Bromine in PDB 5mvl: Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil

The structure of Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil, PDB code: 5mvl was solved by J.S.Hardwick, D.Ptchelkine, S.E.V.Phillips, T.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.67 / 1.41
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	43.517, 43.517, 60.850, 90.00, 90.00, 120.00
R / Rfree (%)	15.7 / 18.2

The structure of Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Bromine atom in the Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil (pdb code 5mvl). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil, PDB code: 5mvl:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil


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 An A-Dna Dodecamer Containing 5-Bromouracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Br2 b:23.7 occ:0.37 BR A:BRU2 0.0 23.7 0.4 C5 A:BRU2 1.9 23.3 1.0 C6 A:BRU2 2.9 23.5 1.0 H6 A:BRU2 2.9 28.2 1.0 C4 A:BRU2 3.0 22.9 1.0 O4 A:BRU2 3.2 26.4 1.0 C4 A:DC1 3.7 28.7 1.0 O A:HOH219 3.7 41.0 0.9 N3 A:DC1 3.7 27.6 1.0 C5 A:DC1 3.7 30.2 1.0 C2 A:DC1 3.8 28.7 1.0 N1 A:DC1 3.8 30.3 1.0 O A:HOH220 3.8 26.2 0.7 C6 A:DC1 3.8 29.9 1.0 OP2 A:BRU2 3.9 31.7 1.0 O A:HOH234 3.9 27.2 0.6 O A:HOH211 4.0 27.6 0.5 C3' A:DC1 4.1 32.3 1.0 O A:HOH204 4.2 50.5 1.0 N1 A:BRU2 4.3 22.6 1.0 N4 A:DC1 4.3 29.8 1.0 N3 A:BRU2 4.3 23.4 1.0 O2 A:DC1 4.4 28.4 1.0 C2' A:DC1 4.4 30.9 1.0 O5' A:BRU2 4.5 28.2 1.0 C1' A:DC1 4.7 32.0 1.0 P A:BRU2 4.7 31.2 1.0 C2 A:BRU2 4.8 23.4 1.0 O3' A:DC1 4.9 31.8 1.0 HN3 A:BRU2 5.0 28.1 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil


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 An A-Dna Dodecamer Containing 5-Bromouracil within 5.0Å range: probe atom residue distance (Å) B Occ B:Br2 b:24.1 occ:0.38 BR B:BRU2 0.0 24.1 0.4 C5 B:BRU2 1.9 24.3 1.0 C6 B:BRU2 2.9 24.8 1.0 C4 B:BRU2 2.9 24.5 1.0 H6 B:BRU2 3.0 29.8 1.0 O4 B:BRU2 3.1 25.9 1.0 O B:HOH130 3.5 52.6 1.0 O B:HOH110 3.7 30.1 0.8 OP2 B:BRU2 3.8 35.4 1.0 C6 B:DC1 3.8 28.2 1.0 C5 B:DC1 3.8 28.5 1.0 N1 B:DC1 3.8 27.5 1.0 O B:HOH123 3.8 28.8 0.9 C4 B:DC1 3.8 26.6 1.0 C2 B:DC1 3.9 25.5 1.0 N3 B:DC1 3.9 25.6 1.0 C3' B:DC1 4.0 31.8 1.0 O B:HOH105 4.1 39.1 0.8 C2' B:DC1 4.2 28.9 1.0 N1 B:BRU2 4.3 24.3 1.0 N3 B:BRU2 4.3 24.9 1.0 O5' B:DC1 4.4 41.0 1.0 O5' B:BRU2 4.5 30.1 1.0 O2 B:DC1 4.5 24.4 1.0 N4 B:DC1 4.5 26.3 1.0 C1' B:DC1 4.6 28.4 1.0 P B:BRU2 4.6 34.1 1.0 H62 B:DA3 4.7 25.3 1.0 C2 B:BRU2 4.8 23.5 1.0 O3' B:DC1 4.8 33.1 1.0 HN3 B:BRU2 4.9 29.9 1.0

J.S.Hardwick, D.Ptchelkine, A.H.El-Sagheer, I.Tear, D.Singleton, S.E.V.Phillips, A.N.Lane, T.Brown. 5-Formylcytosine Does Not Change the Global Structure of Dna. Nat. Struct. Mol. Biol. V. 24 544 2017.
ISSN: ESSN 1545-9985
PubMed: 28504696
DOI: 10.1038/NSMB.3411