mismatched Base Pairs


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 A Brominated Rna Helix with Four Mismatched Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3 b:37.7 occ:1.00 BR A:CBV3 0.0 37.7 1.0 C5 A:CBV3 1.9 28.6 1.0 C6 A:CBV3 2.8 28.0 1.0 C4 A:CBV3 2.9 27.9 1.0 N4 A:CBV3 3.1 29.0 1.0 N7 A:G2 3.4 16.8 1.0 C5 A:G2 3.5 13.8 1.0 C8 A:G2 3.5 16.6 1.0 C4 A:G2 3.7 15.1 1.0 N9 A:G2 3.7 15.4 1.0 O2P A:CBV3 3.9 21.9 1.0 N1 A:CBV3 4.1 27.3 1.0 C3' A:G2 4.1 22.6 1.0 C6 A:G2 4.1 14.7 1.0 N3 A:CBV3 4.1 25.4 1.0 C2' A:G2 4.3 24.0 1.0 O5' A:G2 4.4 28.1 1.0 N3 A:G2 4.4 12.1 1.0 BR A:CBV4 4.4 35.0 1.0 C1' A:G2 4.5 20.2 1.0 O5' A:CBV3 4.6 22.1 1.0 C2 A:CBV3 4.6 27.6 1.0 O6 A:G2 4.6 13.4 1.0 N1 A:G2 4.7 13.4 1.0 OP1 A:G2 4.7 33.3 1.0 P A:CBV3 4.7 24.2 1.0 C2 A:G2 4.8 14.2 1.0 O3' A:G2 4.9 25.1 1.0

Bromine binding site 2 out of 12 in the Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs


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 A Brominated Rna Helix with Four Mismatched Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Br4 b:35.0 occ:1.00 BR A:CBV4 0.0 35.0 1.0 C5 A:CBV4 1.9 21.6 1.0 C6 A:CBV4 2.8 19.3 1.0 C4 A:CBV4 2.9 16.0 1.0 N4 A:CBV4 3.1 7.3 1.0 C5 A:CBV3 3.6 28.6 1.0 C4 A:CBV3 3.7 27.9 1.0 O2P A:CBV4 3.7 25.4 1.0 C6 A:CBV3 3.8 28.0 1.0 O A:HOH7205 3.8 5.1 0.5 N3 A:CBV3 3.9 25.4 1.0 N1 A:CBV3 4.0 27.3 1.0 C2 A:CBV3 4.0 27.6 1.0 N1 A:CBV4 4.1 21.3 1.0 N3 A:CBV4 4.1 17.4 1.0 N4 A:CBV3 4.2 29.0 1.0 O5' A:CBV4 4.3 23.7 1.0 BR A:CBV3 4.4 37.7 1.0 C3' A:CBV3 4.4 22.8 1.0 C2' A:CBV3 4.5 25.9 1.0 P A:CBV4 4.6 26.0 1.0 C2 A:CBV4 4.6 18.2 1.0 O2 A:CBV3 4.7 24.6 1.0 C1' A:CBV3 4.8 26.5 1.0

Bromine binding site 3 out of 12 in the Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs


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 A Brominated Rna Helix with Four Mismatched Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ B:Br18 b:31.0 occ:1.00 BR B:CBV18 0.0 31.0 1.0 C5 B:CBV18 1.9 18.0 1.0 C4 B:CBV18 2.8 9.1 1.0 C6 B:CBV18 2.9 12.0 1.0 N4 B:CBV18 3.0 12.7 1.0 O B:HOH7226 3.3 16.4 0.5 N7 B:G17 3.5 14.3 1.0 C8 B:G17 3.5 15.3 1.0 C5 B:G17 3.6 10.8 1.0 N9 B:G17 3.7 18.6 1.0 C4 B:G17 3.7 13.6 1.0 OP1 B:G17 3.8 41.6 1.0 O2P B:CBV18 3.8 16.1 1.0 O5' B:G17 3.8 39.6 1.0 C3' B:G17 4.0 23.4 1.0 N3 B:CBV18 4.1 14.7 1.0 BR B:CBV19 4.1 19.6 1.0 N1 B:CBV18 4.1 11.4 1.0 C6 B:G17 4.2 9.7 1.0 C2' B:G17 4.3 20.8 1.0 P B:G17 4.4 43.4 1.0 N3 B:G17 4.4 12.2 1.0 O5' B:CBV18 4.5 13.4 1.0 C1' B:G17 4.5 20.7 1.0 P B:CBV18 4.6 18.7 1.0 C2 B:CBV18 4.6 14.5 1.0 O6 B:G17 4.8 6.7 1.0 N1 B:G17 4.8 7.9 1.0 O3' B:G17 4.8 19.0 1.0 C2 B:G17 4.9 13.4 1.0 O4' B:G17 4.9 27.9 1.0 C4' B:G17 4.9 28.2 1.0 C5' B:G17 5.0 32.6 1.0

