Cadmium in PDB 3ccm: Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U, PDB code: 3ccm 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)	49.70 / 2.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.531, 298.177, 573.367, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U 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 G2611U (pdb code 3ccm). 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 G2611U, PDB code: 3ccm:
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 G2611U


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 G2611U within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd8705 b:88.3 occ:1.00 O O:HOH5650 2.4 46.8 1.0 ND1 O:HIS40 2.7 29.1 1.0 O O:HOH5322 3.1 41.2 1.0 CG O:HIS40 3.6 27.9 1.0 CE1 O:HIS40 3.6 27.7 1.0 CB O:HIS40 3.7 30.7 1.0 CG O:ARG37 4.3 38.5 1.0 O O:HOH3002 4.5 56.6 1.0 NE2 O:HIS40 4.7 30.3 1.0 CD2 O:HIS40 4.7 29.4 1.0 CZ O:ARG37 4.7 40.7 1.0 NH1 O:ARG37 4.8 39.5 1.0 NE O:ARG37 4.8 40.0 1.0 O O:ARG37 4.9 34.2 1.0 CB O:ARG37 4.9 37.5 1.0 CA O:ARG37 5.0 36.4 1.0

Cadmium binding site 2 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U


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 G2611U within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd8701 b:62.7 occ:1.00 SG U:CYS36 2.4 44.7 1.0 SG U:CYS6 2.5 41.6 1.0 SG U:CYS9 2.5 48.6 1.0 SG U:CYS32 2.6 30.1 1.0 CB U:CYS6 3.1 47.6 1.0 CB U:CYS9 3.3 46.8 1.0 CB U:CYS36 3.5 42.4 1.0 CB U:CYS32 3.7 33.0 1.0 N U:CYS9 3.7 45.5 1.0 CA U:CYS9 4.0 46.4 1.0 N U:CYS32 4.1 33.5 1.0 OG1 U:THR11 4.4 53.4 1.0 CA U:CYS32 4.5 34.0 1.0 OG U:SER33 4.6 29.7 1.0 CA U:CYS6 4.6 46.6 1.0 CB U:TYR8 4.7 41.9 1.0 N U:GLY10 4.8 49.2 1.0 N U:SER33 4.8 36.7 1.0 C U:CYS9 4.8 47.9 1.0 C U:TYR8 4.9 45.1 1.0 CA U:CYS36 4.9 42.2 1.0

Cadmium binding site 3 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U


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 G2611U within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd8703 b:67.7 occ:1.00 SG Z:CYS84 2.2 41.2 1.0 SG Z:CYS63 2.4 53.4 1.0 SG Z:CYS66 2.5 63.2 1.0 SG Z:CYS81 2.5 43.5 1.0 CB Z:CYS81 3.2 48.4 1.0 CB Z:CYS63 3.3 55.8 1.0 CB Z:CYS84 3.4 46.4 1.0 CB Z:CYS66 3.6 63.5 1.0 N Z:CYS66 3.8 63.0 1.0 N Z:CYS84 3.8 48.8 1.0 CA Z:CYS84 4.2 47.4 1.0 CA Z:CYS66 4.3 63.0 1.0 CB Z:ASN65 4.3 61.2 1.0 CB Z:TYR83 4.6 52.9 1.0 CB Z:TYR86 4.6 43.2 1.0 CD2 Z:TYR83 4.7 56.5 1.0 CA Z:CYS81 4.7 47.1 1.0 CA Z:CYS63 4.7 56.5 1.0 C Z:ASN65 4.9 62.6 1.0 C Z:CYS66 4.9 63.0 1.0 C Z:CYS84 4.9 47.6 1.0 C Z:TYR83 4.9 50.4 1.0 CA Z:ASN65 5.0 61.4 1.0

Cadmium binding site 4 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U


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 G2611U within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8702 b:54.9 occ:1.00 SG 1:CYS22 2.4 20.2 1.0 SG 1:CYS19 2.4 21.2 1.0 SG 1:CYS34 2.5 20.7 1.0 SG 1:CYS37 2.5 17.7 1.0 CB 1:CYS19 3.1 21.9 1.0 CB 1:CYS34 3.2 21.4 1.0 CB 1:CYS22 3.3 23.3 1.0 CB 1:CYS37 3.3 18.0 1.0 N 1:CYS22 3.7 26.5 1.0 N 1:CYS37 3.7 20.7 1.0 CA 1:CYS37 4.0 20.0 1.0 CA 1:CYS22 4.1 24.4 1.0 CB 1:PHE39 4.3 23.9 1.0 CA 1:CYS19 4.6 23.8 1.0 CA 1:CYS34 4.6 22.6 1.0 CB 1:ARG21 4.7 28.9 1.0 C 1:CYS37 4.7 18.8 1.0 N 1:PHE39 4.7 22.8 1.0 N 1:GLY38 4.7 19.5 1.0 C 1:ARG21 4.8 28.0 1.0 CB 1:SER36 4.8 21.7 1.0 O 1:HOH1020 4.8 30.8 1.0 C 1:SER36 4.9 22.6 1.0 C 1:CYS22 4.9 23.2 1.0 N 1:GLY23 4.9 21.4 1.0

Cadmium binding site 5 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U


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 G2611U within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd8704 b:63.9 occ:1.00 SG 3:CYS71 2.3 41.1 1.0 SG 3:CYS74 2.4 51.1 1.0 SG 3:CYS11 2.4 41.9 1.0 O 3:HOH9055 2.5 0.1 1.0 SG 3:CYS14 2.6 53.8 1.0 CB 3:CYS71 3.2 47.1 1.0 CB 3:CYS14 3.3 51.3 1.0 CB 3:CYS11 3.5 44.0 1.0 CB 3:CYS74 3.6 53.2 1.0 N 3:CYS14 3.8 52.7 1.0 N 3:CYS74 4.1 54.9 1.0 CA 3:CYS14 4.1 53.4 1.0 CA 3:CYS74 4.4 54.0 1.0 OE1 3:GLN18 4.4 55.1 1.0 CB 3:HIS13 4.5 49.9 1.0 CA 3:CYS71 4.6 46.5 1.0 C 3:HIS13 4.7 51.0 1.0 CG 3:GLN18 4.9 52.3 1.0 CA 3:CYS11 4.9 44.0 1.0 CB 3:GLN18 5.0 49.8 1.0 O 3:HOH9033 5.0 30.2 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