Cadmium in PDB 3cc4: Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit

The structure of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit, PDB code: 3cc4 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)	49.85 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.780, 299.084, 573.837, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.4

The structure of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit 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 Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit (pdb code 3cc4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit, PDB code: 3cc4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd8705 b:0.2 occ:1.00 ND1 O:HIS40 2.6 28.6 1.0 O O:HOH5650 2.7 56.8 1.0 CE1 O:HIS40 3.5 29.2 1.0 CG O:HIS40 3.7 28.4 1.0 O 0:HOH6086 3.7 52.5 1.0 CB O:HIS40 3.9 32.8 1.0 O 0:HOH4397 4.4 61.7 1.0 CG O:ARG37 4.5 42.0 1.0 CZ O:ARG37 4.7 39.6 1.0 NE2 O:HIS40 4.7 29.8 1.0 CD2 O:HIS40 4.8 29.1 1.0 NE O:ARG37 4.8 40.8 1.0 NH1 O:ARG37 4.9 38.1 1.0 NH2 O:ARG37 5.0 38.1 1.0

Cadmium binding site 2 out of 5 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd8701 b:58.1 occ:1.00 SG U:CYS36 2.6 58.6 1.0 SG U:CYS32 2.6 49.2 1.0 SG U:CYS9 2.6 55.7 1.0 SG U:CYS6 2.6 56.9 1.0 CB U:CYS9 3.3 53.5 1.0 CB U:CYS6 3.4 56.4 1.0 CB U:CYS32 3.4 47.3 1.0 CB U:CYS36 3.5 54.6 1.0 N U:CYS9 3.8 53.3 1.0 N U:CYS32 4.0 46.4 1.0 CA U:CYS9 4.1 54.2 1.0 OG1 U:THR11 4.2 63.6 1.0 CA U:CYS32 4.3 48.3 1.0 OG U:SER33 4.6 53.3 1.0 N U:SER33 4.7 50.6 1.0 CB U:TYR8 4.7 51.2 1.0 N U:GLY10 4.8 56.1 1.0 CA U:CYS6 4.9 57.1 1.0 C U:CYS32 4.9 50.1 1.0 C U:CYS9 5.0 55.3 1.0 CA U:CYS36 5.0 54.8 1.0 C U:TYR8 5.0 52.9 1.0

Cadmium binding site 3 out of 5 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd8703 b:81.9 occ:1.00 SG Z:CYS63 2.6 80.1 1.0 SG Z:CYS84 2.6 77.8 1.0 SG Z:CYS81 2.8 79.8 1.0 SG Z:CYS66 3.0 87.0 1.0 CB Z:CYS63 3.3 79.5 1.0 CB Z:CYS81 3.4 76.8 1.0 CB Z:CYS84 3.7 75.9 1.0 N Z:CYS66 3.9 81.3 1.0 CB Z:CYS66 3.9 83.0 1.0 N Z:CYS84 3.9 75.9 1.0 CB Z:ASN65 4.0 79.4 1.0 CA Z:CYS84 4.4 75.6 1.0 CB Z:TYR83 4.4 77.1 1.0 CA Z:CYS66 4.5 82.2 1.0 CD2 Z:TYR83 4.5 79.9 1.0 CA Z:ASN65 4.8 79.9 1.0 CB Z:TYR86 4.8 66.8 1.0 CA Z:CYS63 4.8 79.9 1.0 C Z:ASN65 4.8 80.7 1.0 N Z:ASN65 4.8 79.5 1.0 CA Z:CYS81 4.9 75.1 1.0

Cadmium binding site 4 out of 5 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8702 b:57.5 occ:1.00 SG 1:CYS37 2.5 37.2 1.0 SG 1:CYS22 2.5 34.1 1.0 SG 1:CYS34 2.6 31.9 1.0 SG 1:CYS19 2.6 33.3 1.0 CB 1:CYS19 3.1 30.9 1.0 CB 1:CYS34 3.3 26.2 1.0 CB 1:CYS22 3.3 31.9 1.0 CB 1:CYS37 3.4 30.9 1.0 N 1:CYS22 3.8 32.9 1.0 N 1:CYS37 3.8 28.0 1.0 CA 1:CYS37 4.1 27.9 1.0 CA 1:CYS22 4.1 31.2 1.0 CB 1:PHE39 4.3 30.5 1.0 CB 1:ARG21 4.6 29.0 1.0 CA 1:CYS19 4.6 30.1 1.0 CA 1:CYS34 4.7 25.9 1.0 C 1:CYS37 4.7 28.4 1.0 C 1:ARG21 4.8 32.2 1.0 CB 1:SER36 4.8 23.6 1.0 N 1:PHE39 4.8 28.4 1.0 N 1:GLY38 4.9 28.2 1.0 N 1:GLY23 4.9 31.3 1.0 C 1:CYS22 4.9 32.6 1.0 C 1:SER36 4.9 27.7 1.0

Cadmium binding site 5 out of 5 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd8704 b:66.2 occ:1.00 SG 3:CYS11 2.6 53.4 1.0 SG 3:CYS71 2.6 61.3 1.0 SG 3:CYS74 2.6 71.0 1.0 O 3:HOH9051 2.7 0.0 1.0 SG 3:CYS14 2.9 71.0 1.0 CB 3:CYS14 3.1 67.4 1.0 CB 3:CYS74 3.4 69.3 1.0 CB 3:CYS71 3.4 61.6 1.0 CB 3:CYS11 3.6 54.7 1.0 N 3:CYS14 3.9 67.9 1.0 CA 3:CYS14 4.0 67.9 1.0 N 3:CYS74 4.1 68.7 1.0 CA 3:CYS74 4.3 69.1 1.0 CB 3:HIS13 4.7 66.5 1.0 C 3:HIS13 4.8 67.5 1.0 OE1 3:GLN18 4.8 70.5 1.0 O 3:HOH9030 4.8 41.1 1.0 CA 3:CYS71 4.8 61.1 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