Cadmium in PDB 1kc8: Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit

The structure of Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit, PDB code: 1kc8 was solved by J.L.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)	19.99 / 3.01
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.902, 300.474, 575.176, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.5

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

Magnesium	(Mg)	117 atoms
Potassium	(K)	3 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 atoms

The binding sites of Cadmium atom in the Co-Crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit (pdb code 1kc8). 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 Blasticidin S Bound to the 50S Ribosomal Subunit, PDB code: 1kc8:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ P:Cd8405 b:0.2 occ:1.00 ND1 P:HIS40 2.6 32.1 1.0 O A:HOH6251 2.9 54.2 1.0 O P:HOH5322 3.1 34.5 1.0 CE1 P:HIS40 3.5 31.8 1.0 CG P:HIS40 3.6 32.6 1.0 CB P:HIS40 3.8 35.2 1.0 CG P:ARG37 4.2 45.7 1.0 O A:HOH4339 4.4 49.2 1.0 CZ P:ARG37 4.6 46.0 1.0 NE2 P:HIS40 4.6 31.3 1.0 NH1 P:ARG37 4.7 45.5 1.0 CD2 P:HIS40 4.7 31.5 1.0 CB P:ARG37 4.7 43.6 1.0 NE P:ARG37 4.8 45.4 1.0 CA P:ARG37 4.8 42.5 1.0 O P:ARG37 4.9 41.4 1.0 CD P:ARG37 5.0 45.0 1.0

Cadmium binding site 2 out of 5 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ V:Cd8401 b:0.0 occ:1.00 CB V:CYS9 2.9 92.1 1.0 N V:CYS9 3.0 90.9 1.0 SG V:CYS36 3.0 96.9 1.0 SG V:CYS6 3.2 98.1 1.0 CB V:CYS36 3.3 91.7 1.0 SG V:CYS9 3.4 94.3 1.0 CA V:CYS9 3.5 91.0 1.0 CB V:CYS6 3.5 96.3 1.0 CB V:TYR8 3.8 88.5 1.0 SG V:CYS32 4.0 94.2 1.0 C V:TYR8 4.1 90.3 1.0 CD2 V:TYR8 4.2 87.7 1.0 N V:GLY10 4.3 89.9 1.0 CA V:TYR8 4.4 89.8 1.0 C V:CYS9 4.4 90.5 1.0 CG V:TYR8 4.5 87.9 1.0 N V:CYS32 4.5 90.0 1.0 CB V:CYS32 4.6 91.2 1.0 N V:TYR8 4.7 90.6 1.0 CA V:CYS36 4.7 91.0 1.0 OG1 V:THR11 4.9 88.2 1.0 CA V:CYS6 4.9 95.8 1.0 OG V:SER33 5.0 89.0 1.0

Cadmium binding site 3 out of 5 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8403 b:0.9 occ:1.00 CB 1:CYS42 2.8 0.8 1.0 SG 1:CYS42 3.3 0.7 1.0 CB 1:CYS60 3.4 95.9 1.0 SG 1:CYS60 3.4 0.5 1.0 N 1:CYS42 3.5 0.4 1.0 CA 1:CYS42 3.7 0.1 1.0 SG 1:CYS39 3.7 99.1 1.0 N 1:CYS60 3.9 96.0 1.0 CB 1:CYS39 4.0 97.2 1.0 CD2 1:HIS59 4.0 99.9 1.0 SG 1:CYS57 4.0 0.0 1.0 CB 1:CYS57 4.1 98.0 1.0 CA 1:CYS60 4.2 94.9 1.0 C 1:CYS42 4.5 0.6 1.0 CG1 1:VAL41 4.5 0.8 1.0 CB 1:HIS59 4.5 98.1 1.0 CB 1:VAL41 4.6 0.2 1.0 CG 1:HIS59 4.6 99.7 1.0 C 1:VAL41 4.7 0.6 1.0 O 1:CYS42 4.9 0.4 1.0 C 1:HIS59 4.9 96.6 1.0

Cadmium binding site 4 out of 5 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 2:Cd8402 b:50.1 occ:1.00 SG 2:CYS34 2.4 30.8 1.0 SG 2:CYS37 2.4 30.1 1.0 SG 2:CYS22 2.5 29.1 1.0 SG 2:CYS19 2.7 31.4 1.0 CB 2:CYS19 3.1 26.6 1.0 CB 2:CYS34 3.2 28.4 1.0 CB 2:CYS22 3.3 28.7 1.0 CB 2:CYS37 3.3 26.0 1.0 N 2:CYS22 3.6 29.8 1.0 N 2:CYS37 3.8 26.0 1.0 CA 2:CYS22 4.0 29.1 1.0 CA 2:CYS37 4.1 25.5 1.0 CB 2:PHE39 4.4 30.0 1.0 O 2:HOH1020 4.4 38.5 1.0 CB 2:ARG21 4.5 28.0 1.0 CA 2:CYS19 4.6 27.5 1.0 C 2:ARG21 4.6 28.6 1.0 CA 2:CYS34 4.7 27.4 1.0 C 2:CYS22 4.8 28.8 1.0 C 2:CYS37 4.8 24.7 1.0 CB 2:SER36 4.9 26.2 1.0 N 2:GLY23 4.9 28.2 1.0 CA 2:ARG21 4.9 28.6 1.0 C 2:SER36 4.9 25.5 1.0 N 2:ARG21 4.9 29.0 1.0 N 2:GLY38 5.0 24.3 1.0

Cadmium binding site 5 out of 5 in the Co-Crystal Structure of Blasticidin S 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 Blasticidin S Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 4:Cd8404 b:0.1 occ:1.00 CB 4:CYS14 2.6 0.8 1.0 SG 4:CYS11 2.8 0.4 1.0 CB 4:CYS11 2.9 0.8 1.0 SG 4:CYS71 3.2 0.1 1.0 N 4:CYS14 3.4 0.9 1.0 CA 4:CYS14 3.5 0.7 1.0 CB 4:CYS71 3.6 0.6 1.0 O 4:HOH8564 3.7 69.6 1.0 SG 4:CYS14 3.7 0.4 1.0 CB 4:CYS74 4.2 0.5 1.0 OE1 4:GLN18 4.3 0.6 1.0 NE2 4:GLN18 4.3 0.8 1.0 CD 4:GLN18 4.3 0.4 1.0 CA 4:CYS11 4.4 0.5 1.0 SG 4:CYS74 4.4 0.3 1.0 O 4:CYS11 4.6 0.1 1.0 O 4:GLU16 4.6 0.2 1.0 C 4:HIS13 4.6 0.8 1.0 C 4:CYS14 4.7 0.7 1.0 C 4:CYS11 4.8 0.2 1.0 CB 4:GLN18 4.8 0.3 1.0 N 4:CYS74 4.9 0.2 1.0 CB 4:HIS13 4.9 0.8 1.0 N 4:ASN15 4.9 0.8 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