Bromine in PDB 367d: 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex

The structure of 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex, PDB code: 367d was solved by A.K.Todd, A.Adams, J.H.Thorpe, W.A.Denny, C.J.Cardin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 1.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	30.096, 30.096, 39.547, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / n/a

The binding sites of Bromine atom in the 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex (pdb code 367d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex, PDB code: 367d:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in the 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br14 b:32.5 occ:1.00 BR A:DA514 0.0 32.5 1.0 C5 A:DA514 2.0 16.2 1.0 C14 A:DA514 2.9 14.9 1.0 N10 A:DA514 2.9 16.4 1.0 C6 A:DA514 3.0 15.6 1.0 C4 B:DC11 3.6 11.4 1.0 C5 B:DC11 3.7 12.8 1.0 N4 B:DC11 3.7 14.2 1.0 O6 B:DG12 3.8 11.5 1.0 O B:HOH33 4.2 32.9 1.0 O B:HOH40 4.2 26.5 1.0 C13 A:DA514 4.2 14.8 1.0 C12 A:DA514 4.2 17.6 1.0 O B:HOH31 4.2 34.6 1.0 OD1 A:DA514 4.2 21.1 1.0 C7 A:DA514 4.3 14.9 1.0 N3 B:DC11 4.3 11.1 1.0 C6 B:DC11 4.3 12.6 1.0 C6 B:DG12 4.3 10.8 1.0 N4 A:DC1 4.6 11.5 1.0 N7 B:DG12 4.6 12.5 1.0 C5 B:DG12 4.7 11.0 1.0 CD1 A:DA514 4.7 21.7 1.0 C8 A:DA514 4.8 15.0 1.0 C2 B:DC11 4.8 11.1 1.0 N1 B:DC11 4.9 12.8 1.0 C4 A:DA514 4.9 17.1 1.0

Bromine binding site 2 out of 6 in the 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br15 b:54.3 occ:1.00 C5 A:DU3 1.9 22.6 1.0 C6 A:DU3 2.9 21.8 1.0 C4 A:DU3 2.9 19.9 1.0 O4 A:DU3 3.1 24.0 1.0 O A:HOH45 3.4 36.6 1.0 C2' A:DG2 3.7 18.8 1.0 O A:HOH82 3.8 31.2 1.0 C8 A:DG2 3.9 17.8 1.0 N9 A:DG2 4.0 16.3 1.0 N3 A:DU3 4.1 20.5 1.0 O A:HOH125 4.2 42.7 1.0 N1 A:DU3 4.2 22.6 1.0 C1' A:DG2 4.3 18.4 1.0 O A:HOH39 4.3 30.8 1.0 N7 A:DG2 4.3 16.4 1.0 C4 A:DG2 4.4 12.9 1.0 N6 A:DA4 4.5 14.8 1.0 CD7 B:DA513 4.6 33.1 1.0 C5 A:DG2 4.6 13.9 1.0 C2 A:DU3 4.8 20.3 1.0 O4 B:DU9 4.9 21.3 1.0

Bromine binding site 3 out of 6 in the 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Br13 b:32.6 occ:1.00 BR B:DA513 0.0 32.6 1.0 C5 B:DA513 2.0 16.2 1.0 C14 B:DA513 2.9 14.3 1.0 N10 B:DA513 2.9 15.7 1.0 C6 B:DA513 2.9 16.6 1.0 O A:HOH97 3.6 43.1 1.0 C4 A:DC5 3.6 11.5 1.0 C5 A:DC5 3.6 12.5 1.0 N4 A:DC5 3.7 13.2 1.0 O6 A:DG6 3.8 11.8 1.0 O A:HOH50 4.2 31.5 1.0 O A:HOH75 4.2 24.7 1.0 OD1 B:DA513 4.2 20.6 1.0 C13 B:DA513 4.2 13.7 1.0 C12 B:DA513 4.2 16.9 1.0 C7 B:DA513 4.3 15.4 1.0 N3 A:DC5 4.3 11.2 1.0 C6 A:DG6 4.3 11.2 1.0 O A:HOH49 4.3 38.0 1.0 C6 A:DC5 4.3 11.6 1.0 N4 B:DC7 4.6 12.2 1.0 N7 A:DG6 4.7 12.9 1.0 C5 A:DG6 4.7 11.6 1.0 CD1 B:DA513 4.7 18.6 1.0 C8 B:DA513 4.7 14.4 1.0 C2 A:DC5 4.8 10.6 1.0 N1 A:DC5 4.9 11.4 1.0 O A:HOH85 4.9 34.6 1.0 C4 B:DA513 4.9 15.9 1.0

