Cadmium in PDB 1q82: Crystal Structure of Cc-Puromycin Bound to the A-Site of the 50S Ribosomal Subunit

The structure of Crystal Structure of Cc-Puromycin Bound to the A-Site of the 50S Ribosomal Subunit, PDB code: 1q82 was solved by J.L.Hansen, T.M.Schmeing, 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 / 2.98
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	213.163, 301.288, 575.397, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.1

The structure of Crystal Structure of Cc-Puromycin Bound to the A-Site of 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 Crystal Structure of Cc-Puromycin Bound to the A-Site of the 50S Ribosomal Subunit (pdb code 1q82). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of Cc-Puromycin Bound to the A-Site of the 50S Ribosomal Subunit, PDB code: 1q82:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of Cc-Puromycin Bound to the A-Site of 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 Crystal Structure of Cc-Puromycin Bound to the A-Site of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ P:Cd8405 b:89.0 occ:1.00 ND1 P:HIS40 2.5 33.1 1.0 O P:HOH5322 2.7 40.5 1.0 O P:HOH5650 2.9 30.0 1.0 CG P:HIS40 3.4 34.4 1.0 CE1 P:HIS40 3.4 34.2 1.0 CB P:HIS40 3.6 36.1 1.0 CG P:ARG37 4.4 49.9 1.0 NE2 P:HIS40 4.6 35.6 1.0 CD2 P:HIS40 4.6 34.2 1.0 CZ P:ARG37 4.7 51.0 1.0 NH1 P:ARG37 4.7 49.0 1.0 O A:HOH3848 4.8 43.3 1.0 CB P:ARG37 4.8 48.3 1.0 CA P:ARG37 4.8 47.5 1.0 O P:ARG37 4.8 46.7 1.0 NE P:ARG37 4.9 50.4 1.0 NH2 P:ARG37 5.0 52.3 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of Cc-Puromycin Bound to the A-Site of 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 Crystal Structure of Cc-Puromycin Bound to the A-Site of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ V:Cd8401 b:0.3 occ:1.00 SG V:CYS36 3.0 97.3 1.0 CB V:CYS9 3.1 92.3 1.0 SG V:CYS6 3.1 0.2 1.0 SG V:CYS32 3.3 89.4 1.0 CB V:CYS6 3.5 99.5 1.0 SG V:CYS9 3.5 92.8 1.0 CB V:CYS36 3.6 94.9 1.0 N V:CYS9 3.6 92.4 1.0 CA V:CYS9 3.9 92.1 1.0 CB V:CYS32 4.1 90.7 1.0 OG1 V:THR11 4.2 91.5 1.0 N V:CYS32 4.4 91.0 1.0 CB V:TYR8 4.5 90.5 1.0 OG V:SER33 4.6 92.8 1.0 N V:GLY10 4.6 91.9 1.0 C V:CYS9 4.7 92.0 1.0 CA V:CYS32 4.8 91.5 1.0 C V:TYR8 4.8 92.2 1.0 CD2 V:TYR8 4.8 87.0 1.0 N V:SER33 4.9 92.8 1.0

Cadmium binding site 3 out of 5 in the Crystal Structure of Cc-Puromycin Bound to the A-Site of 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 Crystal Structure of Cc-Puromycin Bound to the A-Site of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8403 b:0.5 occ:1.00 CB 1:CYS42 3.1 0.5 1.0 CB 1:CYS60 3.2 0.6 1.0 N 1:CYS60 3.6 0.1 1.0 SG 1:CYS60 3.6 0.4 1.0 SG 1:CYS42 3.6 0.1 1.0 SG 1:CYS39 3.7 1.0 1.0 N 1:CYS42 3.8 0.9 1.0 SG 1:CYS57 3.9 0.8 1.0 CD2 1:HIS59 4.0 0.4 1.0 CA 1:CYS60 4.0 0.8 1.0 CA 1:CYS42 4.0 0.0 1.0 CB 1:CYS57 4.0 1.0 1.0 CB 1:CYS39 4.1 0.0 1.0 CB 1:HIS59 4.3 0.1 1.0 CG 1:HIS59 4.5 0.7 1.0 C 1:HIS59 4.6 0.2 1.0 CG1 1:VAL41 4.7 0.6 1.0 CB 1:VAL41 4.8 0.0 1.0 C 1:CYS42 4.8 0.8 1.0 C 1:CYS60 4.9 0.3 1.0 C 1:VAL41 5.0 0.5 1.0 CB 1:TYR62 5.0 0.3 1.0

