Cadmium in PDB 3ccv: Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A, PDB code: 3ccv 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)	49.99 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.752, 299.012, 574.480, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22.5

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A 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 G2616A (pdb code 3ccv). 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 G2616A, PDB code: 3ccv:
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 G2616A


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 G2616A within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd8705 b:84.2 occ:1.00 ND1 O:HIS40 2.6 30.2 1.0 O 0:HOH6276 2.8 40.7 1.0 O 0:HOH6040 3.4 43.2 1.0 CE1 O:HIS40 3.4 31.4 1.0 CG O:HIS40 3.6 29.9 1.0 CB O:HIS40 3.9 33.3 1.0 O 0:HOH4360 4.3 40.1 1.0 CG O:ARG37 4.5 48.2 1.0 NE2 O:HIS40 4.6 32.0 1.0 CD2 O:HIS40 4.7 30.9 1.0 CZ O:ARG37 4.7 46.9 1.0 NE O:ARG37 4.8 48.4 1.0 CB O:ARG37 4.9 45.6 1.0

Cadmium binding site 2 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


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 G2616A within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd8701 b:62.3 occ:1.00 SG U:CYS9 2.3 54.2 1.0 SG U:CYS36 2.4 57.8 1.0 SG U:CYS6 2.4 54.2 1.0 SG U:CYS32 2.4 43.1 1.0 CB U:CYS9 3.2 52.7 1.0 CB U:CYS6 3.2 56.4 1.0 CB U:CYS32 3.4 44.6 1.0 CB U:CYS36 3.5 55.2 1.0 N U:CYS9 3.7 53.4 1.0 N U:CYS32 3.9 44.1 1.0 CA U:CYS9 4.0 52.7 1.0 CA U:CYS32 4.2 45.3 1.0 OG1 U:THR11 4.4 63.0 1.0 OG U:SER33 4.6 53.4 1.0 CB U:TYR8 4.6 52.8 1.0 N U:SER33 4.6 49.4 1.0 CA U:CYS6 4.7 56.8 1.0 N U:GLY10 4.7 53.2 1.0 C U:CYS32 4.8 47.9 1.0 C U:TYR8 4.9 53.4 1.0 C U:CYS9 4.9 52.8 1.0 CA U:CYS36 5.0 54.4 1.0

Cadmium binding site 3 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


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 G2616A within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd8703 b:83.5 occ:1.00 SG Z:CYS84 2.3 70.2 1.0 SG Z:CYS63 2.4 78.0 1.0 SG Z:CYS81 2.5 76.4 1.0 SG Z:CYS66 2.9 88.9 1.0 CB Z:CYS81 3.2 73.7 1.0 CB Z:CYS84 3.4 68.6 1.0 CB Z:CYS63 3.4 79.6 1.0 N Z:CYS66 3.5 88.0 1.0 CB Z:ASN65 3.6 85.2 1.0 CB Z:CYS66 3.6 88.1 1.0 N Z:CYS84 3.8 70.5 1.0 CA Z:CYS84 4.1 69.2 1.0 CA Z:CYS66 4.2 88.2 1.0 CD2 Z:TYR83 4.3 78.2 1.0 CB Z:TYR83 4.4 74.8 1.0 C Z:ASN65 4.5 87.5 1.0 ND2 Z:ASN65 4.5 84.5 1.0 CA Z:ASN65 4.5 86.2 1.0 CG Z:ASN65 4.6 84.9 1.0 CB Z:TYR86 4.6 63.1 1.0 N Z:ASN65 4.7 85.3 1.0 CA Z:CYS81 4.7 72.9 1.0 CA Z:CYS63 4.8 80.7 1.0 CG Z:TYR83 4.8 77.0 1.0 C Z:CYS84 4.8 68.5 1.0 C Z:TYR83 4.9 72.5 1.0 C Z:CYS66 5.0 88.8 1.0

Cadmium binding site 4 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


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 G2616A within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8702 b:60.5 occ:1.00 SG 1:CYS22 2.4 28.5 1.0 SG 1:CYS34 2.4 35.8 1.0 SG 1:CYS37 2.4 30.9 1.0 SG 1:CYS19 2.5 29.6 1.0 CB 1:CYS19 3.1 30.6 1.0 CB 1:CYS22 3.1 30.5 1.0 CB 1:CYS34 3.2 28.7 1.0 CB 1:CYS37 3.3 27.8 1.0 N 1:CYS22 3.6 30.5 1.0 N 1:CYS37 3.8 26.8 1.0 CA 1:CYS22 3.9 30.3 1.0 CB 1:PHE39 4.1 31.6 1.0 CA 1:CYS37 4.1 26.8 1.0 CA 1:CYS19 4.6 31.1 1.0 CA 1:CYS34 4.6 29.2 1.0 CB 1:ARG21 4.7 29.0 1.0 C 1:CYS22 4.7 30.0 1.0 C 1:ARG21 4.7 30.8 1.0 N 1:GLY23 4.7 29.8 1.0 N 1:PHE39 4.7 29.3 1.0 C 1:CYS37 4.8 25.1 1.0 N 1:GLY38 4.9 25.4 1.0 CB 1:SER36 4.9 25.0 1.0 CD 1:ARG21 4.9 29.1 1.0 C 1:SER36 5.0 27.5 1.0 CA 1:ARG21 5.0 30.4 1.0 O 1:HOH8968 5.0 32.4 1.0 N 1:ARG21 5.0 30.5 1.0

Cadmium binding site 5 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


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 G2616A within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd8704 b:76.5 occ:1.00 SG 3:CYS71 2.3 64.5 1.0 SG 3:CYS74 2.4 76.9 1.0 SG 3:CYS11 2.4 64.0 1.0 SG 3:CYS14 2.4 79.6 1.0 CB 3:CYS71 3.1 63.6 1.0 CB 3:CYS14 3.4 75.6 1.0 CB 3:CYS11 3.6 63.6 1.0 CB 3:CYS74 3.6 75.1 1.0 N 3:CYS14 3.8 75.7 1.0 N 3:CYS74 4.1 73.9 1.0 CA 3:CYS14 4.2 76.0 1.0 CG 3:GLN18 4.3 69.6 1.0 CA 3:CYS74 4.4 74.6 1.0 CB 3:HIS13 4.5 74.1 1.0 CA 3:CYS71 4.6 63.3 1.0 O 3:HOH8963 4.6 28.0 1.0 C 3:HIS13 4.8 75.2 1.0 O 3:HOH8985 4.8 0.9 1.0 CB 3:GLN18 4.9 67.6 1.0 NE2 3:GLN18 4.9 71.5 1.0 CA 3:CYS11 4.9 64.5 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