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

The structure of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of Nonspecifically Bound Paromomycin (A1555G Mutant, Br-Derivative), PDB code: 3bnr 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)	50.99 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.189, 77.380, 56.322, 90.00, 115.12, 90.00
R / Rfree (%)	21.5 / 24.5

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

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 Nonspecifically Bound Paromomycin (A1555G Mutant, Br-Derivative) (pdb code 3bnr). 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 Nonspecifically Bound Paromomycin (A1555G Mutant, Br-Derivative), PDB code: 3bnr:
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 Nonspecifically Bound Paromomycin (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 Nonspecifically Bound Paromomycin (A1555G Mutant, Br-Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br11 b:42.9 occ:1.00 BR A:5BU11 0.0 42.9 1.0 C5 A:5BU11 1.9 32.4 1.0 C6 A:5BU11 2.8 28.4 1.0 C4 A:5BU11 2.9 31.8 1.0 O4 A:5BU11 3.2 28.3 1.0 O A:HOH52 3.4 32.9 1.0 O A:HOH38 3.4 42.2 1.0 C5 A:C10 3.6 24.3 1.0 O A:HOH35 3.6 31.6 1.0 C6 A:C10 3.7 23.2 1.0 C4 A:C10 3.7 23.2 1.0 OP2 A:5BU11 3.8 31.9 1.0 N1 A:C10 4.0 24.3 1.0 N3 A:C10 4.0 20.5 1.0 N1 A:5BU11 4.1 30.3 1.0 N3 A:5BU11 4.1 30.0 1.0 C2 A:C10 4.2 24.6 1.0 N4 A:C10 4.2 20.1 1.0 C3' A:C10 4.3 25.1 1.0 O A:HOH65 4.3 37.5 1.0 O5' A:5BU11 4.5 31.1 1.0 C2' A:C10 4.5 25.8 1.0 P A:5BU11 4.7 31.0 1.0 C2 A:5BU11 4.7 30.6 1.0 N4 A:C12 4.7 32.2 1.0 C1' A:C10 4.8 25.0 1.0 O5' A:C10 4.9 30.1 1.0 C5 A:C12 5.0 35.5 1.0 O2 A:C10 5.0 21.8 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 Nonspecifically Bound Paromomycin (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 Nonspecifically Bound Paromomycin (A1555G Mutant, Br-Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ B:Br10 b:43.7 occ:1.00 BR B:5BU10 0.0 43.7 1.0 C5 B:5BU10 1.9 36.5 1.0 C6 B:5BU10 2.8 34.5 1.0 C4 B:5BU10 2.9 37.1 1.0 O4 B:5BU10 3.2 35.2 1.0 O B:HOH49 3.5 36.6 1.0 O A:HOH66 3.5 38.8 1.0 C5 B:C9 3.6 26.5 1.0 C6 B:C9 3.6 28.7 1.0 C4 B:C9 3.7 27.5 1.0 O B:HOH32 3.7 34.3 1.0 N1 B:C9 3.7 27.9 1.0 OP2 B:5BU10 3.7 32.2 1.0 N3 B:C9 3.8 28.2 1.0 C2 B:C9 3.8 29.4 1.0 C3' B:C9 3.9 30.1 1.0 N1 B:5BU10 4.1 33.1 1.0 C2' B:C9 4.2 31.2 1.0 N3 B:5BU10 4.2 35.4 1.0 O5' B:C9 4.3 26.0 1.0 N4 B:C9 4.3 27.1 1.0 O5' B:5BU10 4.4 33.1 1.0 C1' B:C9 4.5 28.8 1.0 O2 B:C9 4.6 30.1 1.0 P B:5BU10 4.6 32.4 1.0 OP2 B:C9 4.7 27.2 1.0 C2 B:5BU10 4.7 34.6 1.0 O3' B:C9 4.8 32.3 1.0 O B:HOH34 4.8 46.0 1.0 C4' B:C9 5.0 28.0 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 Nonspecifically Bound Paromomycin (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 Nonspecifically Bound Paromomycin (A1555G Mutant, Br-Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ C:Br11 b:40.8 occ:1.00 BR C:5BU11 0.0 40.8 1.0 C5 C:5BU11 1.9 29.5 1.0 C6 C:5BU11 2.8 27.5 1.0 C4 C:5BU11 2.9 28.1 1.0 O4 C:5BU11 3.2 29.0 1.0 O C:HOH55 3.3 40.4 1.0 O C:HOH47 3.4 36.4 1.0 O C:HOH28 3.4 31.4 1.0 O C:HOH57 3.4 32.6 1.0 C5 C:C10 3.6 24.9 1.0 C6 C:C10 3.7 24.9 1.0 C4 C:C10 3.7 25.6 1.0 OP2 C:5BU11 3.8 29.3 1.0 N1 C:C10 4.0 25.2 1.0 N3 C:C10 4.0 23.6 1.0 N1 C:5BU11 4.1 25.3 1.0 C2 C:C10 4.1 25.1 1.0 N3 C:5BU11 4.1 24.8 1.0 C3' C:C10 4.3 25.2 1.0 N4 C:C10 4.3 23.1 1.0 O5' C:5BU11 4.4 26.4 1.0 C2' C:C10 4.4 25.0 1.0 N4 C:C12 4.7 28.2 1.0 P C:5BU11 4.7 27.3 1.0 C2 C:5BU11 4.7 26.9 1.0 C1' C:C10 4.8 25.3 1.0 C5 C:C12 4.9 30.7 1.0 O2 C:C10 4.9 21.5 1.0 O5' C:C10 4.9 28.2 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 Nonspecifically Bound Paromomycin (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 Nonspecifically Bound Paromomycin (A1555G Mutant, Br-Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ D:Br9 b:47.4 occ:1.00 BR D:5BU9 0.0 47.4 1.0 C5 D:5BU9 1.9 41.0 1.0 C6 D:5BU9 2.8 39.3 1.0 C4 D:5BU9 2.9 39.9 1.0 O4 D:5BU9 3.2 39.5 1.0 O D:HOH46 3.5 42.2 1.0 O D:HOH56 3.5 46.0 1.0 C6 D:C8 3.5 32.4 1.0 C5 D:C8 3.6 30.7 1.0 O D:HOH55 3.6 45.4 1.0 OP2 D:5BU9 3.7 36.7 1.0 N1 D:C8 3.7 33.5 1.0 C4 D:C8 3.7 30.9 1.0 C2 D:C8 3.9 33.8 1.0 N3 D:C8 3.9 31.6 1.0 C3' D:C8 3.9 33.5 1.0 C2' D:C8 4.1 34.7 1.0 N1 D:5BU9 4.1 38.9 1.0 N3 D:5BU9 4.1 38.9 1.0 O5' D:C8 4.3 27.2 1.0 O5' D:5BU9 4.4 36.5 1.0 N4 D:C8 4.4 26.2 1.0 C1' D:C8 4.5 33.3 1.0 P D:5BU9 4.5 36.1 1.0 OP2 D:C8 4.6 24.9 1.0 O2 D:C8 4.7 36.6 1.0 C2 D:5BU9 4.7 38.8 1.0 O3' D:C8 4.8 35.4 1.0 O4' D:C8 5.0 30.4 1.0 C4' D:C8 5.0 31.8 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