Bromine in PDB 7xdj: Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex

The structure of Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex, PDB code: 7xdj was solved by C.M.Chien, R.B.Satange, M.H.Hou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.84 / 2.44
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	132.522, 132.522, 49.595, 90, 90, 120
R / Rfree (%)	20.1 / 23.6

The structure of Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Magnesium	(Mg)	3 atoms

The binding sites of Bromine atom in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex (pdb code 7xdj). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex, PDB code: 7xdj:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex


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 Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Br7 b:68.9 occ:1.00 BR B:BRU7 0.0 68.9 1.0 C5 B:BRU7 2.0 52.0 1.0 C4 B:BRU7 2.9 45.9 1.0 C6 B:BRU7 2.9 48.7 1.0 O4 B:BRU7 3.1 43.9 1.0 C2' B:DC6 3.7 56.3 1.0 N3 B:BRU7 4.2 43.6 1.0 N1 B:BRU7 4.2 47.7 1.0 C6 B:DC6 4.2 47.4 1.0 N1 B:DC6 4.3 50.6 1.0 C1' B:DC6 4.5 61.5 1.0 C2 B:BRU7 4.6 48.4 1.0 C5 B:DC6 4.7 51.2 1.0 C3' B:DC6 5.0 53.4 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex


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 Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Br7 b:74.9 occ:1.00 BR F:BRU7 0.0 74.9 1.0 C5 F:BRU7 1.9 47.2 1.0 C6 F:BRU7 2.9 41.4 1.0 C4 F:BRU7 2.9 42.8 1.0 O4 F:BRU7 3.1 41.4 1.0 C8 M:DA1 3.7 37.8 1.0 C2' F:DC6 3.7 53.7 1.0 N7 M:DA1 3.7 37.7 1.0 O4' M:DA1 3.8 45.7 1.0 C5 I:DC5 3.8 51.1 1.0 C5 M:DA1 3.9 43.3 1.0 N9 M:DA1 3.9 41.4 1.0 C5' M:DA1 3.9 56.4 1.0 C4 M:DA1 4.0 43.3 1.0 C6 L:QUI101 4.1 42.5 1.0 C6 F:DC6 4.1 48.1 1.0 N1 F:BRU7 4.2 44.8 1.0 N3 F:BRU7 4.2 45.1 1.0 N4 I:DC5 4.2 39.4 1.0 N1 F:DC6 4.3 56.9 1.0 C5 L:QUI101 4.4 39.1 1.0 C4 I:DC5 4.4 43.6 1.0 C4' M:DA1 4.5 59.4 1.0 C1' F:DC6 4.5 61.0 1.0 C1' M:DA1 4.5 44.7 1.0 C6 M:DA1 4.6 49.0 1.0 C2 F:BRU7 4.6 44.4 1.0 C5 F:DC6 4.6 45.2 1.0 N3 M:DA1 4.7 49.0 1.0 C6 I:DC5 4.7 43.7 1.0 C2 F:DC6 4.9 52.8 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex


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 Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Br7 b:72.8 occ:1.00 BR J:BRU7 0.0 72.8 1.0 C5 J:BRU7 2.0 63.0 1.0 C6 J:BRU7 2.9 56.5 1.0 C4 J:BRU7 3.0 53.1 1.0 O4 J:BRU7 3.2 48.1 1.0 C5 N:DC2 3.6 46.0 1.0 C2' J:DC6 4.0 57.1 1.0 N4 N:DC2 4.0 45.2 1.0 N1 J:BRU7 4.2 46.1 1.0 C6 J:DC6 4.2 49.3 1.0 C6 H:QUI102 4.2 48.6 1.0 N3 J:BRU7 4.2 54.3 1.0 C4 N:DC2 4.2 45.7 1.0 N1 J:DC6 4.4 53.1 1.0 C6 N:DC2 4.5 46.7 1.0 C5 J:DC6 4.6 44.4 1.0 C2 J:BRU7 4.6 43.8 1.0 C5 H:QUI102 4.8 49.0 1.0 C1' J:DC6 4.8 61.3 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex


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 Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ N:Br7 b:67.5 occ:1.00 BR N:BRU7 0.0 67.5 1.0 C5 N:BRU7 1.9 55.5 1.0 C6 N:BRU7 2.9 47.5 1.0 C4 N:BRU7 2.9 43.8 1.0 O4 N:BRU7 3.1 44.4 1.0 C5 J:DC2 3.5 44.1 1.0 N7 E:DA1 3.8 42.5 1.0 C8 E:DA1 3.8 40.3 1.0 C5 E:DA1 3.8 42.8 1.0 C5' E:DA1 3.9 60.2 1.0 C2' N:DC6 3.9 65.6 1.0 C6 L:QUI102 3.9 41.6 1.0 C4 E:DA1 4.0 43.6 1.0 N9 E:DA1 4.0 46.6 1.0 O5' E:DA1 4.0 73.2 1.0 O4' E:DA1 4.0 57.4 1.0 N4 J:DC2 4.0 44.8 1.0 C6 N:DC6 4.1 41.0 1.0 N1 N:BRU7 4.1 42.1 1.0 N3 N:BRU7 4.2 47.9 1.0 C4 J:DC2 4.2 46.1 1.0 N1 N:DC6 4.3 49.5 1.0 C6 J:DC2 4.4 45.3 1.0 C6 E:DA1 4.4 46.4 1.0 C4' E:DA1 4.5 58.8 1.0 C5 N:DC6 4.5 39.3 1.0 C1' N:DC6 4.6 60.0 1.0 C2 N:BRU7 4.6 42.4 1.0 C5 L:QUI102 4.7 43.1 1.0 N3 E:DA1 4.7 42.8 1.0 C1' E:DA1 4.7 60.2 1.0 C7 L:QUI102 4.8 42.4 1.0 N6 E:DA1 5.0 44.0 1.0

R.Satange, S.H.Kao, C.M.Chien, S.H.Chou, C.C.Lin, S.Neidle, M.H.Hou. Staggered Intercalation of Dna Duplexes with Base-Pair Modulation By Two Distinct Drug Molecules Induces Asymmetric Backbone Twisting and Structure Polymorphism. Nucleic Acids Res. V. 50 8867 2022.
ISSN: ESSN 1362-4962
PubMed: 35871296
DOI: 10.1093/NAR/GKAC629