Bromine in PDB 366d: 1.3 A Structure Determination of the D(Cg(5-Bru)Acg)2/6- Bromo-9-Amino-Daca Complex

The structure of 1.3 A Structure Determination of the D(Cg(5-Bru)Acg)2/6- Bromo-9-Amino-Daca Complex, PDB code: 366d 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)	8.00 / 1.30
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	30.110, 30.110, 39.560, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The binding sites of Bromine atom in the 1.3 A Structure Determination of the D(Cg(5-Bru)Acg)2/6- Bromo-9-Amino-Daca Complex (pdb code 366d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the 1.3 A Structure Determination of the D(Cg(5-Bru)Acg)2/6- Bromo-9-Amino-Daca Complex, PDB code: 366d:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the 1.3 A Structure Determination of the D(Cg(5-Bru)Acg)2/6- 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 1.3 A Structure Determination of the D(Cg(5-Bru)Acg)2/6- Bromo-9-Amino-Daca Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1003 b:30.3 occ:0.61 BR A:BRU1003 0.0 30.3 0.6 BR A:BRU1003 1.3 18.4 0.4 C5 A:BRU1003 1.9 19.4 0.6 C6 A:BRU1003 2.8 20.1 0.6 H6 A:BRU1003 2.8 24.1 0.6 C4 A:BRU1003 2.8 16.8 0.6 C5 A:BRU1003 2.9 19.0 0.4 O4 A:BRU1003 3.2 15.7 0.6 H2' A:DG1002 3.2 29.6 1.0 O4 A:BRU1003 3.3 18.0 0.4 C4 A:BRU1003 3.4 15.2 0.4 H2'' A:DG1002 3.6 29.6 1.0 O A:HOH4020 3.7 32.3 1.0 H8 A:DG1002 3.8 24.7 1.0 C2' A:DG1002 3.8 24.7 1.0 C8 A:DG1002 3.8 20.6 1.0 C6 A:BRU1003 3.9 18.1 0.4 H6 A:BRU1003 4.0 21.7 0.6 N9 A:DG1002 4.0 18.3 1.0 N3 A:BRU1003 4.0 15.5 0.6 N1 A:BRU1003 4.1 18.8 0.6 N7 A:DG1002 4.2 18.0 1.0 C1' A:DG1002 4.4 22.4 1.0 H62 A:DA1004 4.4 22.3 1.0 O A:HOH4006 4.5 35.9 1.0 C4 A:DG1002 4.5 15.1 1.0 HD71 A:DA63013 4.5 53.3 0.6 H61 A:DA1004 4.6 22.3 1.0 C2 A:BRU1003 4.6 14.7 0.6 C5 A:DG1002 4.7 15.9 1.0 HN3 A:BRU1003 4.7 18.6 0.6 N6 A:DA1004 4.7 18.6 1.0 N3 A:BRU1003 4.8 15.7 0.4 H2' A:BRU1003 4.8 26.9 0.6 H1' A:DG1002 4.8 26.9 1.0 HD72 A:DA63013 4.9 53.3 0.6

Bromine binding site 2 out of 4 in the 1.3 A Structure Determination of the D(Cg(5-Bru)Acg)2/6- 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 1.3 A Structure Determination of the D(Cg(5-Bru)Acg)2/6- Bromo-9-Amino-Daca Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1003 b:18.4 occ:0.39 BR A:BRU1003 0.0 18.4 0.4 C5 A:BRU1003 1.2 19.4 0.6 BR A:BRU1003 1.3 30.3 0.6 H6 A:BRU1003 1.6 24.1 0.6 C6 A:BRU1003 1.6 20.1 0.6 C5 A:BRU1003 1.9 19.0 0.4 C4 A:BRU1003 2.5 16.8 0.6 C6 A:BRU1003 2.8 18.1 0.4 H6 A:BRU1003 2.8 21.7 0.6 C4 A:BRU1003 2.8 15.2 0.4 N1 A:BRU1003 2.9 18.8 0.6 O4 A:BRU1003 3.1 18.0 0.4 H2'' A:DG1002 3.2 29.6 1.0 O4 A:BRU1003 3.4 15.7 0.6 N3 A:BRU1003 3.4 15.5 0.6 H2' A:DG1002 3.5 29.6 1.0 O A:HOH4006 3.5 35.9 1.0 H62 A:DA1004 3.5 22.3 1.0 H2' A:BRU1003 3.6 26.9 0.6 C2 A:BRU1003 3.7 14.7 0.6 C2' A:DG1002 3.7 24.7 1.0 C1' A:BRU1003 3.9 21.7 0.6 N6 A:DA1004 3.9 18.6 1.0 H61 A:DA1004 4.0 22.3 1.0 N3 A:BRU1003 4.0 15.7 0.4 N1 A:BRU1003 4.1 17.8 0.4 C2' A:BRU1003 4.1 22.4 0.6 N9 A:DG1002 4.2 18.3 1.0 HN3 A:BRU1003 4.2 18.6 0.6 C1' A:DG1002 4.3 22.4 1.0 O4' A:BRU1003 4.3 19.7 0.6 C8 A:DG1002 4.4 20.6 1.0 H2'' A:BRU1003 4.4 26.9 0.6 H1' A:DG1002 4.5 26.9 1.0 OP2 A:BRU1003 4.5 23.6 0.4 H8 A:DG1002 4.5 24.7 1.0 C4 A:DG1002 4.6 15.1 1.0 C2 A:BRU1003 4.6 14.5 0.4 H2' A:BRU1003 4.6 26.5 0.6 H1' A:BRU1003 4.7 26.1 0.6 HN3 A:BRU1003 4.7 18.8 0.6 O A:HOH4020 4.7 32.3 1.0 C6 A:DA1004 4.7 16.3 1.0 N7 A:DG1002 4.9 18.0 1.0 O2 A:BRU1003 4.9 14.9 0.6 HD71 A:DA63013 4.9 53.3 0.6 C5 A:DG1002 5.0 15.9 1.0 O5' A:BRU1003 5.0 23.9 0.6

