Cadmium in PDB 1k73: 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: 1k73 was solved by J.Hansen, N.Ban, P.Nissen, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.01
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	213.245, 300.750, 574.806, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.6

The structure of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit also contains other interesting chemical elements:

Magnesium	(Mg)	117 atoms
Potassium	(K)	2 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 atoms

The binding sites of Cadmium atom in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit (pdb code 1k73). 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: 1k73:
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 P:Cd8405 b:82.8 occ:1.00 ND1 P:HIS40 2.7 35.8 1.0 O A:HOH6020 2.8 30.9 1.0 O P:HOH5650 2.8 35.1 1.0 CG P:HIS40 3.5 36.7 1.0 CE1 P:HIS40 3.6 35.4 1.0 CB P:HIS40 3.7 38.5 1.0 CG P:ARG37 4.3 49.2 1.0 CD2 P:HIS40 4.7 36.1 1.0 NE2 P:HIS40 4.7 36.1 1.0 CZ P:ARG37 4.7 47.4 1.0 NH1 P:ARG37 4.8 45.6 1.0 O A:HOH4332 4.8 52.5 1.0 CB P:ARG37 4.8 47.6 1.0 CA P:ARG37 4.9 46.6 1.0 NE P:ARG37 4.9 48.2 1.0 O P:ARG37 4.9 46.4 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 V:Cd8401 b:59.7 occ:1.00 SG V:CYS6 2.2 58.2 1.0 SG V:CYS36 2.3 53.0 1.0 SG V:CYS32 2.5 30.7 1.0 SG V:CYS9 2.6 56.5 1.0 CB V:CYS6 3.2 58.1 1.0 CB V:CYS9 3.4 54.3 1.0 CB V:CYS36 3.5 52.5 1.0 N V:CYS9 3.7 52.9 1.0 CB V:CYS32 3.8 38.4 1.0 N V:CYS32 4.0 41.5 1.0 CA V:CYS9 4.1 52.7 1.0 CB V:TYR8 4.3 50.9 1.0 CA V:CYS32 4.5 42.0 1.0 OG V:SER33 4.6 48.9 1.0 OG1 V:THR11 4.6 56.9 1.0 CA V:CYS6 4.6 57.4 1.0 N V:GLY10 4.7 53.4 1.0 C V:TYR8 4.8 52.6 1.0 N V:SER33 4.8 45.8 1.0 C V:CYS9 4.8 52.7 1.0 CD2 V:TYR8 4.9 48.6 1.0 CA V:CYS36 4.9 52.1 1.0 CA V:TYR8 4.9 51.8 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 1:Cd8403 b:60.3 occ:1.00 SG 1:CYS60 2.3 46.6 1.0 SG 1:CYS57 2.4 60.8 1.0 SG 1:CYS39 2.5 54.2 1.0 SG 1:CYS42 2.7 61.7 1.0 CB 1:CYS57 3.2 62.6 1.0 CB 1:CYS39 3.3 57.8 1.0 CB 1:CYS42 3.4 65.4 1.0 CB 1:CYS60 3.5 50.9 1.0 N 1:CYS42 3.8 68.8 1.0 N 1:CYS60 3.9 56.1 1.0 CA 1:CYS42 4.2 67.5 1.0 CA 1:CYS60 4.3 53.5 1.0 CB 1:HIS59 4.6 65.3 1.0 CD2 1:HIS59 4.7 69.4 1.0 CB 1:TYR62 4.7 57.4 1.0 CB 1:VAL41 4.7 68.7 1.0 CA 1:CYS57 4.8 61.9 1.0 C 1:CYS42 4.8 68.4 1.0 CA 1:CYS39 4.8 61.8 1.0 CG1 1:VAL41 4.9 67.5 1.0 C 1:HIS59 5.0 59.9 1.0 C 1:VAL41 5.0 69.7 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 2:Cd8402 b:59.1 occ:1.00 SG 2:CYS37 2.5 42.0 1.0 SG 2:CYS19 2.5 44.6 1.0 SG 2:CYS22 2.6 34.0 1.0 SG 2:CYS34 2.6 34.9 1.0 CB 2:CYS19 3.0 38.7 1.0 CB 2:CYS34 3.2 33.4 1.0 CB 2:CYS22 3.2 33.1 1.0 CB 2:CYS37 3.4 34.4 1.0 N 2:CYS22 3.6 34.0 1.0 N 2:CYS37 3.9 30.8 1.0 CA 2:CYS22 4.0 34.4 1.0 CA 2:CYS37 4.2 31.2 1.0 CB 2:PHE39 4.3 37.0 1.0 CA 2:CYS19 4.5 36.8 1.0 CB 2:ARG21 4.5 33.4 1.0 C 2:ARG21 4.6 34.9 1.0 CA 2:CYS34 4.7 34.5 1.0 O 2:HOH8420 4.7 23.0 1.0 C 2:CYS22 4.8 34.3 1.0 N 2:GLY23 4.8 32.3 1.0 C 2:CYS37 4.9 31.4 1.0 CB 2:SER36 4.9 29.2 1.0 CA 2:ARG21 4.9 33.4 1.0 C 2:SER36 4.9 30.4 1.0 N 2:ARG21 4.9 35.7 1.0 C 2:CYS19 4.9 37.3 1.0 N 2:PHE39 5.0 34.4 1.0 N 2:GLY38 5.0 29.1 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 4:Cd8404 b:62.3 occ:1.00 SG 4:CYS71 2.0 54.2 1.0 SG 4:CYS11 2.3 64.0 1.0 SG 4:CYS74 2.6 59.8 1.0 CB 4:CYS71 2.8 55.9 1.0 SG 4:CYS14 3.1 67.9 1.0 O 4:HOH8561 3.1 0.9 1.0 CB 4:CYS14 3.2 64.4 1.0 CB 4:CYS74 3.4 61.1 1.0 CB 4:CYS11 3.5 58.6 1.0 N 4:CYS14 3.9 62.8 1.0 N 4:CYS74 4.1 63.5 1.0 CA 4:CYS14 4.1 64.9 1.0 CA 4:CYS71 4.2 57.5 1.0 CA 4:CYS74 4.3 62.5 1.0 OE1 4:GLN18 4.6 70.1 1.0 CB 4:HIS13 4.8 59.4 1.0 C 4:CYS71 4.9 58.6 1.0 CA 4:CYS11 4.9 57.6 1.0 O 4:LYS76 5.0 59.5 1.0 CD 4:GLN18 5.0 67.3 1.0

J.Hansen, P.B.Moore, T.A.Steitz. Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit J.Mol.Biol. V. 330 1061 2003.
ISSN: ISSN 0022-2836
PubMed: 12860128
DOI: 10.1016/S0022-2836(03)00668-5