Bromine binding site 4 out of 12 in the Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs


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 A Brominated Rna Helix with Four Mismatched Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ B:Br19 b:19.6 occ:1.00 BR B:CBV19 0.0 19.6 1.0 C5 B:CBV19 1.9 11.0 1.0 C4 B:CBV19 2.8 8.1 1.0 C6 B:CBV19 2.9 5.5 1.0 N4 B:CBV19 3.0 3.4 1.0 C5 B:CBV18 3.5 18.0 1.0 C6 B:CBV18 3.6 12.0 1.0 O2P B:CBV19 3.6 4.4 1.0 O B:HOH6200 3.7 3.4 0.5 C4 B:CBV18 3.8 9.1 1.0 N1 B:CBV18 3.9 11.4 1.0 N3 B:CBV18 4.1 14.7 1.0 N3 B:CBV19 4.1 7.6 1.0 C2 B:CBV18 4.1 14.5 1.0 N1 B:CBV19 4.1 3.4 1.0 BR B:CBV18 4.1 31.0 1.0 C3' B:CBV18 4.2 7.7 1.0 C2' B:CBV18 4.3 11.7 1.0 N4 B:CBV18 4.4 12.7 1.0 O5' B:CBV19 4.4 6.8 1.0 P B:CBV19 4.6 7.5 1.0 C2 B:CBV19 4.6 7.2 1.0 O5' B:CBV18 4.7 13.4 1.0 C1' B:CBV18 4.7 9.9 1.0 N7 B:A20 4.7 5.8 1.0 O2P B:CBV18 4.8 16.1 1.0 O2 B:CBV18 4.9 11.1 1.0 O3' B:CBV18 5.0 8.2 1.0

Bromine binding site 5 out of 12 in the Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs


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 A Brominated Rna Helix with Four Mismatched Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ C:Br33 b:41.6 occ:1.00 BR C:CBV33 0.0 41.6 1.0 C5 C:CBV33 1.9 30.9 1.0 C6 C:CBV33 2.8 28.8 1.0 C4 C:CBV33 2.9 29.1 1.0 N4 C:CBV33 3.2 19.4 1.0 N7 C:G32 3.7 33.8 1.0 O2P C:CBV33 3.7 36.9 1.0 C5 C:G32 3.8 33.8 1.0 C8 C:G32 3.8 34.6 1.0 C4 C:G32 3.9 32.4 1.0 N9 C:G32 3.9 34.2 1.0 C3' C:G32 4.0 38.6 1.0 N1 C:CBV33 4.1 24.2 1.0 N3 C:CBV33 4.1 26.2 1.0 C6 C:G32 4.3 30.4 1.0 BR C:CBV34 4.4 35.6 1.0 C5' C:G32 4.4 44.2 1.0 O5' C:CBV33 4.5 30.5 1.0 C2' C:G32 4.5 37.9 1.0 P C:CBV33 4.6 36.6 1.0 C2 C:CBV33 4.6 26.7 1.0 N3 C:G32 4.6 30.0 1.0 C4' C:G32 4.7 41.0 1.0 C1' C:G32 4.7 37.9 1.0 O3' C:G32 4.8 37.1 1.0 O6 C:G32 4.8 33.0 1.0 N1 C:G32 4.9 25.8 1.0 OP1 C:G32 4.9 57.7 1.0

Bromine binding site 6 out of 12 in the Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs


