Bromine in PDB 3bno: Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site (Br-Derivative)

The structure of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site (Br-Derivative), PDB code: 3bno 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)	36.88 / 2.35
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.140, 45.460, 52.130, 71.43, 73.42, 74.05
R / Rfree (%)	22.6 / 25.5

The binding sites of Bromine atom in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site (Br-Derivative) (pdb code 3bno). 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 (Br-Derivative), PDB code: 3bno:
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 (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 (Br-Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br9 b:72.3 occ:0.55 BR A:5BU9 0.0 72.3 0.6 C5 A:5BU9 1.9 76.6 1.0 C6 A:5BU9 2.8 74.3 1.0 C4 A:5BU9 2.9 75.5 1.0 O4 A:5BU9 3.2 80.2 1.0 C5 A:C8 3.5 74.3 1.0 C4 A:C8 3.6 74.5 1.0 OP2 A:5BU9 3.6 71.1 1.0 C6 A:C8 3.7 76.3 1.0 N3 A:C8 4.0 75.4 1.0 N4 A:C8 4.0 69.3 1.0 N1 A:C8 4.1 75.1 1.0 N3 A:5BU9 4.1 76.0 1.0 N1 A:5BU9 4.1 75.6 1.0 C2 A:C8 4.2 76.7 1.0 C3' A:C8 4.3 72.6 1.0 O5' A:C8 4.3 73.1 1.0 N4 A:C10 4.4 80.1 1.0 OP2 A:C8 4.4 73.9 1.0 O5' A:5BU9 4.4 70.4 1.0 P A:5BU9 4.6 73.5 1.0 C2' A:C8 4.7 74.0 1.0 C2 A:5BU9 4.7 75.2 1.0 C5 A:C10 4.8 77.0 1.0 C1' A:C8 4.9 74.6 1.0 O3' A:C8 5.0 70.3 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site (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 (Br-Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ B:Br9 b:65.9 occ:0.71 BR B:5BU9 0.0 65.9 0.7 C5 B:5BU9 1.9 65.2 1.0 C6 B:5BU9 2.9 66.7 1.0 C4 B:5BU9 2.9 66.0 1.0 O4 B:5BU9 3.2 67.6 1.0 C6 B:C8 3.5 65.0 1.0 C5 B:C8 3.5 59.0 1.0 OP2 B:C8 3.6 44.8 1.0 O5' B:C8 3.9 52.5 1.0 OP2 B:5BU9 3.9 66.5 1.0 N3 B:5BU9 4.2 67.1 1.0 N1 B:5BU9 4.2 67.4 1.0 C3' B:C8 4.3 58.9 1.0 N1 B:C8 4.4 65.9 1.0 P B:C8 4.4 47.0 1.0 O5' B:5BU9 4.5 62.8 1.0 C4 B:C8 4.5 61.8 1.0 C2' B:C8 4.7 59.6 1.0 C2 B:5BU9 4.7 68.3 1.0 P B:5BU9 4.8 63.8 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site (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 (Br-Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ C:Br9 b:67.5 occ:0.63 BR C:5BU9 0.0 67.5 0.6 C5 C:5BU9 1.9 62.1 1.0 C6 C:5BU9 2.9 61.8 1.0 C4 C:5BU9 2.9 60.8 1.0 O4 C:5BU9 3.2 61.6 1.0 C5 C:C8 3.4 59.5 1.0 C6 C:C8 3.5 61.1 1.0 OP2 C:5BU9 3.7 57.7 1.0 C4 C:C8 3.7 62.2 1.0 N1 C:C8 3.9 63.6 1.0 N3 C:C8 4.1 60.7 1.0 C3' C:C8 4.1 51.4 1.0 N3 C:5BU9 4.2 58.7 1.0 N1 C:5BU9 4.2 62.3 1.0 C2 C:C8 4.2 63.2 1.0 C2' C:C8 4.3 56.1 1.0 N4 C:C8 4.3 65.1 1.0 O5' C:5BU9 4.4 55.4 1.0 O5' C:C8 4.5 61.0 1.0 P C:5BU9 4.6 55.7 1.0 C1' C:C8 4.7 56.5 1.0 OP2 C:C8 4.7 61.4 1.0 C2 C:5BU9 4.7 63.2 1.0 N4 C:C10 4.8 49.7 1.0 C5 C:C10 4.8 53.5 1.0 O3' C:C8 4.9 48.4 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site (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 (Br-Derivative) within 5.0Å range: probe atom residue distance (Å) B Occ D:Br9 b:65.8 occ:0.65 BR D:5BU9 0.0 65.8 0.7 C5 D:5BU9 1.9 60.2 1.0 C6 D:5BU9 2.8 61.0 1.0 C4 D:5BU9 2.9 62.3 1.0 O4 D:5BU9 3.2 63.8 1.0 C5 D:C8 3.4 59.3 1.0 C6 D:C8 3.4 62.5 1.0 OP2 D:5BU9 3.6 72.3 1.0 OP2 D:C8 3.8 38.9 1.0 O5' D:C8 3.8 51.9 1.0 N1 D:5BU9 4.1 60.6 1.0 C3' D:C8 4.1 61.4 1.0 N3 D:5BU9 4.2 62.1 1.0 C4 D:C8 4.2 62.3 1.0 N1 D:C8 4.2 61.3 1.0 O5' D:5BU9 4.3 62.7 1.0 P D:C8 4.4 48.1 1.0 P D:5BU9 4.5 65.8 1.0 C2' D:C8 4.7 60.8 1.0 C2 D:5BU9 4.7 60.7 1.0 N4 D:C8 4.8 58.9 1.0 N3 D:C8 4.9 63.6 1.0 O3' D:C8 4.9 63.9 1.0 C2 D:C8 4.9 63.3 1.0 C1' D:C8 4.9 60.6 1.0 C5' D:C8 4.9 52.9 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