Potassium 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:

Bromine

(Br)

4 atoms

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium 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 Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 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 Potassium with other atoms in the K 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:K24 b:26.3 occ:1.00 O2 A:C23 2.8 22.9 1.0 O2' A:C23 2.9 25.5 1.0 O D:HOH40 2.9 37.3 1.0 O D:HOH27 2.9 24.6 1.0 O2 C:C10 2.9 21.5 1.0 O B:HOH24 3.0 25.3 1.0 C2' A:C23 3.6 24.6 1.0 N2 B:G2 3.6 24.0 1.0 N6 D:A15 3.7 23.4 1.0 C1' A:C23 3.8 22.6 1.0 C1' C:C10 3.8 25.3 1.0 C2 A:C23 3.9 24.1 1.0 O2' C:C10 3.9 21.5 1.0 C2 C:C10 3.9 25.1 1.0 O2' D:C14 4.2 32.8 1.0 O2 C:C9 4.3 22.4 1.0 N1 C:C10 4.3 25.2 1.0 N2 D:G13 4.3 27.8 1.0 C2' C:C10 4.3 25.0 1.0 N1 A:C23 4.4 23.9 1.0 C6 D:A15 4.5 27.4 1.0 O2 B:C3 4.6 20.7 1.0 N7 D:A15 4.7 31.6 1.0 N3 C:C9 4.7 20.7 1.0 O4' C:C10 4.8 25.7 1.0 C2 C:C9 4.9 23.5 1.0 C5 D:A15 4.9 29.4 1.0 C2 B:G2 4.9 27.6 1.0 N3 C:C10 5.0 23.6 1.0 O4' A:C23 5.0 21.8 1.0 O2 D:C14 5.0 33.2 1.0

Potassium binding site 2 out of 2 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 Potassium with other atoms in the K 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 C:K25 b:31.9 occ:1.00 O2 A:C10 2.7 21.8 1.0 O D:HOH24 2.8 27.6 1.0 O2 C:C23 2.8 26.2 1.0 O2' C:C23 2.9 23.4 1.0 O A:HOH26 2.9 23.4 1.0 O B:HOH25 3.0 27.4 1.0 N2 D:G1 3.6 32.3 1.0 C1' A:C10 3.7 25.0 1.0 C2' C:C23 3.7 24.9 1.0 C2 A:C10 3.7 24.6 1.0 N6 B:A16 3.8 34.6 1.0 C1' C:C23 3.9 24.7 1.0 C2 C:C23 4.0 27.0 1.0 O2' A:C10 4.0 20.6 1.0 O2' B:C15 4.0 36.4 1.0 N1 A:C10 4.1 24.3 1.0 C2' A:C10 4.2 25.8 1.0 O2 A:C9 4.4 25.4 1.0 N2 B:G14 4.4 30.0 1.0 N1 C:C23 4.5 25.1 1.0 C6 B:A16 4.5 34.5 1.0 N7 B:A16 4.5 36.1 1.0 O2 D:C2 4.5 28.2 1.0 O B:HOH69 4.6 32.1 1.0 O4' A:C10 4.7 25.9 1.0 C5 B:A16 4.7 35.6 1.0 N3 A:C9 4.7 21.4 1.0 N3 A:C10 4.8 20.5 1.0 C2 A:C9 4.9 24.9 1.0 O2 B:C15 4.9 29.7 1.0 C2 D:G1 5.0 34.6 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