Cadmium in PDB 3g71: Co-Crystal Structure of Bruceantin Bound to the Large Ribosomal Subunit

The structure of Co-Crystal Structure of Bruceantin Bound to the Large Ribosomal Subunit, PDB code: 3g71 was solved by G.Gurel, G.Blaha, 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)	49.76 / 2.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.207, 299.544, 574.251, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.3

The structure of Co-Crystal Structure of Bruceantin Bound to the Large Ribosomal Subunit also contains other interesting chemical elements:

Strontium	(Sr)	108 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-Crystal Structure of Bruceantin Bound to the Large Ribosomal Subunit (pdb code 3g71). 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 Bruceantin Bound to the Large Ribosomal Subunit, PDB code: 3g71:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Co-Crystal Structure of Bruceantin Bound to the Large 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 Bruceantin Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd8705 b:0.2 occ:1.00 ND1 O:HIS40 2.6 37.4 1.0 O 0:HOH5650 2.6 49.0 1.0 O 0:HOH5322 3.1 56.5 1.0 CE1 O:HIS40 3.5 37.6 1.0 CG O:HIS40 3.6 38.2 1.0 CB O:HIS40 3.8 43.2 1.0 O 0:HOH3002 4.5 67.3 1.0 NE2 O:HIS40 4.6 37.3 1.0 CD2 O:HIS40 4.7 37.8 1.0 CZ O:ARG37 4.8 55.5 1.0 CG O:ARG37 4.9 56.8 1.0 CA O:GLY62 4.9 56.4 1.0 NH2 O:ARG37 4.9 53.9 1.0 O O:ARG37 5.0 52.5 1.0

Cadmium binding site 2 out of 5 in the Co-Crystal Structure of Bruceantin Bound to the Large 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 Bruceantin Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd8701 b:71.8 occ:1.00 SG U:CYS32 2.5 54.9 1.0 SG U:CYS36 2.6 68.2 1.0 SG U:CYS9 2.6 71.0 1.0 SG U:CYS6 2.6 71.4 1.0 CB U:CYS9 3.4 70.6 1.0 CB U:CYS6 3.4 72.3 1.0 CB U:CYS32 3.4 57.6 1.0 CB U:CYS36 3.6 66.1 1.0 N U:CYS9 3.8 71.3 1.0 N U:CYS32 3.9 57.9 1.0 CA U:CYS9 4.2 71.2 1.0 CA U:CYS32 4.2 58.1 1.0 OG1 U:THR11 4.3 81.9 1.0 N U:SER33 4.6 61.3 1.0 OG U:SER33 4.6 64.3 1.0 CB U:TYR8 4.6 68.8 1.0 N U:GLY10 4.8 72.4 1.0 C U:CYS32 4.9 60.8 1.0 CA U:CYS6 4.9 71.8 1.0 C U:TYR8 5.0 70.5 1.0 C U:CYS9 5.0 72.1 1.0

Cadmium binding site 3 out of 5 in the Co-Crystal Structure of Bruceantin Bound to the Large 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 Bruceantin Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd8703 b:0.1 occ:1.00 SG Z:CYS84 2.9 0.8 1.0 SG Z:CYS66 3.0 0.2 1.0 SG Z:CYS81 3.4 0.5 1.0 SG Z:CYS63 3.5 0.1 1.0 N Z:CYS84 3.5 0.1 1.0 CB Z:CYS81 3.6 1.0 1.0 CB Z:CYS84 3.7 0.6 1.0 CB Z:TYR83 3.8 0.8 1.0 CB Z:CYS63 4.1 1.0 1.0 CA Z:CYS84 4.1 0.6 1.0 CD2 Z:TYR83 4.2 0.7 1.0 CB Z:CYS66 4.4 0.3 1.0 CB Z:TYR86 4.4 0.3 1.0 C Z:TYR83 4.5 0.1 1.0 CB Z:ASN65 4.5 0.7 1.0 CG Z:TYR83 4.5 0.4 1.0 CA Z:TYR83 4.6 0.7 1.0 N Z:CYS66 4.7 0.9 1.0 C Z:CYS84 4.8 0.3 1.0 N Z:TYR83 4.8 0.4 1.0 CA Z:CYS81 5.0 0.8 1.0

Cadmium binding site 4 out of 5 in the Co-Crystal Structure of Bruceantin Bound to the Large 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 Bruceantin Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8702 b:72.7 occ:1.00 SG 1:CYS37 2.4 41.4 1.0 SG 1:CYS22 2.4 42.7 1.0 SG 1:CYS34 2.5 42.6 1.0 SG 1:CYS19 2.6 45.2 1.0 CB 1:CYS19 3.2 42.2 1.0 CB 1:CYS34 3.3 39.0 1.0 CB 1:CYS22 3.3 42.1 1.0 CB 1:CYS37 3.4 41.0 1.0 N 1:CYS22 3.8 41.9 1.0 N 1:CYS37 3.8 40.5 1.0 CA 1:CYS22 4.1 42.1 1.0 CA 1:CYS37 4.2 40.4 1.0 CB 1:PHE39 4.3 45.3 1.0 CB 1:ARG21 4.6 40.0 1.0 CA 1:CYS19 4.7 43.2 1.0 CA 1:CYS34 4.7 40.2 1.0 CB 1:SER36 4.7 39.1 1.0 C 1:CYS37 4.8 38.7 1.0 C 1:ARG21 4.8 41.2 1.0 N 1:PHE39 4.9 42.6 1.0 C 1:CYS22 4.9 41.1 1.0 N 1:GLY23 4.9 41.1 1.0 O 1:HOH1020 4.9 45.8 1.0 N 1:GLY38 4.9 39.1 1.0 C 1:SER36 4.9 40.0 1.0

Cadmium binding site 5 out of 5 in the Co-Crystal Structure of Bruceantin Bound to the Large 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 Bruceantin Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd8704 b:94.4 occ:1.00 SG 3:CYS74 2.6 0.9 1.0 SG 3:CYS71 2.6 86.7 1.0 SG 3:CYS11 2.7 86.2 1.0 CB 3:CYS14 2.9 96.0 1.0 CB 3:CYS71 3.6 87.8 1.0 OE1 3:GLN18 3.6 95.5 1.0 CB 3:CYS11 3.6 84.5 1.0 SG 3:CYS14 3.8 98.5 1.0 O 3:HOH6741 3.8 0.0 1.0 CB 3:CYS74 3.9 99.3 1.0 N 3:CYS14 3.9 96.2 1.0 CA 3:CYS14 4.0 96.2 1.0 N 3:CYS74 4.3 98.0 1.0 CD 3:GLN18 4.6 93.9 1.0 CA 3:CYS74 4.7 98.7 1.0 CB 3:HIS13 4.8 93.8 1.0 O 3:HOH3785 4.9 54.3 1.0 C 3:HIS13 5.0 95.5 1.0

G.Gurel, G.Blaha, P.B.Moore, T.A.Steitz. U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: the Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome. J.Mol.Biol. V. 389 146 2009.
ISSN: ISSN 0022-2836
PubMed: 19362093
DOI: 10.1016/J.JMB.2009.04.005