Cadmium in PDB 1m90: Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit

The structure of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit, PDB code: 1m90 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 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.661, 299.773, 573.684, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.2

The structure of Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit also contains other interesting chemical elements:

Magnesium	(Mg)	119 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 Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit (pdb code 1m90). 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 Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit, PDB code: 1m90:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin 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 Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ P:Cd8405 b:0.7 occ:1.00 ND1 P:HIS40 2.5 31.6 1.0 O A:HOH5786 2.9 80.6 1.0 O P:HOH5322 3.1 33.4 1.0 CE1 P:HIS40 3.4 32.8 1.0 CG P:HIS40 3.6 31.1 1.0 CB P:HIS40 3.8 33.5 1.0 CG P:ARG37 4.2 44.2 1.0 O A:HOH3873 4.5 57.0 1.0 NE2 P:HIS40 4.6 32.9 1.0 CD2 P:HIS40 4.7 31.3 1.0 CB P:ARG37 4.7 41.4 1.0 CZ P:ARG37 4.8 44.3 1.0 NE P:ARG37 4.8 44.7 1.0 CA P:ARG37 4.8 39.8 1.0 NH1 P:ARG37 4.9 44.0 1.0 CD P:ARG37 5.0 44.3 1.0

Cadmium binding site 2 out of 5 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin 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 Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ V:Cd8401 b:62.7 occ:1.00 SG V:CYS32 2.4 34.3 1.0 SG V:CYS36 2.4 53.5 1.0 SG V:CYS9 2.5 54.3 1.0 SG V:CYS6 2.6 56.1 1.0 CB V:CYS6 3.3 56.0 1.0 CB V:CYS9 3.4 54.1 1.0 CB V:CYS36 3.5 53.0 1.0 CB V:CYS32 3.6 41.7 1.0 N V:CYS9 3.8 55.1 1.0 N V:CYS32 4.0 43.7 1.0 CA V:CYS9 4.2 55.2 1.0 CA V:CYS32 4.4 44.0 1.0 OG1 V:THR11 4.4 60.0 1.0 OG V:SER33 4.4 47.5 1.0 CB V:TYR8 4.6 53.4 1.0 N V:SER33 4.7 47.2 1.0 CA V:CYS6 4.8 56.4 1.0 N V:GLY10 4.8 55.0 1.0 C V:CYS32 4.9 46.3 1.0 CA V:CYS36 4.9 51.4 1.0 C V:TYR8 4.9 55.0 1.0 C V:CYS9 5.0 55.4 1.0

Cadmium binding site 3 out of 5 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin 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 Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8403 b:62.4 occ:1.00 SG 1:CYS39 2.4 67.8 1.0 SG 1:CYS60 2.4 55.0 1.0 SG 1:CYS57 2.5 62.8 1.0 SG 1:CYS42 2.9 68.7 1.0 CB 1:CYS39 3.2 66.9 1.0 CB 1:CYS57 3.3 63.5 1.0 CB 1:CYS42 3.3 68.1 1.0 CB 1:CYS60 3.6 56.1 1.0 N 1:CYS42 3.7 68.8 1.0 N 1:CYS60 4.0 58.8 1.0 CA 1:CYS42 4.1 68.4 1.0 CA 1:CYS60 4.4 57.7 1.0 CB 1:HIS59 4.6 64.8 1.0 CA 1:CYS39 4.7 67.8 1.0 C 1:CYS42 4.7 68.7 1.0 CD2 1:HIS59 4.7 67.9 1.0 CB 1:VAL41 4.7 68.5 1.0 CB 1:TYR62 4.7 49.4 1.0 CA 1:CYS57 4.8 61.9 1.0 CG1 1:VAL41 4.8 68.7 1.0 C 1:VAL41 4.9 68.7 1.0 O 1:CYS42 5.0 70.0 1.0

Cadmium binding site 4 out of 5 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin 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 Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 2:Cd8402 b:56.0 occ:1.00 SG 2:CYS37 2.4 30.8 1.0 SG 2:CYS22 2.5 27.3 1.0 SG 2:CYS34 2.5 33.1 1.0 SG 2:CYS19 2.6 31.3 1.0 CB 2:CYS19 3.1 29.6 1.0 CB 2:CYS22 3.2 28.3 1.0 CB 2:CYS34 3.2 29.3 1.0 CB 2:CYS37 3.3 29.5 1.0 N 2:CYS22 3.6 30.8 1.0 N 2:CYS37 3.7 28.2 1.0 CA 2:CYS22 4.0 30.0 1.0 CA 2:CYS37 4.0 29.1 1.0 CB 2:PHE39 4.3 30.5 1.0 CA 2:CYS19 4.6 30.3 1.0 CB 2:ARG21 4.6 30.6 1.0 CA 2:CYS34 4.7 29.1 1.0 C 2:ARG21 4.7 30.9 1.0 C 2:CYS37 4.7 28.4 1.0 C 2:CYS22 4.7 29.7 1.0 CB 2:SER36 4.8 26.7 1.0 N 2:GLY23 4.8 29.6 1.0 C 2:SER36 4.8 27.9 1.0 N 2:PHE39 4.8 29.9 1.0 O 2:HOH1020 4.9 23.8 1.0 CD 2:ARG21 4.9 31.7 1.0 N 2:GLY38 4.9 27.9 1.0 CA 2:ARG21 5.0 30.7 1.0 N 2:ARG21 5.0 30.4 1.0

Cadmium binding site 5 out of 5 in the Co-Crystal Structure of Cca-Phe-Caproic Acid-Biotin and Sparsomycin 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 Cca-Phe-Caproic Acid-Biotin and Sparsomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 4:Cd8404 b:57.4 occ:1.00 SG 4:CYS71 2.3 48.8 1.0 SG 4:CYS74 2.4 59.4 1.0 SG 4:CYS11 2.5 50.9 1.0 SG 4:CYS14 2.7 63.3 1.0 O 4:HOH8561 3.0 0.1 1.0 CB 4:CYS71 3.1 51.6 1.0 CB 4:CYS14 3.1 59.7 1.0 CB 4:CYS74 3.4 57.4 1.0 CB 4:CYS11 3.5 49.6 1.0 N 4:CYS14 3.7 59.2 1.0 CA 4:CYS14 4.0 59.2 1.0 N 4:CYS74 4.0 58.7 1.0 CA 4:CYS74 4.3 57.7 1.0 CA 4:CYS71 4.5 52.0 1.0 CB 4:HIS13 4.7 58.7 1.0 C 4:HIS13 4.9 59.0 1.0 OE1 4:GLN18 4.9 63.1 1.0 CA 4:CYS11 5.0 50.3 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