Bromine in PDB 6v9d: Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin

The structure of Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin, PDB code: 6v9d was solved by R.J.Trachman, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.36 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	48.917, 48.917, 122.972, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 27.2

The structure of Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Bromine atom in the Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin (pdb code 6v9d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin, PDB code: 6v9d:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ B:Br103 b:34.3 occ:1.00 C5 B:U2 1.9 27.7 1.0 C4 B:U2 2.8 31.2 1.0 C6 B:U2 2.9 29.5 1.0 O4 B:U2 3.0 31.3 1.0 N7 B:A1 3.5 26.6 1.0 C8 B:A1 3.6 25.6 1.0 OP2 B:U2 3.8 30.1 1.0 C5 B:A1 4.0 28.3 1.0 N3 B:U2 4.1 32.0 1.0 O5' B:A1 4.1 39.1 1.0 N9 B:A1 4.1 26.6 1.0 C3' B:A1 4.2 25.3 1.0 N1 B:U2 4.2 30.8 1.0 C4 B:A1 4.4 28.6 1.0 O5' B:U2 4.5 32.4 1.0 P B:U2 4.6 31.1 1.0 C6 B:A1 4.7 31.7 1.0 C2 B:U2 4.7 29.9 1.0 N4 B:C3 4.7 33.1 1.0 C2' B:A1 4.8 28.5 1.0 O3' B:A1 4.9 27.9 1.0 C5' B:A1 5.0 30.0 1.0 C1' B:A1 5.0 27.2 1.0

Bromine binding site 2 out of 2 in the Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Co-Crystal Structure of the Fluorogenic Mango-IV Homodimer Bound to TO1-Biotin within 5.0Å range: probe atom residue distance (Å) B Occ E:Br102 b:46.0 occ:1.00 C5 E:U2 2.0 38.5 1.0 C6 E:U2 2.9 35.5 1.0 C4 E:U2 3.0 39.8 1.0 C8 E:A1 3.3 41.8 1.0 O4 E:U2 3.3 39.7 1.0 N9 E:A1 3.3 37.6 1.0 OP2 E:U2 3.4 25.8 1.0 C4 E:A1 3.6 34.8 1.0 O2' E:A1 3.6 45.7 1.0 C1' E:A1 3.6 40.0 1.0 N7 E:A1 3.7 36.7 1.0 C5 E:A1 3.8 34.0 1.0 N1 E:U2 4.2 34.0 1.0 C2' E:A1 4.2 34.1 1.0 N3 E:U2 4.2 35.7 1.0 N3 E:A1 4.3 35.8 1.0 O5' E:U2 4.3 42.8 1.0 P E:U2 4.4 30.1 1.0 N4 E:C3 4.7 33.6 1.0 C6 E:A1 4.7 39.5 1.0 C2 E:U2 4.8 35.1 1.0 O4' E:A1 4.8 34.0 1.0 C5 E:C3 4.9 31.4 1.0 C2 E:A1 5.0 33.4 1.0

R.J.Trachman 3Rd, R.Cojocaru, D.Wu, G.Piszczek, M.Ryckelynck, P.J.Unrau, A.R.Ferre-D'amare. Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields An Rna Fret Pair. Structure 2020.
ISSN: ISSN 0969-2126
PubMed: 32386573
DOI: 10.1016/J.STR.2020.04.007