Bromine in PDB 1f1t: Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine

The structure of Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine, PDB code: 1f1t was solved by C.Baugh, D.Grate, C.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.00 / 2.80
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.297, 55.297, 143.920, 90.00, 90.00, 120.00
R / Rfree (%)	26.1 / 28.2

The structure of Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine also contains other interesting chemical elements:

Strontium

(Sr)

8 atoms

The binding sites of Bromine atom in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine (pdb code 1f1t). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 5 binding sites of Bromine where determined in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine, PDB code: 1f1t:
Jump to Bromine binding site number: 1; 2; 3; 4; 5;

Bromine binding site 1 out of 5 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


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 the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br4 b:61.9 occ:1.00 BR A:5BU4 0.0 61.9 1.0 C5 A:5BU4 1.9 59.1 1.0 C6 A:5BU4 2.8 58.7 1.0 C4 A:5BU4 2.8 58.8 1.0 O4 A:5BU4 3.1 58.4 1.0 N7 A:A3 3.4 61.5 1.0 OP2 A:5BU4 3.6 59.6 1.0 C8 A:A3 3.6 61.7 1.0 C5 A:A3 3.7 61.4 1.0 N9 A:A3 4.0 61.7 1.0 N3 A:5BU4 4.1 58.1 1.0 N1 A:5BU4 4.1 57.7 1.0 C4 A:A3 4.1 61.5 1.0 C3' A:A3 4.3 61.8 1.0 C6 A:A3 4.3 61.3 1.0 O5' A:5BU4 4.4 58.7 1.0 O A:HOH305 4.5 20.3 1.0 P A:5BU4 4.5 59.6 1.0 C2' A:A3 4.6 61.9 1.0 C2 A:5BU4 4.7 58.0 1.0 N6 A:A3 4.7 61.1 1.0 O5' A:A3 4.7 66.2 1.0 C1' A:A3 4.9 62.0 1.0 N3 A:A3 5.0 61.3 1.0 O3' A:A3 5.0 60.5 1.0

Bromine binding site 2 out of 5 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


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 the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br11 b:48.6 occ:1.00 BR A:5BU11 0.0 48.6 1.0 C5 A:5BU11 1.9 46.5 1.0 C6 A:5BU11 2.8 46.2 1.0 C4 A:5BU11 2.8 46.2 1.0 O4 A:5BU11 3.1 46.0 1.0 N1 A:C10 3.5 40.5 1.0 C6 A:C10 3.5 40.3 1.0 C2 A:C10 3.6 40.4 1.0 C5 A:C10 3.7 40.3 1.0 OP2 A:5BU11 3.7 42.8 1.0 N3 A:C10 3.7 40.4 1.0 C4 A:C10 3.8 40.2 1.0 C2' A:C10 3.8 41.2 1.0 C3' A:C10 3.8 41.4 1.0 N3 A:5BU11 4.0 45.8 1.0 N1 A:5BU11 4.1 45.5 1.0 O2 A:C10 4.1 40.4 1.0 C1' A:C10 4.2 40.9 1.0 O5' A:5BU11 4.4 43.4 1.0 P A:5BU11 4.5 43.0 1.0 N4 A:C10 4.6 40.3 1.0 C2 A:5BU11 4.6 45.6 1.0 O5' A:C10 4.7 39.9 1.0 O3' A:C10 4.7 42.1 1.0 O4' A:C10 4.7 40.9 1.0 C4' A:C10 4.9 40.9 1.0 OP2 A:C10 4.9 39.6 1.0 O3' A:A9 5.0 39.1 1.0

Bromine binding site 3 out of 5 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


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 the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br25 b:58.5 occ:1.00 BR A:5BU25 0.0 58.5 1.0 C5 A:5BU25 1.9 55.8 1.0 C6 A:5BU25 2.8 55.2 1.0 C4 A:5BU25 2.8 55.6 1.0 O4 A:5BU25 3.1 55.5 1.0 OP2 A:5BU25 3.4 48.9 1.0 C1' A:G24 3.5 46.2 1.0 O4' A:G24 3.7 45.7 1.0 C8 A:G24 4.0 46.6 1.0 O2' A:G24 4.1 46.4 1.0 N3 A:5BU25 4.1 55.1 1.0 N1 A:5BU25 4.1 54.1 1.0 N9 A:G24 4.2 46.5 1.0 C2' A:G24 4.3 46.4 1.0 C4' A:G24 4.4 45.5 1.0 P A:5BU25 4.5 49.0 1.0 OP2 A:A27 4.6 50.5 1.0 O3' A:G24 4.6 47.9 1.0 C2 A:5BU25 4.7 54.5 1.0 C3' A:G24 4.7 46.5 1.0 O5' A:5BU25 4.8 50.0 1.0 C5' A:5BU25 4.8 51.2 1.0

Bromine binding site 4 out of 5 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


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 the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br32 b:43.8 occ:1.00 BR A:5BU32 0.0 43.8 1.0 C5 A:5BU32 1.9 41.6 1.0 C4 A:5BU32 2.8 41.4 1.0 C6 A:5BU32 2.8 41.2 1.0 O4 A:5BU32 3.0 41.3 1.0 O2' A:A31 3.4 38.1 1.0 OP1 A:5BU32 3.7 38.5 1.0 O3' A:A31 3.8 38.6 1.0 N3 A:5BU32 4.1 40.9 1.0 N1 A:5BU32 4.1 40.3 1.0 P A:5BU32 4.3 38.3 1.0 O5' A:5BU32 4.4 38.3 1.0 C2' A:A31 4.6 38.6 1.0 C2 A:5BU32 4.6 40.6 1.0 C3' A:A31 4.8 38.7 1.0

Bromine binding site 5 out of 5 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br36 b:49.4 occ:1.00 BR A:5BU36 0.0 49.4 1.0 C5 A:5BU36 1.9 46.3 1.0 C6 A:5BU36 2.8 45.6 1.0 C4 A:5BU36 2.8 46.0 1.0 O4 A:5BU36 3.0 46.0 1.0 OP2 A:5BU36 3.4 36.5 1.0 C4 A:A35 3.7 31.4 1.0 N9 A:A35 3.7 31.7 1.0 C8 A:A35 3.7 31.6 1.0 C5 A:A35 3.7 31.1 1.0 N7 A:A35 3.7 31.5 1.0 C3' A:A35 4.0 33.5 1.0 C2' A:A35 4.0 32.8 1.0 N3 A:5BU36 4.0 45.3 1.0 N1 A:5BU36 4.1 44.5 1.0 N3 A:A35 4.2 31.2 1.0 C6 A:A35 4.4 30.9 1.0 O5' A:5BU36 4.4 37.7 1.0 C1' A:A35 4.4 32.3 1.0 P A:5BU36 4.5 36.3 1.0 C2 A:5BU36 4.6 44.9 1.0 C2 A:A35 4.7 31.0 1.0 O3' A:A35 4.8 35.0 1.0 N1 A:A35 4.8 30.9 1.0 O4' A:A35 4.9 32.4 1.0 C4' A:A35 5.0 33.0 1.0

C.Baugh, D.Grate, C.Wilson. 2.8 A Crystal Structure of the Malachite Green Aptamer. J.Mol.Biol. V. 301 117 2000.
ISSN: ISSN 0022-2836
PubMed: 10926496
DOI: 10.1006/JMBI.2000.3951