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 A Brominated Rna Helix with Four Mismatched Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ C:Br34 b:35.6 occ:1.00 BR C:CBV34 0.0 35.6 1.0 C5 C:CBV34 1.9 22.8 1.0 C6 C:CBV34 2.8 21.0 1.0 C4 C:CBV34 2.9 24.6 1.0 N4 C:CBV34 3.2 21.7 1.0 C4 C:CBV33 3.4 29.1 1.0 C5 C:CBV33 3.4 30.9 1.0 N3 C:CBV33 3.6 26.2 1.0 C6 C:CBV33 3.6 28.8 1.0 O2P C:CBV34 3.6 29.1 1.0 C2 C:CBV33 3.7 26.7 1.0 N1 C:CBV33 3.7 24.2 1.0 N4 C:CBV33 4.0 19.4 1.0 N1 C:CBV34 4.1 17.6 1.0 N3 C:CBV34 4.2 18.3 1.0 C3' C:CBV33 4.2 24.3 1.0 O5' C:CBV34 4.3 22.8 1.0 C2' C:CBV33 4.3 22.0 1.0 BR C:CBV33 4.4 41.6 1.0 O2 C:CBV33 4.4 24.9 1.0 P C:CBV34 4.5 22.9 1.0 C1' C:CBV33 4.6 21.3 1.0 C2 C:CBV34 4.7 19.4 1.0 O5' C:CBV33 4.9 30.5 1.0 O3' C:CBV33 4.9 27.4 1.0

Bromine binding site 7 out of 12 in the Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs


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 A Brominated Rna Helix with Four Mismatched Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ D:Br48 b:31.6 occ:1.00 BR D:CBV48 0.0 31.6 1.0 C5 D:CBV48 1.9 14.7 1.0 C6 D:CBV48 2.8 11.7 1.0 C4 D:CBV48 2.8 13.1 1.0 N4 D:CBV48 3.0 5.6 1.0 OP2 D:G47 3.5 49.4 1.0 N7 D:G47 3.5 8.6 1.0 C8 D:G47 3.6 14.9 1.0 C5 D:G47 3.6 10.2 1.0 N9 D:G47 3.8 16.7 1.0 C4 D:G47 3.8 12.7 1.0 O5' D:G47 3.9 46.3 1.0 BR D:CBV49 4.0 27.4 1.0 N3 D:CBV48 4.1 11.7 1.0 N1 D:CBV48 4.1 9.0 1.0 C3' D:G47 4.1 29.4 1.0 O2P D:CBV48 4.2 19.1 1.0 C6 D:G47 4.2 15.6 1.0 P D:G47 4.3 50.6 1.0 C2' D:G47 4.4 26.3 1.0 N3 D:G47 4.5 9.0 1.0 C1' D:G47 4.6 25.9 1.0 O5' D:CBV48 4.6 17.6 1.0 C2 D:CBV48 4.6 12.5 1.0 O D:HOH7328 4.7 14.2 0.5 O6 D:G47 4.8 18.0 1.0 N1 D:G47 4.8 12.8 1.0 C2 D:G47 4.9 7.3 1.0 P D:CBV48 4.9 18.2 1.0 N4 D:CBV49 4.9 18.0 1.0 C4' D:G47 4.9 33.9 1.0 O4' D:G47 4.9 32.8 1.0 C5' D:G47 5.0 39.5 1.0

Bromine binding site 8 out of 12 in the Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs


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 A Brominated Rna Helix with Four Mismatched Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ D:Br49 b:27.4 occ:1.00 BR D:CBV49 0.0 27.4 1.0 C5 D:CBV49 1.9 12.3 1.0 C6 D:CBV49 2.8 9.7 1.0 C4 D:CBV49 2.8 11.4 1.0 N4 D:CBV49 3.0 18.0 1.0 C5 D:CBV48 3.4 14.7 1.0 C6 D:CBV48 3.4 11.7 1.0 C4 D:CBV48 3.7 13.1 1.0 O2P D:CBV49 3.7 13.1 1.0 N1 D:CBV48 3.7 9.0 1.0 N3 D:CBV48 4.0 11.7 1.0 C2 D:CBV48 4.0 12.5 1.0 BR D:CBV48 4.0 31.6 1.0 N3 D:CBV49 4.1 4.7 1.0 C3' D:CBV48 4.1 12.8 1.0 N1 D:CBV49 4.1 3.9 1.0 C2' D:CBV48 4.1 14.8 1.0 N4 D:CBV48 4.3 5.6 1.0 O5' D:CBV49 4.4 9.7 1.0 C1' D:CBV48 4.5 9.6 1.0 P D:CBV49 4.6 12.5 1.0 C2 D:CBV49 4.6 2.4 1.0 N7 D:A50 4.7 10.4 1.0 O2 D:CBV48 4.8 16.1 1.0 O5' D:CBV48 4.8 17.6 1.0 O3' D:CBV48 4.9 14.9 1.0

