Cadmium in PDB 3ccq: Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U, PDB code: 3ccq was solved by G.Blaha, G.Gurel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.330, 299.618, 575.237, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.3

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U also contains other interesting chemical elements:

Strontium	(Sr)	108 atoms
Magnesium	(Mg)	93 atoms
Potassium	(K)	2 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	75 atoms

The binding sites of Cadmium atom in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U (pdb code 3ccq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U, PDB code: 3ccq:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd8705 b:0.4 occ:1.00 ND1 O:HIS40 2.7 40.1 1.0 O O:HOH5650 3.1 78.3 1.0 CE1 O:HIS40 3.5 41.5 1.0 O 0:HOH6070 3.5 49.2 1.0 CG O:HIS40 3.7 40.9 1.0 CB O:HIS40 3.9 43.9 1.0 CG O:ARG37 4.5 54.6 1.0 O O:HOH3002 4.6 47.4 1.0 NE2 O:HIS40 4.7 41.7 1.0 CD2 O:HIS40 4.8 41.7 1.0 CZ O:ARG37 4.8 54.9 1.0 NE O:ARG37 4.9 55.1 1.0 NH1 O:ARG37 4.9 53.1 1.0

Cadmium binding site 2 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd8701 b:63.8 occ:1.00 SG U:CYS32 2.4 53.4 1.0 SG U:CYS36 2.4 67.1 1.0 SG U:CYS6 2.4 60.0 1.0 SG U:CYS9 2.6 63.6 1.0 CB U:CYS9 3.2 62.6 1.0 CB U:CYS6 3.2 62.3 1.0 CB U:CYS32 3.4 54.4 1.0 CB U:CYS36 3.6 63.9 1.0 N U:CYS9 3.6 62.9 1.0 N U:CYS32 3.9 53.7 1.0 CA U:CYS9 4.0 62.9 1.0 CA U:CYS32 4.2 55.0 1.0 OG1 U:THR11 4.3 66.8 1.0 N U:SER33 4.5 57.9 1.0 OG U:SER33 4.5 62.0 1.0 CB U:TYR8 4.7 61.2 1.0 N U:GLY10 4.7 63.4 1.0 CA U:CYS6 4.7 63.1 1.0 C U:CYS9 4.7 62.9 1.0 C U:CYS32 4.7 57.1 1.0 C U:TYR8 4.8 62.4 1.0 CA U:CYS36 5.0 63.0 1.0

Cadmium binding site 3 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd8703 b:75.3 occ:1.00 SG Z:CYS63 2.3 66.8 1.0 SG Z:CYS84 2.3 74.0 1.0 SG Z:CYS81 2.6 77.7 1.0 SG Z:CYS66 2.9 87.5 1.0 CB Z:CYS63 3.2 71.3 1.0 CB Z:CYS81 3.2 76.3 1.0 CB Z:CYS84 3.3 74.3 1.0 N Z:CYS66 3.5 81.6 1.0 CB Z:CYS66 3.6 83.0 1.0 N Z:CYS84 3.7 75.8 1.0 CB Z:ASN65 3.8 81.4 1.0 CA Z:CYS84 4.1 74.6 1.0 CA Z:CYS66 4.2 81.2 1.0 CD2 Z:TYR83 4.4 83.5 1.0 CB Z:TYR83 4.4 80.0 1.0 C Z:ASN65 4.5 81.3 1.0 CA Z:ASN65 4.6 80.5 1.0 CA Z:CYS63 4.6 74.2 1.0 N Z:ASN65 4.7 78.8 1.0 CB Z:TYR86 4.7 69.9 1.0 CA Z:CYS81 4.7 75.7 1.0 C Z:CYS84 4.8 74.3 1.0 ND2 Z:ASN65 4.9 84.5 1.0 C Z:TYR83 4.9 77.6 1.0 CG Z:ASN65 4.9 83.2 1.0 C Z:CYS66 4.9 80.2 1.0 CG Z:TYR83 4.9 82.2 1.0 C Z:CYS63 5.0 75.8 1.0

Cadmium binding site 4 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8702 b:67.1 occ:1.00 SG 1:CYS34 2.4 38.7 1.0 SG 1:CYS37 2.4 43.1 1.0 SG 1:CYS22 2.4 41.3 1.0 SG 1:CYS19 2.5 41.2 1.0 CB 1:CYS19 3.1 40.5 1.0 CB 1:CYS34 3.1 33.4 1.0 CB 1:CYS22 3.1 38.5 1.0 CB 1:CYS37 3.5 39.1 1.0 N 1:CYS22 3.6 38.8 1.0 N 1:CYS37 3.9 36.6 1.0 CA 1:CYS22 3.9 38.7 1.0 CB 1:PHE39 4.0 42.8 1.0 CA 1:CYS37 4.2 37.7 1.0 CA 1:CYS34 4.5 34.4 1.0 CA 1:CYS19 4.5 40.9 1.0 CB 1:ARG21 4.7 38.5 1.0 N 1:PHE39 4.7 40.7 1.0 N 1:GLY23 4.7 37.9 1.0 C 1:ARG21 4.8 39.4 1.0 C 1:CYS22 4.8 38.5 1.0 C 1:CYS37 4.8 37.6 1.0 CB 1:SER36 4.9 31.1 1.0 CD 1:ARG21 4.9 38.2 1.0 N 1:GLY38 5.0 37.5 1.0 C 1:CYS19 5.0 41.8 1.0

Cadmium binding site 5 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation A2488U within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd8704 b:74.1 occ:1.00 SG 3:CYS14 2.2 75.9 1.0 SG 3:CYS74 2.3 71.9 1.0 SG 3:CYS71 2.4 62.9 1.0 SG 3:CYS11 2.5 58.5 1.0 O 3:HOH9052 2.5 0.2 1.0 CB 3:CYS71 3.1 64.9 1.0 CB 3:CYS74 3.3 70.4 1.0 CB 3:CYS11 3.5 59.0 1.0 CB 3:CYS14 3.5 72.5 1.0 N 3:CYS14 3.8 72.3 1.0 N 3:CYS74 4.0 71.5 1.0 CA 3:CYS74 4.2 71.0 1.0 CA 3:CYS14 4.3 72.6 1.0 CB 3:HIS13 4.4 71.0 1.0 CA 3:CYS71 4.6 65.9 1.0 NE2 3:GLN18 4.7 78.3 1.0 C 3:HIS13 4.8 72.0 1.0 CG 3:GLN18 4.9 73.6 1.0 CA 3:CYS11 4.9 59.6 1.0 C 3:CYS74 5.0 70.8 1.0

G.Blaha, G.Gurel, S.J.Schroeder, P.B.Moore, T.A.Steitz. Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant. J.Mol.Biol. V. 379 505 2008.
ISSN: ISSN 0022-2836
PubMed: 18455733
DOI: 10.1016/J.JMB.2008.03.075