Bromine binding site 4 out of 6 in the 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Br15 b:21.4 occ:0.50 BR B:DA515 0.0 21.4 0.5 C8 B:DA515 1.6 8.7 0.5 C5 B:DA515 2.0 9.1 0.5 C13 B:DA515 2.4 7.7 0.5 C9 B:DA515 2.4 11.4 0.5 C7 B:DA515 2.8 10.2 0.5 C14 B:DA515 3.1 10.2 0.5 N10 B:DA515 3.1 10.1 0.5 C6 B:DA515 3.1 9.8 0.5 O2 A:DC1 3.3 10.7 1.0 C14 B:DA515 3.6 9.7 0.5 C11 B:DA515 3.8 10.2 0.5 C6 B:DA515 3.9 9.6 0.5 C2 A:DC1 3.9 10.1 1.0 C1' A:DC1 4.0 12.5 1.0 N1 A:DC1 4.3 10.5 1.0 O A:HOH18 4.3 14.1 1.0 O4' A:DC1 4.3 11.4 1.0 C13 B:DA515 4.3 8.0 0.5 C5 B:DA515 4.4 8.3 0.5 C7 B:DA515 4.4 9.6 0.5 C12 B:DA515 4.5 11.0 0.5 C1 B:DA515 4.5 11.4 0.5 C12 B:DA515 4.7 10.6 0.5 N2 B:DG12 4.7 11.5 1.0 N10 B:DA515 4.8 8.8 0.5 N3 A:DC1 4.8 9.9 1.0 C8 B:DA515 4.9 9.6 0.5

Bromine binding site 5 out of 6 in the 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Br15 b:21.7 occ:0.50 BR B:DA515 0.0 21.7 0.5 C8 B:DA515 1.6 9.6 0.5 C5 B:DA515 2.0 8.3 0.5 C13 B:DA515 2.3 8.0 0.5 C9 B:DA515 2.5 10.7 0.5 C7 B:DA515 2.7 9.6 0.5 C14 B:DA515 3.0 9.7 0.5 N10 B:DA515 3.1 8.8 0.5 C6 B:DA515 3.1 9.6 0.5 C14 B:DA515 3.6 10.2 0.5 C11 B:DA515 3.9 10.4 0.5 C6 B:DA515 3.9 9.8 0.5 N4 A:DC1 3.9 11.5 1.0 C4 A:DC1 4.2 11.0 1.0 C13 B:DA515 4.3 7.7 0.5 O6 B:DG12 4.3 11.5 1.0 O B:HOH33 4.4 32.9 1.0 C5 B:DA515 4.4 9.1 0.5 C7 B:DA515 4.4 10.2 0.5 C12 B:DA515 4.5 10.6 0.5 C1 B:DA515 4.6 12.1 0.5 N3 A:DC1 4.7 9.9 1.0 C12 B:DA515 4.7 11.0 0.5 N10 B:DA515 4.7 10.1 0.5 C5 A:DC1 4.7 11.1 1.0 C8 B:DA515 4.9 8.7 0.5

Bromine binding site 6 out of 6 in the 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of 1.2 A Structure Determination of the D(Cg(5-Bru)Acg)2/5-Bromo-9-Amino- Daca Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Br16 b:54.9 occ:1.00 C5 B:DU9 2.0 22.3 1.0 C6 B:DU9 2.9 21.3 1.0 C4 B:DU9 3.0 19.5 1.0 O4 B:DU9 3.1 21.3 1.0 C2' B:DG8 3.7 19.2 1.0 O B:HOH48 3.9 31.7 1.0 C8 B:DG8 3.9 17.3 1.0 N9 B:DG8 4.0 14.7 1.0 N3 B:DU9 4.2 20.2 1.0 N1 B:DU9 4.2 22.8 1.0 C1' B:DG8 4.3 16.8 1.0 O B:HOH35 4.3 30.1 1.0 N7 B:DG8 4.4 16.2 1.0 C4 B:DG8 4.5 13.4 1.0 N6 B:DA10 4.5 15.2 1.0 C5 B:DG8 4.7 14.1 1.0 C2 B:DU9 4.8 19.6 1.0 O4 A:DU3 4.9 24.0 1.0

A.K.Todd, A.Adams, J.H.Thorpe, W.A.Denny, L.P.G.Wakelin, C.J.Cardin. Major Groove Binding and 'Dna-Induced' Fit in the Intercalation of A Derivative of the Mixed Topoisomerase I/II Poison N-(2-(Dimethlyamino)Ethyl)Acridine-4-Carboxamide (Daca) Into Dna: X-Ray Structure Complexed to D(Cg(5BR-U)Acg)2 at 1.3-Angstrom Resolution J.Med.Chem. V. 42 536 1999.
ISSN: ISSN 0022-2623
PubMed: 10052960
DOI: 10.1021/JM980479U