Cadmium in PDB 3i56: Co-Crystal Structure of Triacetyloleandomcyin Bound to the Large Ribosomal Subunit

The structure of Co-Crystal Structure of Triacetyloleandomcyin Bound to the Large Ribosomal Subunit, PDB code: 3i56 was solved by G.Gurel, G.Blaha, T.A.Steitz, P.B.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.430, 300.773, 575.414, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.3

The structure of Co-Crystal Structure of Triacetyloleandomcyin 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 Triacetyloleandomcyin Bound to the Large Ribosomal Subunit (pdb code 3i56). 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 Triacetyloleandomcyin Bound to the Large Ribosomal Subunit, PDB code: 3i56:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Co-Crystal Structure of Triacetyloleandomcyin 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 Triacetyloleandomcyin Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd8705 b:91.6 occ:1.00 O 0:HOH5650 2.6 28.5 1.0 ND1 O:HIS40 2.7 27.6 1.0 O O:HOH5322 3.0 28.8 1.0 CE1 O:HIS40 3.6 26.8 1.0 CG O:HIS40 3.7 28.5 1.0 CB O:HIS40 3.8 29.9 1.0 O 0:HOH3002 4.6 55.3 1.0 CZ O:ARG37 4.7 37.4 1.0 NE2 O:HIS40 4.8 26.0 1.0 CG O:ARG37 4.8 40.1 1.0 CD2 O:HIS40 4.8 27.5 1.0 NH1 O:ARG37 4.9 35.6 1.0 NH2 O:ARG37 4.9 36.4 1.0 CA O:GLY62 4.9 39.1 1.0 NE O:ARG37 5.0 38.6 1.0 O O:ARG37 5.0 37.9 1.0

Cadmium binding site 2 out of 5 in the Co-Crystal Structure of Triacetyloleandomcyin 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 Triacetyloleandomcyin Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd8701 b:58.4 occ:1.00 SG U:CYS32 2.4 20.7 1.0 SG U:CYS36 2.4 48.2 1.0 SG U:CYS6 2.5 48.2 1.0 SG U:CYS9 2.5 43.7 1.0 CB U:CYS6 3.4 49.0 1.0 CB U:CYS32 3.5 27.8 1.0 CB U:CYS9 3.5 44.1 1.0 CB U:CYS36 3.6 46.7 1.0 N U:CYS9 3.8 44.6 1.0 N U:CYS32 3.9 30.3 1.0 CA U:CYS9 4.2 44.8 1.0 CA U:CYS32 4.2 31.9 1.0 OG1 U:THR11 4.4 56.0 1.0 CB U:TYR8 4.6 41.8 1.0 OG U:SER33 4.6 39.7 1.0 N U:SER33 4.6 36.5 1.0 CA U:CYS6 4.8 49.5 1.0 N U:GLY10 4.8 46.8 1.0 C U:CYS32 4.9 35.0 1.0 C U:TYR8 4.9 44.0 1.0 CA U:CYS36 5.0 45.7 1.0

Cadmium binding site 3 out of 5 in the Co-Crystal Structure of Triacetyloleandomcyin 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 Triacetyloleandomcyin Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd8703 b:55.6 occ:1.00 SG Z:CYS84 2.3 39.2 1.0 SG Z:CYS81 2.4 54.5 1.0 SG Z:CYS63 2.5 54.1 1.0 SG Z:CYS66 2.7 65.4 1.0 CB Z:CYS63 3.3 54.3 1.0 CB Z:CYS81 3.3 56.0 1.0 CB Z:CYS84 3.4 44.7 1.0 CB Z:CYS66 3.5 66.1 1.0 N Z:CYS66 3.7 66.2 1.0 N Z:CYS84 3.9 48.6 1.0 CB Z:ASN65 4.1 65.6 1.0 CA Z:CYS66 4.2 65.8 1.0 CA Z:CYS84 4.2 46.0 1.0 CD2 Z:TYR83 4.6 58.7 1.0 C Z:ASN65 4.7 65.8 1.0 CB Z:TYR83 4.7 55.6 1.0 CB Z:TYR86 4.7 46.8 1.0 CA Z:CYS63 4.7 55.4 1.0 CA Z:CYS81 4.8 55.0 1.0 CA Z:ASN65 4.8 65.1 1.0 N Z:GLY67 4.9 66.2 1.0 N Z:ASN65 4.9 64.0 1.0 C Z:CYS84 4.9 47.0 1.0

Cadmium binding site 4 out of 5 in the Co-Crystal Structure of Triacetyloleandomcyin 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 Triacetyloleandomcyin Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8702 b:58.9 occ:1.00 SG 1:CYS37 2.3 27.4 1.0 SG 1:CYS34 2.4 25.4 1.0 SG 1:CYS22 2.5 28.4 1.0 SG 1:CYS19 2.7 30.8 1.0 CB 1:CYS19 3.2 26.8 1.0 CB 1:CYS34 3.2 18.4 1.0 CB 1:CYS37 3.3 20.2 1.0 CB 1:CYS22 3.4 27.6 1.0 N 1:CYS22 3.7 28.3 1.0 N 1:CYS37 3.9 21.0 1.0 CA 1:CYS37 4.1 21.2 1.0 CA 1:CYS22 4.1 27.6 1.0 CB 1:PHE39 4.3 29.5 1.0 CB 1:ARG21 4.5 27.9 1.0 C 1:ARG21 4.7 28.7 1.0 CA 1:CYS19 4.7 27.9 1.0 CA 1:CYS34 4.7 19.1 1.0 C 1:CYS37 4.7 21.0 1.0 N 1:GLY38 4.8 22.0 1.0 N 1:PHE39 4.8 26.5 1.0 C 1:CYS22 4.9 27.4 1.0 CA 1:ARG21 4.9 28.0 1.0 N 1:GLY23 4.9 27.1 1.0 CB 1:SER36 5.0 18.2 1.0 CD 1:ARG21 5.0 26.6 1.0 C 1:SER36 5.0 20.1 1.0 N 1:ARG21 5.0 28.3 1.0

Cadmium binding site 5 out of 5 in the Co-Crystal Structure of Triacetyloleandomcyin 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 Triacetyloleandomcyin Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd8704 b:56.2 occ:1.00 SG 3:CYS14 2.4 65.5 1.0 SG 3:CYS71 2.4 42.4 1.0 SG 3:CYS11 2.5 53.1 1.0 SG 3:CYS74 2.5 54.8 1.0 O 3:HOH6741 2.6 0.7 1.0 CB 3:CYS71 3.3 46.7 1.0 CB 3:CYS11 3.4 51.5 1.0 CB 3:CYS14 3.4 61.6 1.0 CB 3:CYS74 3.6 56.4 1.0 N 3:CYS74 4.1 56.1 1.0 N 3:CYS14 4.2 60.7 1.0 CA 3:CYS74 4.4 56.7 1.0 CA 3:CYS14 4.4 61.0 1.0 OE1 3:GLN18 4.7 59.2 1.0 O 3:HOH3785 4.7 11.6 1.0 CA 3:CYS71 4.8 47.7 1.0 CB 3:HIS13 4.8 58.1 1.0 CA 3:CYS11 4.9 51.5 1.0

G.Gurel, G.Blaha, T.A.Steitz, P.B.Moore. Structures of Triacetyloleandomycin and Mycalamide A Bind to the Large Ribosomal Subunit of Haloarcula Marismortui. Antimicrob.Agents Chemother. V. 53 5010 2009.
ISSN: ISSN 0066-4804
PubMed: 19738021
DOI: 10.1128/AAC.00817-09