Bromine in PDB 3bnq: Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)

The structure of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative), PDB code: 3bnq was solved by J.Kondo, E.Westhof, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.79 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.266, 76.056, 55.912, 90.00, 117.06, 90.00
R / Rfree (%)	22.9 / 26.9

The structure of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) also contains other interesting chemical elements:

Strontium	(Sr)	8 atoms
Potassium	(K)	2 atoms

The binding sites of Bromine atom in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) (pdb code 3bnq). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative), PDB code: 3bnq:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)


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 Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br11 b:40.5 occ:1.00 BR A:5BU11 0.0 40.5 1.0 C5 A:5BU11 1.9 31.8 1.0 C6 A:5BU11 2.8 29.9 1.0 C4 A:5BU11 2.9 28.6 1.0 O4 A:5BU11 3.2 26.3 1.0 O A:HOH313 3.2 37.1 1.0 O A:HOH328 3.4 34.9 1.0 C5 A:C10 3.5 29.5 1.0 C4 A:C10 3.6 28.8 1.0 C6 A:C10 3.6 29.2 1.0 O A:HOH314 3.7 37.5 1.0 O A:HOH309 3.8 34.0 1.0 OP2 A:5BU11 3.8 29.5 1.0 N3 A:C10 3.9 29.5 1.0 N1 A:C10 4.0 32.4 1.0 C2 A:C10 4.1 33.9 1.0 N1 A:5BU11 4.1 30.9 1.0 N3 A:5BU11 4.2 23.4 1.0 N4 A:C10 4.2 28.5 1.0 C3' A:C10 4.3 29.6 1.0 O5' A:5BU11 4.5 30.5 1.0 C2' A:C10 4.5 30.8 1.0 N4 A:C12 4.6 28.4 1.0 P A:5BU11 4.7 29.5 1.0 C2 A:5BU11 4.7 28.0 1.0 C1' A:C10 4.8 34.7 1.0 O5' A:C10 4.9 32.7 1.0 O2 A:C10 4.9 30.5 1.0 C5 A:C12 5.0 34.5 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)


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 Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ B:Br11 b:44.0 occ:1.00 BR B:5BU11 0.0 44.0 1.0 C5 B:5BU11 1.9 40.8 1.0 C6 B:5BU11 2.8 38.3 1.0 C4 B:5BU11 2.9 40.4 1.0 O4 B:5BU11 3.2 37.5 1.0 C5 B:C10 3.6 30.2 1.0 C4 B:C10 3.6 30.5 1.0 C6 B:C10 3.6 30.5 1.0 N3 B:C10 3.7 30.6 1.0 OP2 B:5BU11 3.8 34.6 1.0 N1 B:C10 3.8 29.0 1.0 C2 B:C10 3.8 30.3 1.0 C3' B:C10 4.1 36.7 1.0 N1 B:5BU11 4.1 36.2 1.0 N3 B:5BU11 4.1 38.5 1.0 N4 B:C10 4.2 28.1 1.0 C2' B:C10 4.3 36.7 1.0 O5' B:5BU11 4.5 38.4 1.0 O5' B:C10 4.5 32.5 1.0 O2 B:C10 4.6 31.1 1.0 O B:HOH222 4.6 38.1 1.0 C1' B:C10 4.6 34.3 1.0 P B:5BU11 4.6 36.5 1.0 C2 B:5BU11 4.7 36.6 1.0 OP2 B:C10 4.9 33.4 1.0 O3' B:C10 4.9 38.6 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)


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 Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ C:Br11 b:43.8 occ:1.00 BR C:5BU11 0.0 43.8 1.0 C5 C:5BU11 1.9 30.2 1.0 C6 C:5BU11 2.8 27.6 1.0 C4 C:5BU11 2.9 29.2 1.0 O4 C:5BU11 3.2 25.3 1.0 O C:HOH319 3.4 35.6 1.0 C5 C:C10 3.5 30.9 1.0 C4 C:C10 3.6 32.5 1.0 C6 C:C10 3.7 30.7 1.0 OP2 C:5BU11 3.9 32.6 1.0 N3 C:C10 3.9 26.1 1.0 N1 C:C10 3.9 29.6 1.0 C2 C:C10 4.0 30.4 1.0 N1 C:5BU11 4.1 27.6 1.0 N3 C:5BU11 4.1 24.6 1.0 N4 C:C10 4.2 27.7 1.0 O C:HOH330 4.3 43.6 1.0 C3' C:C10 4.4 30.8 1.0 O C:HOH306 4.4 77.6 0.8 O5' C:5BU11 4.4 33.4 1.0 C2' C:C10 4.5 27.4 1.0 C2 C:5BU11 4.7 28.5 1.0 P C:5BU11 4.7 32.1 1.0 N4 C:C12 4.7 33.5 1.0 C1' C:C10 4.8 28.9 1.0 O2 C:C10 4.8 29.9 1.0 C5 C:C12 5.0 31.6 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)


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 Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ D:Br9 b:55.8 occ:1.00 BR D:5BU9 0.0 55.8 1.0 C5 D:5BU9 1.9 50.6 1.0 C6 D:5BU9 2.8 49.1 1.0 C4 D:5BU9 2.9 46.8 1.0 O4 D:5BU9 3.2 47.7 1.0 C5 D:C8 3.5 35.4 1.0 C6 D:C8 3.5 33.5 1.0 C4 D:C8 3.6 32.3 1.0 N1 D:C8 3.8 37.5 1.0 OP2 D:5BU9 3.8 48.1 1.0 N3 D:C8 3.8 34.8 1.0 C2 D:C8 3.9 36.8 1.0 C3' D:C8 4.0 39.6 1.0 N3 D:5BU9 4.1 46.9 1.0 N1 D:5BU9 4.1 47.3 1.0 N4 D:C8 4.3 34.8 1.0 C2' D:C8 4.3 40.0 1.0 O5' D:C8 4.4 33.8 1.0 O5' D:5BU9 4.4 46.0 1.0 C1' D:C8 4.6 37.6 1.0 O2 D:C8 4.6 44.6 1.0 P D:5BU9 4.6 46.4 1.0 C2 D:5BU9 4.7 47.2 1.0 OP2 D:C8 4.7 34.2 1.0 O3' D:C8 4.9 45.2 1.0

J.Kondo, E.Westhof. The Bacterial and Mitochondrial Ribosomal A-Site Molecular Switches Possess Different Conformational Substates Nucleic Acids Res. V. 36 2654 2008.
ISSN: ISSN 0305-1048
PubMed: 18346970
DOI: 10.1093/NAR/GKN112