Cadmium in PDB 1nji: Structure of Chloramphenicol Bound to the 50S Ribosomal Subunit

The structure of Structure of Chloramphenicol Bound to the 50S Ribosomal Subunit, PDB code: 1nji was solved by J.L.Hansen, 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)	50.00 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.720, 299.750, 573.430, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.9

The structure of Structure of Chloramphenicol Bound to the 50S Ribosomal Subunit also contains other interesting chemical elements:

Magnesium	(Mg)	117 atoms
Potassium	(K)	2 atoms
Chlorine	(Cl)	24 atoms
Sodium	(Na)	85 atoms

The binding sites of Cadmium atom in the Structure of Chloramphenicol Bound to the 50S Ribosomal Subunit (pdb code 1nji). 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 Chloramphenicol Bound to the 50S Ribosomal Subunit, PDB code: 1nji:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Structure of Chloramphenicol 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 Structure of Chloramphenicol Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ P:Cd8405 b:90.7 occ:1.00 ND1 P:HIS40 2.6 28.6 1.0 O A:HOH6249 2.9 46.4 1.0 O P:HOH5322 2.9 30.5 1.0 CG P:HIS40 3.5 27.5 1.0 CE1 P:HIS40 3.5 29.0 1.0 CB P:HIS40 3.7 29.6 1.0 CG P:ARG37 4.4 37.0 1.0 NE2 P:HIS40 4.6 29.2 1.0 CD2 P:HIS40 4.7 28.6 1.0 O A:HOH4328 4.8 53.6 1.0 CZ P:ARG37 4.8 34.9 1.0 CB P:ARG37 4.9 36.7 1.0 NE P:ARG37 4.9 36.0 1.0 CA P:ARG37 4.9 36.7 1.0 NH1 P:ARG37 4.9 34.5 1.0 O P:ARG37 5.0 36.1 1.0

Cadmium binding site 2 out of 5 in the Structure of Chloramphenicol 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 Structure of Chloramphenicol Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ V:Cd8401 b:63.9 occ:1.00 SG V:CYS9 2.1 52.8 1.0 SG V:CYS36 2.2 52.4 1.0 SG V:CYS6 2.4 50.9 1.0 SG V:CYS32 2.5 25.7 1.0 CB V:CYS9 3.1 48.4 1.0 CB V:CYS6 3.4 51.6 1.0 CB V:CYS36 3.5 49.8 1.0 CB V:CYS32 3.7 34.5 1.0 N V:CYS9 3.7 47.8 1.0 CA V:CYS9 4.0 48.2 1.0 N V:CYS32 4.3 34.2 1.0 OG1 V:THR11 4.3 55.9 1.0 CA V:CYS32 4.5 34.1 1.0 CB V:TYR8 4.6 45.1 1.0 N V:GLY10 4.7 49.1 1.0 OG V:SER33 4.7 36.6 1.0 C V:CYS9 4.8 48.6 1.0 CA V:CYS6 4.8 51.2 1.0 C V:TYR8 4.8 47.6 1.0 CA V:CYS36 4.9 48.0 1.0 CD2 V:TYR8 4.9 40.0 1.0 N V:SER33 5.0 36.9 1.0

Cadmium binding site 3 out of 5 in the Structure of Chloramphenicol 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 Structure of Chloramphenicol Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8403 b:56.4 occ:1.00 SG 1:CYS60 2.1 45.6 1.0 SG 1:CYS57 2.3 49.7 1.0 SG 1:CYS39 2.4 48.4 1.0 SG 1:CYS42 2.6 64.0 1.0 CB 1:CYS42 3.3 61.6 1.0 CB 1:CYS57 3.3 52.5 1.0 CB 1:CYS60 3.4 45.1 1.0 CB 1:CYS39 3.4 51.6 1.0 N 1:CYS42 3.7 61.5 1.0 N 1:CYS60 3.9 47.8 1.0 CA 1:CYS42 4.1 61.3 1.0 CA 1:CYS60 4.2 46.6 1.0 CB 1:HIS59 4.6 56.0 1.0 CB 1:VAL41 4.6 61.0 1.0 CD2 1:HIS59 4.6 59.2 1.0 C 1:CYS42 4.7 61.8 1.0 CG1 1:VAL41 4.7 61.4 1.0 CB 1:TYR62 4.8 48.5 1.0 CA 1:CYS39 4.8 52.3 1.0 C 1:VAL41 4.8 61.1 1.0 CA 1:CYS57 4.9 51.9 1.0 C 1:HIS59 5.0 51.4 1.0 CG 1:HIS59 5.0 58.6 1.0

Cadmium binding site 4 out of 5 in the Structure of Chloramphenicol 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 Structure of Chloramphenicol Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 2:Cd8402 b:57.2 occ:1.00 SG 2:CYS19 2.3 29.6 1.0 SG 2:CYS22 2.4 31.2 1.0 SG 2:CYS37 2.4 29.3 1.0 SG 2:CYS34 2.6 28.5 1.0 CB 2:CYS19 3.0 26.1 1.0 CB 2:CYS34 3.2 26.1 1.0 CB 2:CYS22 3.3 30.0 1.0 CB 2:CYS37 3.4 25.8 1.0 N 2:CYS22 3.6 29.0 1.0 N 2:CYS37 3.9 26.1 1.0 CA 2:CYS22 4.1 30.4 1.0 CA 2:CYS37 4.2 26.7 1.0 CB 2:ARG21 4.3 27.6 1.0 CB 2:PHE39 4.3 28.2 1.0 CA 2:CYS19 4.5 27.6 1.0 C 2:ARG21 4.6 30.0 1.0 CA 2:CYS34 4.6 27.4 1.0 O 2:HOH1020 4.8 21.6 1.0 CA 2:ARG21 4.8 28.3 1.0 C 2:CYS22 4.8 28.5 1.0 C 2:CYS37 4.9 24.1 1.0 N 2:ARG21 4.9 28.2 1.0 N 2:GLY23 4.9 27.7 1.0 CB 2:SER36 4.9 25.5 1.0 C 2:CYS19 4.9 27.4 1.0 CD 2:ARG21 4.9 31.6 1.0 N 2:PHE39 4.9 27.0 1.0 N 2:GLY38 5.0 22.6 1.0 C 2:SER36 5.0 24.7 1.0

Cadmium binding site 5 out of 5 in the Structure of Chloramphenicol 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 Structure of Chloramphenicol Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 4:Cd8404 b:59.2 occ:1.00 SG 4:CYS11 2.2 56.4 1.0 SG 4:CYS71 2.2 37.0 1.0 SG 4:CYS74 2.4 50.3 1.0 SG 4:CYS14 2.7 61.5 1.0 CB 4:CYS14 3.0 57.3 1.0 CB 4:CYS71 3.2 43.4 1.0 O 4:HOH8559 3.2 0.5 1.0 CB 4:CYS11 3.4 51.9 1.0 CB 4:CYS74 3.5 51.7 1.0 N 4:CYS14 3.5 55.8 1.0 CA 4:CYS14 3.8 56.6 1.0 N 4:CYS74 4.2 53.5 1.0 CA 4:CYS74 4.4 52.4 1.0 CB 4:HIS13 4.5 52.3 1.0 CA 4:CYS71 4.6 44.5 1.0 C 4:HIS13 4.7 54.8 1.0 CA 4:CYS11 4.8 51.6 1.0 OE1 4:GLN18 4.9 60.1 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