Bromine in PDB 9lnj: Crystal Structure of VANC21 in Complex with Its Target Dna (5- Bromouridine Substituted).

The structure of Crystal Structure of VANC21 in Complex with Its Target Dna (5- Bromouridine Substituted)., PDB code: 9lnj was solved by Y.Tanaka, W.Shihoya, H.Hirano, Y.Itoh, T.Kakutani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.26 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.35, 77.16, 59, 90, 93.3, 90
R / Rfree (%)	17.6 / 20.8

The structure of Crystal Structure of VANC21 in Complex with Its Target Dna (5- Bromouridine Substituted). also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Bromine atom in the Crystal Structure of VANC21 in Complex with Its Target Dna (5- Bromouridine Substituted). (pdb code 9lnj). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Crystal Structure of VANC21 in Complex with Its Target Dna (5- Bromouridine Substituted)., PDB code: 9lnj:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the Crystal Structure of VANC21 in Complex with Its Target Dna (5- Bromouridine Substituted).


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 VANC21 in Complex with Its Target Dna (5- Bromouridine Substituted). within 5.0Å range: probe atom residue distance (Å) B Occ B:Br12 b:35.2 occ:1.00 BR B:BRU12 0.0 35.2 1.0 C5 B:BRU12 1.9 28.2 1.0 C6 B:BRU12 2.8 27.9 1.0 C4 B:BRU12 2.9 27.7 1.0 O4 B:BRU12 3.1 25.9 1.0 C6 B:DC11 3.5 27.2 1.0 N1 B:DC11 3.7 27.1 1.0 C2' B:DC11 3.7 29.7 1.0 C5 B:DC11 3.8 26.6 1.0 N3 B:BRU12 4.1 25.3 1.0 N1 B:BRU12 4.1 30.0 1.0 C2 B:DC11 4.2 30.8 1.0 C1' B:DC11 4.2 30.2 1.0 C4 B:DC11 4.3 26.8 1.0 N3 B:DC11 4.5 26.9 1.0 C2 B:BRU12 4.7 34.0 1.0 O2 B:DC11 4.9 28.0 1.0

Bromine binding site 2 out of 3 in the Crystal Structure of VANC21 in Complex with Its Target Dna (5- Bromouridine Substituted).


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 VANC21 in Complex with Its Target Dna (5- Bromouridine Substituted). within 5.0Å range: probe atom residue distance (Å) B Occ B:Br13 b:104.8 occ:1.00 BR B:BRU13 0.0 104.8 1.0 C5 B:BRU13 1.9 65.1 1.0 C6 B:BRU13 2.8 67.8 1.0 C4 B:BRU13 2.9 63.7 1.0 O4 B:BRU13 3.1 62.0 1.0 OP2 B:BRU13 3.2 67.5 1.0 N3 B:BRU13 4.1 62.8 1.0 N1 B:BRU13 4.1 70.6 1.0 P B:BRU13 4.5 61.0 1.0 C2 B:BRU13 4.7 67.7 1.0 C2' B:BRU12 4.7 39.0 1.0 O5' B:BRU13 4.9 63.6 1.0 O3' B:BRU12 4.9 48.7 1.0

Bromine binding site 3 out of 3 in the Crystal Structure of VANC21 in Complex with Its Target Dna (5- Bromouridine Substituted).


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 VANC21 in Complex with Its Target Dna (5- Bromouridine Substituted). within 5.0Å range: probe atom residue distance (Å) B Occ C:Br13 b:45.3 occ:1.00 BR C:BRU13 0.0 45.3 1.0 C5 C:BRU13 1.9 32.5 1.0 C6 C:BRU13 2.8 33.3 1.0 C4 C:BRU13 2.8 32.6 1.0 O4 C:BRU13 3.1 35.8 1.0 N7 C:DG12 3.6 40.5 1.0 C8 C:DG12 3.6 38.7 1.0 C5 C:DG12 4.0 34.9 1.0 N9 C:DG12 4.0 38.1 1.0 OP2 C:BRU13 4.1 35.6 1.0 N3 C:BRU13 4.1 33.9 1.0 N1 C:BRU13 4.1 30.5 1.0 C4 C:DG12 4.2 35.9 1.0 C3' C:DG12 4.3 37.5 1.0 C2' C:DG12 4.6 41.1 1.0 C6 C:DG12 4.7 35.4 1.0 C2 C:BRU13 4.7 33.6 1.0 O5' C:BRU13 4.7 38.8 1.0 C1' C:DG12 4.8 37.5 1.0 P C:BRU13 4.9 39.1 1.0

Y.Tanaka, A.Osakabe, W.Shihoya, H.Hirano, Y.Itoh, T.Kakutani, O.Nureki. Structure and Evolution of the Sequence-Specific Anti-Silencing Factor VANC21 and Its Target Dna. Genes Genet Syst 2025.
ISSN: ISSN 1880-5779
PubMed: 41260640
DOI: 10.1266/GGS.25-00096