Cadmium in PDB 1yi2: Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yi2 was solved by D.Tu, 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)	30.00 / 2.65
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.435, 299.989, 574.176, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.4

The structure of Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium	(Mg)	116 atoms
Potassium	(K)	2 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 atoms

The binding sites of Cadmium atom in the Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1yi2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yi2:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd8705 b:74.3 occ:1.00 O O:HOH5650 2.3 30.5 1.0 ND1 O:HIS40 2.5 35.1 1.0 O 0:HOH5998 2.7 27.5 1.0 CE1 O:HIS40 3.5 36.8 1.0 CG O:HIS40 3.5 35.0 1.0 CB O:HIS40 3.7 38.0 1.0 CG O:ARG37 4.4 51.8 1.0 O O:HOH3002 4.6 52.8 1.0 NE2 O:HIS40 4.6 36.9 1.0 CD2 O:HIS40 4.6 35.4 1.0 CZ O:ARG37 4.7 47.6 1.0 CB O:ARG37 4.7 48.8 1.0 NH1 O:ARG37 4.7 46.7 1.0 NE O:ARG37 4.8 49.7 1.0 CA O:ARG37 4.9 47.5 1.0 O O:ARG37 4.9 49.3 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd8701 b:67.3 occ:1.00 SG U:CYS32 2.4 42.7 1.0 SG U:CYS36 2.4 57.2 1.0 SG U:CYS6 2.5 54.8 1.0 SG U:CYS9 2.5 58.9 1.0 CB U:CYS6 3.2 58.1 1.0 CB U:CYS9 3.4 57.9 1.0 CB U:CYS36 3.6 56.7 1.0 CB U:CYS32 3.6 47.9 1.0 N U:CYS9 3.8 57.6 1.0 N U:CYS32 4.0 48.8 1.0 CA U:CYS9 4.2 58.4 1.0 OG1 U:THR11 4.3 66.7 1.0 CA U:CYS32 4.4 49.1 1.0 CB U:TYR8 4.5 53.8 1.0 OG U:SER33 4.5 52.5 1.0 CA U:CYS6 4.7 58.4 1.0 N U:SER33 4.7 51.1 1.0 N U:GLY10 4.8 60.1 1.0 C U:CYS32 4.9 50.9 1.0 C U:TYR8 4.9 56.6 1.0 CA U:CYS36 5.0 55.5 1.0 C U:CYS9 5.0 59.5 1.0

Cadmium binding site 3 out of 5 in the Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd8703 b:63.5 occ:1.00 SG Z:CYS60 2.2 59.3 1.0 SG Z:CYS39 2.3 61.9 1.0 SG Z:CYS57 2.5 63.0 1.0 SG Z:CYS42 2.8 76.3 1.0 CB Z:CYS39 3.2 63.8 1.0 CB Z:CYS57 3.2 64.8 1.0 CB Z:CYS60 3.3 61.0 1.0 N Z:CYS42 3.7 75.6 1.0 CB Z:CYS42 3.7 75.0 1.0 N Z:CYS60 3.7 63.4 1.0 CB Z:ASN41 3.9 76.0 1.0 CA Z:CYS60 4.1 62.1 1.0 CA Z:CYS42 4.3 75.2 1.0 CD2 Z:TYR59 4.5 73.2 1.0 CB Z:TYR59 4.5 68.8 1.0 CB Z:TYR62 4.6 59.3 1.0 CA Z:CYS39 4.6 65.5 1.0 CA Z:CYS57 4.7 63.6 1.0 C Z:ASN41 4.7 75.5 1.0 CA Z:ASN41 4.8 74.9 1.0 C Z:CYS60 4.8 62.7 1.0 C Z:TYR59 4.9 64.9 1.0 N Z:ASN41 4.9 73.8 1.0 CG Z:TYR59 5.0 71.4 1.0

Cadmium binding site 4 out of 5 in the Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8702 b:63.1 occ:1.00 SG 1:CYS37 2.4 39.8 1.0 SG 1:CYS22 2.5 39.5 1.0 SG 1:CYS34 2.5 37.9 1.0 SG 1:CYS19 2.6 35.5 1.0 CB 1:CYS22 3.1 37.2 1.0 CB 1:CYS19 3.1 34.0 1.0 CB 1:CYS34 3.2 31.3 1.0 CB 1:CYS37 3.2 32.2 1.0 N 1:CYS22 3.6 38.6 1.0 N 1:CYS37 3.8 33.6 1.0 CA 1:CYS22 3.9 38.1 1.0 CA 1:CYS37 4.1 33.3 1.0 CB 1:PHE39 4.3 37.4 1.0 CA 1:CYS19 4.6 37.1 1.0 CA 1:CYS34 4.6 33.1 1.0 CB 1:ARG21 4.7 37.9 1.0 C 1:ARG21 4.7 38.7 1.0 C 1:CYS22 4.7 37.7 1.0 CB 1:SER36 4.7 35.1 1.0 O 1:HOH8721 4.8 44.1 1.0 C 1:CYS37 4.8 32.8 1.0 N 1:GLY23 4.9 38.0 1.0 C 1:SER36 4.9 34.8 1.0 CD 1:ARG21 4.9 38.8 1.0 N 1:PHE39 4.9 34.9 1.0 N 1:GLY38 5.0 33.5 1.0 CA 1:ARG21 5.0 38.2 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Erythromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd8704 b:62.1 occ:1.00 SG 3:CYS71 2.4 49.9 1.0 SG 3:CYS74 2.4 69.1 1.0 SG 3:CYS11 2.4 61.0 1.0 SG 3:CYS14 2.5 73.4 1.0 O 3:HOH8865 3.0 0.2 1.0 CB 3:CYS71 3.1 54.9 1.0 CB 3:CYS14 3.3 67.7 1.0 CB 3:CYS74 3.4 65.5 1.0 CB 3:CYS11 3.5 59.2 1.0 N 3:CYS14 3.7 66.8 1.0 N 3:CYS74 4.1 65.7 1.0 CA 3:CYS14 4.1 67.5 1.0 CA 3:CYS74 4.3 65.2 1.0 OE1 3:GLN18 4.4 76.1 1.0 CB 3:HIS13 4.6 62.5 1.0 CA 3:CYS71 4.6 56.1 1.0 C 3:HIS13 4.8 65.8 1.0 O 3:HOH8839 4.9 48.3 1.0 CA 3:CYS11 4.9 57.6 1.0

D.Tu, G.Blaha, P.B.Moore, T.A.Steitz. Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide A Structural Explanation For Resistance. Cell(Cambridge,Mass.) V. 121 257 2005.
ISSN: ISSN 0092-8674
PubMed: 15851032
DOI: 10.1016/J.CELL.2005.02.005