Cadmium binding site 4 out of 5 in the Crystal Structure of Cc-Puromycin Bound to the A-Site of 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 Crystal Structure of Cc-Puromycin Bound to the A-Site of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 2:Cd8402 b:57.1 occ:1.00 SG 2:CYS37 2.3 34.4 1.0 SG 2:CYS22 2.4 31.8 1.0 SG 2:CYS19 2.5 38.4 1.0 SG 2:CYS34 2.6 31.2 1.0 CB 2:CYS19 3.0 32.7 1.0 CB 2:CYS34 3.2 30.4 1.0 CB 2:CYS22 3.2 31.2 1.0 CB 2:CYS37 3.3 31.2 1.0 N 2:CYS22 3.6 32.1 1.0 N 2:CYS37 3.8 30.4 1.0 CA 2:CYS22 4.0 31.8 1.0 CA 2:CYS37 4.1 30.6 1.0 CB 2:PHE39 4.3 39.5 1.0 O 2:HOH1020 4.4 22.8 1.0 CB 2:ARG21 4.5 32.1 1.0 CA 2:CYS19 4.5 32.7 1.0 C 2:ARG21 4.6 32.4 1.0 CA 2:CYS34 4.6 31.2 1.0 CB 2:SER36 4.7 29.6 1.0 C 2:CYS22 4.8 32.3 1.0 C 2:CYS37 4.8 30.5 1.0 N 2:GLY23 4.8 32.3 1.0 CA 2:ARG21 4.9 32.1 1.0 CD 2:ARG21 4.9 31.5 1.0 N 2:ARG21 4.9 32.6 1.0 C 2:SER36 4.9 29.9 1.0 N 2:GLY38 4.9 31.5 1.0 N 2:PHE39 4.9 36.4 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of Cc-Puromycin Bound to the A-Site of 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 Crystal Structure of Cc-Puromycin Bound to the A-Site of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 4:Cd8404 b:0.5 occ:1.00 CB 4:CYS14 2.8 0.8 1.0 CB 4:CYS11 3.1 0.4 1.0 SG 4:CYS11 3.1 0.6 1.0 N 4:CYS14 3.2 0.4 1.0 SG 4:CYS71 3.3 0.8 1.0 CB 4:CYS71 3.6 0.3 1.0 CA 4:CYS14 3.6 0.9 1.0 O 4:HOH8559 3.8 85.7 1.0 CB 4:CYS74 4.0 0.3 1.0 SG 4:CYS14 4.0 0.4 1.0 SG 4:CYS74 4.0 0.5 1.0 OE1 4:GLN18 4.3 0.4 1.0 C 4:HIS13 4.4 0.8 1.0 CA 4:CYS11 4.5 1.0 1.0 CB 4:HIS13 4.5 0.0 1.0 CD 4:GLN18 4.6 0.2 1.0 NE2 4:GLN18 4.6 1.0 1.0 O 4:CYS11 4.7 0.5 1.0 C 4:CYS14 4.7 0.1 1.0 C 4:CYS11 4.8 0.9 1.0 CA 4:HIS13 4.9 0.5 1.0 O 4:GLU16 4.9 0.8 1.0 N 4:ASN15 4.9 0.9 1.0 N 4:CYS74 4.9 0.1 1.0 N 4:HIS13 4.9 0.1 1.0

J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz. Structural Insights Into Peptide Bond Formation Proc.Natl.Acad.Sci.Usa V. 99 11670 2002.
ISSN: ISSN 0027-8424
PubMed: 12185246
DOI: 10.1073/PNAS.172404099