Cobalt in PDB 3bnl: Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3

The structure of Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3, PDB code: 3bnl 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)	36.00 / 2.60
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	73.599, 73.599, 63.496, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.1

The binding sites of Cobalt atom in the Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3 (pdb code 3bnl). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3, PDB code: 3bnl:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co23 b:40.0 occ:1.00 CO A:NCO23 0.0 40.0 1.0 N2 A:NCO23 1.9 35.8 1.0 N6 A:NCO23 1.9 35.2 1.0 N4 A:NCO23 1.9 39.5 1.0 N5 A:NCO23 2.0 50.1 1.0 N1 A:NCO23 2.0 24.0 1.0 N3 A:NCO23 2.0 36.2 1.0 O4 B:U5 3.6 22.9 1.0 OP2 A:A17 3.7 26.7 1.0 O6 A:G18 4.1 22.3 1.0 O A:HOH29 4.1 22.7 1.0 O6 B:G4 4.2 44.4 1.0 N7 A:G18 4.4 36.3 1.0 C4 B:U5 4.8 27.2 1.0 C6 A:G18 4.9 36.3 1.0 P A:A17 5.0 42.2 1.0

Cobalt binding site 2 out of 8 in the Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co24 b:85.1 occ:0.74 CO A:NCO24 0.0 85.1 0.7 N2 A:NCO24 1.9 68.0 0.7 N6 A:NCO24 2.0 68.3 0.7 N5 A:NCO24 2.0 70.7 0.7 N4 A:NCO24 2.0 71.9 0.7 N1 A:NCO24 2.0 78.0 0.7 N3 A:NCO24 2.0 72.3 0.7 O A:HOH30 3.7 50.0 1.0 OP2 A:G15 4.1 57.6 1.0 OP2 A:U14 4.2 44.0 1.0 OP1 B:G4 4.2 42.6 1.0 OP2 B:U5 4.5 35.2 1.0

Cobalt binding site 3 out of 8 in the Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co25 b:99.0 occ:0.78 CO A:NCO25 0.0 99.0 0.8 N2 A:NCO25 1.9 80.3 0.8 N5 A:NCO25 1.9 87.2 0.8 N4 A:NCO25 1.9 84.4 0.8 N6 A:NCO25 2.0 80.9 0.8 N3 A:NCO25 2.0 80.6 0.8 N1 A:NCO25 2.0 78.0 0.8 N7 A:G13 4.4 35.9 1.0 O6 A:G13 4.6 40.1 1.0 N7 A:G12 4.7 41.8 1.0 O4 A:U14 4.7 40.4 1.0 OP2 A:G12 5.0 48.5 1.0

Cobalt binding site 4 out of 8 in the Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co23 b:72.3 occ:0.90 CO B:NCO23 0.0 72.3 0.9 N2 B:NCO23 1.9 64.3 0.9 N6 B:NCO23 1.9 53.9 0.9 N5 B:NCO23 1.9 61.0 0.9 N4 B:NCO23 2.0 54.3 0.9 N1 B:NCO23 2.0 71.6 0.9 N3 B:NCO23 2.0 30.3 0.9 OP1 A:A16 3.5 71.8 1.0 OP1 B:C3 3.6 33.7 1.0 P B:C3 4.6 38.8 1.0 OP2 B:C3 4.6 37.1 1.0 P A:A16 5.0 63.5 1.0

Cobalt binding site 5 out of 8 in the Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co24 b:47.5 occ:1.00 CO B:NCO24 0.0 47.5 1.0 N2 B:NCO24 1.9 37.2 1.0 N6 B:NCO24 1.9 46.2 1.0 N4 B:NCO24 1.9 44.8 1.0 N5 B:NCO24 1.9 49.2 1.0 N1 B:NCO24 2.0 42.5 1.0 N3 B:NCO24 2.0 30.0 1.0 O4 A:U5 3.6 29.8 1.0 O6 B:G18 3.9 24.5 1.0 O B:HOH44 4.0 58.3 1.0 O A:HOH43 4.2 33.5 1.0 O6 A:G4 4.2 39.9 1.0 OP2 B:A17 4.3 49.5 1.0 N7 B:G18 4.3 36.1 1.0 OP1 B:A17 4.5 50.5 1.0 C6 B:G18 4.7 37.2 1.0 O4 B:U19 4.8 35.9 1.0 C4 A:U5 4.8 24.3 1.0 C5 B:G18 4.9 22.6 1.0 P B:A17 4.9 39.6 1.0

Cobalt binding site 6 out of 8 in the Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co25 b:81.0 occ:0.72 CO B:NCO25 0.0 81.0 0.7 N2 B:NCO25 1.9 59.1 0.7 N6 B:NCO25 1.9 56.6 0.7 N5 B:NCO25 2.0 69.5 0.7 N4 B:NCO25 2.0 62.7 0.7 N1 B:NCO25 2.0 70.6 0.7 N3 B:NCO25 2.0 69.2 0.7 O B:HOH43 3.7 43.4 1.0 OP2 B:U14 4.0 48.1 1.0 OP2 B:G15 4.1 55.0 1.0 OP1 A:G4 4.4 47.5 1.0 OP2 A:U5 4.6 30.8 1.0 P B:U14 4.8 60.3 1.0 O5' B:U14 4.8 52.9 1.0 OP1 B:U14 4.9 69.1 1.0

Cobalt binding site 7 out of 8 in the Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co26 b:98.0 occ:0.76 CO B:NCO26 0.0 98.0 0.8 N2 B:NCO26 1.9 73.2 0.8 N5 B:NCO26 2.0 73.1 0.8 N4 B:NCO26 2.0 72.6 0.8 N6 B:NCO26 2.0 79.8 0.8 N3 B:NCO26 2.0 78.0 0.8 N1 B:NCO26 2.0 69.9 0.8 O B:HOH42 4.5 52.6 1.0 O A:HOH37 4.5 42.8 1.0 O4 B:U14 4.5 35.9 1.0 N7 B:G13 4.8 33.2 1.0

Cobalt binding site 8 out of 8 in the Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of the Bacterial Ribosomal Decoding A Site in the Presence of [Co(NH3)6]CL3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co27 b:72.2 occ:0.82 CO B:NCO27 0.0 72.2 0.8 N2 B:NCO27 1.9 49.1 0.8 N6 B:NCO27 1.9 58.2 0.8 N4 B:NCO27 1.9 56.2 0.8 N5 B:NCO27 1.9 55.8 0.8 N1 B:NCO27 2.0 70.4 0.8 N3 B:NCO27 2.0 21.4 0.8 OP1 B:A16 3.5 73.7 1.0 OP1 A:C3 3.6 33.6 1.0 OP2 A:C3 4.5 31.6 1.0 P A:C3 4.5 37.0 1.0 C5' B:A16 4.8 85.4 1.0 P B:A16 4.8 69.5 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