Bromine binding site 3 out of 4 in the 1.3 A Structure Determination of the D(Cg(5-Bru)Acg)2/6- 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 1.3 A Structure Determination of the D(Cg(5-Bru)Acg)2/6- Bromo-9-Amino-Daca Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3013 b:45.0 occ:1.00 BR A:DA63013 0.0 45.0 1.0 C6 A:DA63013 1.8 17.3 1.0 C5 A:DA63013 2.7 21.3 1.0 C7 A:DA63013 2.7 18.8 1.0 H5 A:DA63013 2.8 25.6 1.0 H7 A:DA63013 2.8 22.5 1.0 HD83 A:DA63015 3.0 43.2 0.5 H6 A:DC1005 3.3 20.2 1.0 H2'' A:DC1005 3.3 20.2 1.0 C6 A:DC1005 3.3 16.8 1.0 HD71 A:DA63015 3.5 46.0 0.5 H2' A:DC1005 3.5 20.2 1.0 C5 A:DC1005 3.6 16.1 1.0 N7 A:DG1006 3.7 16.9 1.0 CD8 A:DA63015 3.7 28.8 0.5 H5 A:DC1005 3.8 19.4 1.0 HD81 A:DA63015 3.8 43.2 0.5 C2' A:DC1005 3.8 16.9 1.0 N1 A:DC1005 3.8 15.7 1.0 O A:HOH4018 3.8 41.9 1.0 C8 A:DA63013 4.0 17.3 1.0 C14 A:DA63013 4.0 18.1 1.0 O A:HOH4017 4.0 42.0 1.0 ND2 A:DA63015 4.0 27.6 0.5 CD7 A:DA63015 4.0 30.7 0.5 C8 A:DG1006 4.0 16.7 1.0 H8 A:DG1006 4.1 20.0 1.0 O A:HOH4029 4.1 30.6 0.5 HD72 A:DA63015 4.1 46.0 0.5 O A:HOH4009 4.1 38.6 1.0 C1' A:DC1005 4.3 15.2 1.0 C4 A:DC1005 4.3 16.1 1.0 C5 A:DG1006 4.4 14.3 1.0 C13 A:DA63013 4.5 18.2 1.0 C2 A:DC1005 4.6 14.3 1.0 HD82 A:DA63015 4.6 43.2 0.5 H5' A:DG1006 4.6 28.2 1.0 H8 A:DA63013 4.7 20.8 1.0 H1' A:DC1005 4.7 18.3 1.0 N3 A:DC1005 4.8 13.8 1.0 N9 A:DG1006 4.9 16.8 1.0 HD73 A:DA63015 4.9 46.0 0.5 C6 A:DG1006 5.0 13.6 1.0

Bromine binding site 4 out of 4 in the 1.3 A Structure Determination of the D(Cg(5-Bru)Acg)2/6- 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 1.3 A Structure Determination of the D(Cg(5-Bru)Acg)2/6- Bromo-9-Amino-Daca Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3015 b:22.2 occ:0.50 BR A:DA63015 0.0 22.2 0.5 C6 A:DA63015 1.8 22.0 0.5 C7 A:DA63015 2.7 21.4 0.5 C5 A:DA63015 2.7 17.9 0.5 H7 A:DA63015 2.8 14.1 0.5 H5 A:DA63015 2.9 5.7 0.5 C8 A:DA63015 4.1 21.1 0.5 C14 A:DA63015 4.1 18.8 0.5 C13 A:DA63015 4.5 18.3 0.5 H8 A:DA63015 4.8 5.7 0.5

A.K.Todd, A.Adams, J.H.Thorpe, W.A.Denny, L.P.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-(Dimethylamino)Ethyl)Acridine-4-Carboxamide (Daca) Into Dna: X-Ray Structure Complexed to D(Cg(5-Bru)Acg)2 at 1.3-A Resolution. J.Med.Chem. V. 42 536 1999.
ISSN: ISSN 0022-2623
PubMed: 10052960
DOI: 10.1021/JM980479U