Bromine binding site 9 out of 12 in the Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs


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 A Brominated Rna Helix with Four Mismatched Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ E:Br63 b:39.9 occ:1.00 BR E:CBV63 0.0 39.9 1.0 C5 E:CBV63 1.9 27.3 1.0 C6 E:CBV63 2.8 25.0 1.0 C4 E:CBV63 2.9 22.4 1.0 N4 E:CBV63 3.0 16.4 1.0 N7 E:G62 3.5 21.2 1.0 C5 E:G62 3.5 21.3 1.0 O2P E:CBV63 3.6 26.5 1.0 C8 E:G62 3.6 19.1 1.0 C4 E:G62 3.8 20.9 1.0 N9 E:G62 3.8 22.1 1.0 C6 E:G62 4.1 18.1 1.0 N3 E:CBV63 4.1 19.6 1.0 N1 E:CBV63 4.1 23.4 1.0 C3' E:G62 4.1 23.6 1.0 C2' E:G62 4.3 22.9 1.0 O5' E:CBV63 4.4 22.8 1.0 O5' E:G62 4.4 29.9 1.0 N3 E:G62 4.5 17.2 1.0 BR E:CBV64 4.5 32.3 1.0 P E:CBV63 4.5 25.6 1.0 O6 E:G62 4.6 19.0 1.0 OP1 E:G62 4.6 34.9 1.0 C2 E:CBV63 4.6 22.8 1.0 C1' E:G62 4.7 22.0 1.0 N1 E:G62 4.7 22.6 1.0 C2 E:G62 4.8 20.3 1.0 O3' E:G62 4.9 22.7 1.0

Bromine binding site 10 out of 12 in the Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs


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 A Brominated Rna Helix with Four Mismatched Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ E:Br64 b:32.3 occ:1.00 BR E:CBV64 0.0 32.3 1.0 C5 E:CBV64 1.9 23.3 1.0 C6 E:CBV64 2.8 18.6 1.0 C4 E:CBV64 2.8 23.9 1.0 N4 E:CBV64 3.0 22.8 1.0 C5 E:CBV63 3.6 27.3 1.0 O2P E:CBV64 3.7 19.9 1.0 C4 E:CBV63 3.7 22.4 1.0 C6 E:CBV63 3.7 25.0 1.0 N3 E:CBV63 3.9 19.6 1.0 N1 E:CBV63 3.9 23.4 1.0 C2 E:CBV63 4.0 22.8 1.0 N1 E:CBV64 4.1 19.0 1.0 N3 E:CBV64 4.1 21.6 1.0 O5' E:CBV64 4.3 19.8 1.0 N4 E:CBV63 4.3 16.4 1.0 C3' E:CBV63 4.4 27.7 1.0 C2' E:CBV63 4.5 29.3 1.0 BR E:CBV63 4.5 39.9 1.0 P E:CBV64 4.5 21.8 1.0 C2 E:CBV64 4.6 18.7 1.0 O2 E:CBV63 4.7 20.2 1.0 C1' E:CBV63 4.8 27.6 1.0 O3' E:CBV63 5.0 26.5 1.0

A.C.Anderson, R.H.O'neil, D.J.Filman, C.A.Frederick. Crystal Structure of A Brominated Rna Helix with Four Mismatched Base Pairs: An Investigation Into Rna Conformational Variability. Biochemistry V. 38 12577 1999.
ISSN: ISSN 0006-2960
PubMed: 10504226
DOI: 10.1021/BI9904508