Bromine in PDB 3vaf: Structure of U2AF65 Variant with BRU3 Dna

The structure of Structure of U2AF65 Variant with BRU3 Dna, PDB code: 3vaf was solved by J.L.Jenkins, C.L.Kielkopf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.51 / 2.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	164.296, 36.981, 99.431, 90.00, 125.67, 90.00
R / Rfree (%)	23.1 / 28.9

The binding sites of Bromine atom in the Structure of U2AF65 Variant with BRU3 Dna (pdb code 3vaf). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Structure of U2AF65 Variant with BRU3 Dna, PDB code: 3vaf:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Structure of U2AF65 Variant with BRU3 Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of U2AF65 Variant with BRU3 Dna within 5.0Å range: probe atom residue distance (Å) B Occ P:Br4 b:20.9 occ:0.70 BR P:BRU4 0.0 20.9 0.7 C5 P:BRU4 1.9 24.5 1.0 C6 P:BRU4 2.9 24.1 1.0 C4 P:BRU4 3.0 23.9 1.0 O4 P:BRU4 3.2 23.6 1.0 O2 P:DU3 3.3 27.3 1.0 OD1 A:ASN155 3.6 21.7 1.0 O P:HOH203 3.6 18.7 1.0 CA A:ASN155 3.7 24.2 1.0 N A:ASN155 3.9 23.4 1.0 CB A:ASN155 4.0 24.1 1.0 O3' P:DU3 4.1 30.1 1.0 C1' P:DU3 4.1 29.6 1.0 CG A:ASN155 4.1 24.1 1.0 N1 P:BRU4 4.2 23.4 1.0 N3 P:BRU4 4.2 24.1 1.0 C2 P:DU3 4.4 29.7 1.0 C2' P:DU3 4.5 30.1 1.0 OP2 P:BRU4 4.7 29.4 1.0 O A:ASN196 4.7 26.8 1.0 C2 P:BRU4 4.7 23.8 1.0 CZ B:PHE304 4.8 24.0 1.0 N1 P:DU3 4.8 29.2 1.0 C3' P:DU3 4.9 30.8 1.0 CE1 B:PHE304 5.0 23.8 1.0 CB A:ASN196 5.0 30.7 1.0

Bromine binding site 2 out of 4 in the Structure of U2AF65 Variant with BRU3 Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of U2AF65 Variant with BRU3 Dna within 5.0Å range: probe atom residue distance (Å) B Occ P:Br5 b:29.9 occ:0.30 BR P:BRU5 0.0 29.9 0.3 C5 P:BRU5 1.9 30.2 1.0 C6 P:BRU5 2.9 31.1 1.0 C4 P:BRU5 3.0 30.3 1.0 O4 P:BRU5 3.2 29.8 1.0 OP1 P:BRU4 3.6 29.1 1.0 CE1 A:TYR152 3.9 22.5 1.0 O P:HOH206 4.0 31.0 1.0 CZ A:TYR152 4.0 22.0 1.0 OH A:TYR152 4.1 21.6 1.0 NE2 A:HIS230 4.1 28.4 0.5 O5' P:BRU4 4.1 27.1 1.0 C5' P:BRU4 4.1 26.0 1.0 N1 P:BRU5 4.2 30.1 1.0 P P:BRU4 4.2 29.6 1.0 N3 P:BRU5 4.2 30.3 1.0 CE1 A:HIS230 4.4 28.6 0.5 OP2 P:BRU5 4.4 24.6 1.0 OP2 P:BRU4 4.5 29.4 1.0 CD1 A:TYR152 4.5 22.0 1.0 C2 P:BRU5 4.7 30.7 1.0 CE A:LYS225 4.7 28.2 1.0 O5' P:BRU5 4.8 27.8 1.0 CE2 A:TYR152 4.8 22.2 1.0 NZ A:LYS225 4.8 30.4 1.0 O2 A:SO4403 4.8 42.6 1.0

Bromine binding site 3 out of 4 in the Structure of U2AF65 Variant with BRU3 Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of U2AF65 Variant with BRU3 Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Br4 b:22.8 occ:0.40 BR E:BRU4 0.0 22.8 0.4 C5 E:BRU4 1.9 23.5 1.0 C6 E:BRU4 3.0 24.5 1.0 C4 E:BRU4 3.0 24.0 1.0 O2 E:DU3 3.1 34.8 1.0 O4 E:BRU4 3.1 24.5 1.0 C1' E:DU3 3.8 33.6 1.0 CA B:ASN155 3.9 25.2 1.0 O3' E:DU3 4.0 29.0 1.0 N B:ASN155 4.0 23.6 1.0 C2 E:DU3 4.1 34.8 1.0 N3 E:BRU4 4.2 23.5 1.0 N1 E:BRU4 4.2 23.7 1.0 OD1 B:ASN155 4.3 26.5 1.0 C2' E:DU3 4.3 31.8 1.0 CB B:ASN155 4.3 25.2 1.0 O B:HOH533 4.4 39.8 1.0 N1 E:DU3 4.4 34.5 1.0 O4' E:DU3 4.7 34.1 1.0 C3' E:DU3 4.7 31.6 1.0 C2 E:BRU4 4.7 23.1 1.0 CG B:ASN155 4.7 26.7 1.0 ND2 B:ASN196 4.8 36.2 1.0 OP2 E:BRU4 4.8 28.0 1.0 CB B:ASN196 4.9 32.6 1.0 O B:ASN196 5.0 26.9 1.0 P E:BRU4 5.0 26.7 1.0

Bromine binding site 4 out of 4 in the Structure of U2AF65 Variant with BRU3 Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of U2AF65 Variant with BRU3 Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Br5 b:22.0 occ:0.60 BR E:BRU5 0.0 22.0 0.6 C5 E:BRU5 1.9 23.6 1.0 C6 E:BRU5 2.9 23.9 1.0 C4 E:BRU5 3.0 24.3 1.0 OP1 E:BRU4 3.0 27.1 1.0 O4 E:BRU5 3.2 23.4 1.0 P E:BRU4 3.7 26.7 1.0 CE1 B:TYR152 3.7 22.8 1.0 CZ B:TYR152 3.7 23.2 1.0 C5' E:BRU4 3.8 25.8 1.0 OH B:TYR152 3.8 23.9 1.0 O5' E:BRU4 3.8 26.7 1.0 OP2 E:BRU4 3.9 28.0 1.0 O E:HOH106 4.1 35.7 1.0 N1 E:BRU5 4.2 24.2 1.0 N3 E:BRU5 4.2 23.1 1.0 NZ B:LYS225 4.3 27.5 1.0 CD1 B:TYR152 4.3 21.5 1.0 CE2 B:TYR152 4.3 23.9 1.0 CE B:LYS225 4.7 25.4 1.0 NE2 B:HIS230 4.7 35.7 1.0 C2 E:BRU5 4.7 23.8 1.0 OP2 E:BRU5 4.8 29.8 1.0 CD2 B:TYR152 4.8 23.3 1.0 CG B:TYR152 4.8 21.9 1.0 C4' E:BRU4 5.0 24.9 1.0

J.L.Jenkins, A.A.Agrawal, A.Gupta, M.R.Green, C.L.Kielkopf. U2AF65 Adapts to Diverse Pre-Mrna Splice Sites Through Conformational Selection of Specific and Promiscuous Rna Recognition Motifs. Nucleic Acids Res. V. 41 3859 2013.
ISSN: ISSN 0305-1048
PubMed: 23376934
DOI: 10.1093/NAR/GKT046