Cadmium in PDB 3cd6: Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin

The structure of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin, PDB code: 3cd6 was solved by G.Blaha, G.Gurel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.95 / 2.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.805, 299.997, 576.002, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.1

The structure of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin also contains other interesting chemical elements:

Strontium	(Sr)	107 atoms
Magnesium	(Mg)	93 atoms
Potassium	(K)	2 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	75 atoms

The binding sites of Cadmium atom in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin (pdb code 3cd6). 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-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin, PDB code: 3cd6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd8705 b:88.6 occ:1.00 ND1 O:HIS40 2.5 36.7 1.0 O 0:HOH6297 2.6 52.7 1.0 O 0:HOH6064 2.9 41.5 1.0 CE1 O:HIS40 3.4 35.9 1.0 CG O:HIS40 3.6 36.2 1.0 CB O:HIS40 3.8 39.5 1.0 NE2 O:HIS40 4.5 37.0 1.0 O 0:HOH4384 4.6 65.4 1.0 CD2 O:HIS40 4.7 36.4 1.0 CG O:ARG37 4.7 46.2 1.0 CZ O:ARG37 4.8 42.2 1.0 NE O:ARG37 4.9 44.7 1.0 NH1 O:ARG37 5.0 41.7 1.0 CB O:ARG37 5.0 44.9 1.0

Cadmium binding site 2 out of 5 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd8701 b:78.0 occ:1.00 SG U:CYS36 2.6 73.7 1.0 SG U:CYS32 2.7 63.8 1.0 SG U:CYS6 2.8 80.7 1.0 SG U:CYS9 2.8 78.1 1.0 CB U:CYS9 3.3 77.6 1.0 CB U:CYS6 3.5 80.4 1.0 CB U:CYS32 3.5 63.9 1.0 CB U:CYS36 3.6 71.1 1.0 N U:CYS9 3.9 77.0 1.0 N U:CYS32 3.9 63.5 1.0 CA U:CYS9 4.2 77.3 1.0 CA U:CYS32 4.2 64.6 1.0 OG1 U:THR11 4.3 83.0 1.0 OG U:SER33 4.4 68.6 1.0 N U:SER33 4.6 66.2 1.0 CB U:TYR8 4.8 73.5 1.0 C U:CYS32 4.8 65.6 1.0 N U:GLY10 4.8 78.7 1.0 C U:CYS9 5.0 77.7 1.0 CA U:CYS6 5.0 80.3 1.0

Cadmium binding site 3 out of 5 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd8703 b:0.0 occ:1.00 SG Z:CYS84 2.9 0.0 1.0 SG Z:CYS66 3.2 0.7 1.0 CB Z:ASN65 3.4 0.6 1.0 SG Z:CYS81 3.4 0.2 1.0 N Z:CYS66 3.5 0.9 1.0 CB Z:CYS66 3.6 0.2 1.0 CB Z:CYS84 3.9 0.9 1.0 CD2 Z:TYR83 4.0 0.7 1.0 C Z:ASN65 4.2 0.8 1.0 CA Z:CYS66 4.2 0.8 1.0 CA Z:ASN65 4.2 0.7 1.0 N Z:CYS84 4.3 0.4 1.0 CG Z:ASN65 4.5 0.8 1.0 CB Z:CYS81 4.5 0.4 1.0 CB Z:CYS63 4.5 0.3 1.0 SG Z:CYS63 4.5 1.0 1.0 CB Z:TYR83 4.6 0.5 1.0 N Z:ASN65 4.6 0.3 1.0 ND2 Z:ASN65 4.7 0.5 1.0 CA Z:CYS84 4.7 0.8 1.0 CG Z:TYR83 4.8 0.2 1.0 CE2 Z:TYR83 4.8 0.8 1.0 CB Z:TYR86 5.0 0.2 1.0

Cadmium binding site 4 out of 5 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8702 b:54.2 occ:1.00 SG 1:CYS37 2.4 33.7 1.0 SG 1:CYS34 2.5 34.2 1.0 SG 1:CYS22 2.5 34.6 1.0 SG 1:CYS19 2.6 32.5 1.0 CB 1:CYS19 3.1 30.2 1.0 CB 1:CYS22 3.2 31.7 1.0 CB 1:CYS37 3.3 31.0 1.0 CB 1:CYS34 3.3 31.6 1.0 N 1:CYS22 3.7 33.0 1.0 N 1:CYS37 3.9 30.5 1.0 CA 1:CYS22 4.0 31.8 1.0 CA 1:CYS37 4.1 29.5 1.0 CB 1:PHE39 4.4 32.9 1.0 CB 1:ARG21 4.6 29.9 1.0 CA 1:CYS19 4.6 33.5 1.0 CA 1:CYS34 4.7 31.6 1.0 C 1:ARG21 4.7 32.2 1.0 C 1:CYS37 4.8 28.7 1.0 C 1:CYS22 4.8 30.4 1.0 N 1:GLY38 4.8 29.3 1.0 N 1:PHE39 4.9 31.8 1.0 CB 1:SER36 4.9 31.2 1.0 N 1:GLY23 4.9 31.1 1.0 C 1:SER36 4.9 30.9 1.0 CD 1:ARG21 5.0 28.2 1.0

Cadmium binding site 5 out of 5 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd8704 b:0.0 occ:1.00 CB 3:CYS11 3.1 0.3 1.0 CB 3:CYS14 3.2 0.8 1.0 CB 3:GLN18 3.3 0.8 1.0 SG 3:CYS71 3.5 0.3 1.0 SG 3:CYS11 3.5 0.3 1.0 SG 3:CYS14 3.7 0.1 1.0 CG 3:GLN18 3.7 0.3 1.0 NE2 3:GLN18 3.8 0.0 1.0 CD 3:GLN18 3.9 0.3 1.0 O 3:GLU16 4.0 0.7 1.0 N 3:GLN18 4.3 0.2 1.0 CA 3:GLN18 4.3 0.4 1.0 CG 3:GLU16 4.4 0.2 1.0 CA 3:CYS11 4.6 0.6 1.0 OE1 3:GLN18 4.6 1.0 1.0 CA 3:CYS14 4.6 0.5 1.0 SG 3:CYS74 4.6 0.6 1.0 C 3:GLU16 4.7 0.7 1.0 CB 3:CYS71 4.8 0.1 1.0 CE1 3:HIS20 4.9 0.7 1.0 N 3:CYS11 4.9 0.4 1.0 N 3:CYS14 5.0 0.1 1.0 C 3:HIS17 5.0 0.1 1.0

G.Blaha, G.Gurel, S.J.Schroeder, P.B.Moore, T.A.Steitz. Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant. J.Mol.Biol. V. 379 505 2008.
ISSN: ISSN 0022-2836
PubMed: 18455733
DOI: 10.1016/J.JMB.2008.03.075