Cadmium in PDB 2otj: 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui

The structure of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otj was solved by G.Blaha, S.J.Schroeder, J.Tirado-Rives, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.70 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.738, 299.519, 573.593, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.8

The structure of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium	(Mg)	117 atoms
Potassium	(K)	2 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 atoms

The binding sites of Cadmium atom in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui (pdb code 2otj). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otj:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd8705 b:0.9 occ:1.00 ND1 O:HIS40 2.7 41.7 1.0 O O:HOH5650 3.0 79.3 1.0 CE1 O:HIS40 3.5 41.4 1.0 CG O:HIS40 3.7 42.3 1.0 CB O:HIS40 4.0 44.5 1.0 O 0:HOH4372 4.6 68.3 1.0 CD1 O:LEU7 4.6 54.4 1.0 NE2 O:HIS40 4.7 41.1 1.0 CD2 O:HIS40 4.8 42.0 1.0 CG1 O:VAL79 4.8 52.6 1.0 O 0:HOH6049 4.8 58.4 1.0 CD2 O:LEU33 4.8 56.0 1.0 CG O:ARG37 5.0 53.0 1.0 CA O:GLY62 5.0 48.5 1.0 CB O:VAL79 5.0 52.6 1.0

Cadmium binding site 2 out of 5 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd8701 b:67.9 occ:1.00 SG U:CYS9 2.3 60.3 1.0 SG U:CYS32 2.4 48.9 1.0 SG U:CYS6 2.5 61.1 1.0 SG U:CYS36 2.5 58.1 1.0 CB U:CYS6 3.1 62.2 1.0 CB U:CYS9 3.2 60.6 1.0 CB U:CYS32 3.5 50.5 1.0 CB U:CYS36 3.6 58.8 1.0 N U:CYS9 3.6 60.4 1.0 CA U:CYS9 4.0 60.5 1.0 N U:CYS32 4.0 51.8 1.0 CA U:CYS32 4.3 52.0 1.0 OG1 U:THR11 4.4 63.9 1.0 CB U:TYR8 4.5 59.3 1.0 CA U:CYS6 4.6 62.6 1.0 OG U:SER33 4.7 54.7 1.0 N U:GLY10 4.7 60.7 1.0 N U:SER33 4.8 53.8 1.0 C U:CYS9 4.8 60.6 1.0 C U:TYR8 4.8 60.3 1.0 C U:CYS32 4.9 53.2 1.0 CD2 U:TYR8 5.0 56.5 1.0 CA U:CYS36 5.0 59.0 1.0

Cadmium binding site 3 out of 5 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd8703 b:71.6 occ:1.00 SG Z:CYS39 2.2 67.0 1.0 SG Z:CYS60 2.2 66.2 1.0 SG Z:CYS57 2.6 68.8 1.0 SG Z:CYS42 2.8 76.6 1.0 CB Z:CYS39 3.0 68.4 1.0 CB Z:CYS57 3.2 68.2 1.0 CB Z:CYS60 3.4 66.1 1.0 N Z:CYS60 3.7 67.2 1.0 CB Z:CYS42 3.7 75.1 1.0 N Z:CYS42 3.8 74.0 1.0 CA Z:CYS60 4.1 66.7 1.0 CB Z:ASN41 4.1 73.6 1.0 CA Z:CYS42 4.3 74.4 1.0 CB Z:TYR59 4.3 69.5 1.0 CA Z:CYS39 4.4 69.5 1.0 CD2 Z:TYR59 4.6 71.5 1.0 CA Z:CYS57 4.7 67.6 1.0 CB Z:TYR62 4.7 62.0 1.0 C Z:TYR59 4.8 68.0 1.0 C Z:ASN41 4.8 73.7 1.0 C Z:CYS60 4.8 66.3 1.0 C Z:CYS39 4.9 70.3 1.0 CA Z:ASN41 4.9 73.1 1.0 CG Z:TYR59 4.9 71.0 1.0 N Z:ASN41 4.9 72.2 1.0 N Z:ASP61 5.0 66.0 1.0

Cadmium binding site 4 out of 5 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8702 b:65.5 occ:1.00 SG 1:CYS34 2.4 32.5 1.0 SG 1:CYS37 2.4 37.6 1.0 SG 1:CYS22 2.4 40.9 1.0 SG 1:CYS19 2.5 36.9 1.0 CB 1:CYS19 3.0 36.7 1.0 CB 1:CYS34 3.2 32.5 1.0 CB 1:CYS22 3.3 40.2 1.0 CB 1:CYS37 3.4 33.5 1.0 N 1:CYS22 3.7 40.7 1.0 N 1:CYS37 3.9 33.2 1.0 CA 1:CYS22 4.0 40.7 1.0 CA 1:CYS37 4.2 33.4 1.0 CB 1:PHE39 4.2 37.1 1.0 CA 1:CYS19 4.5 36.6 1.0 CA 1:CYS34 4.6 33.8 1.0 CB 1:ARG21 4.7 39.2 1.0 C 1:CYS22 4.7 40.5 1.0 N 1:GLY23 4.7 39.5 1.0 C 1:ARG21 4.8 40.2 1.0 C 1:CYS37 4.9 33.3 1.0 CB 1:SER36 4.9 33.1 1.0 N 1:PHE39 4.9 35.4 1.0 O 1:GLU24 4.9 41.2 1.0 O 1:HOH8720 5.0 26.4 1.0 C 1:SER36 5.0 32.9 1.0 N 1:GLU24 5.0 41.3 1.0 N 1:GLY38 5.0 32.8 1.0 C 1:CYS19 5.0 37.4 1.0

Cadmium binding site 5 out of 5 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd8704 b:66.0 occ:1.00 SG 3:CYS74 2.3 69.5 1.0 SG 3:CYS71 2.3 61.6 1.0 SG 3:CYS11 2.5 64.3 1.0 SG 3:CYS14 2.6 73.3 1.0 O 3:HOH8854 3.0 0.6 1.0 CB 3:CYS14 3.0 70.7 1.0 CB 3:CYS71 3.2 62.9 1.0 N 3:CYS14 3.4 70.3 1.0 CB 3:CYS74 3.5 68.0 1.0 CB 3:CYS11 3.5 63.7 1.0 CA 3:CYS14 3.7 70.5 1.0 N 3:CYS74 4.1 68.5 1.0 CA 3:CYS74 4.3 67.9 1.0 CB 3:HIS13 4.4 70.0 1.0 C 3:HIS13 4.6 70.3 1.0 CA 3:CYS71 4.6 63.1 1.0 CG 3:GLN18 4.8 68.4 1.0 O 3:HOH8833 4.9 55.0 1.0 CA 3:HIS13 4.9 69.9 1.0 CA 3:CYS11 4.9 64.2 1.0

S.J.Schroeder, G.Blaha, J.Tirado-Rives, T.A.Steitz, P.B.Moore. The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula Marismortui: 13-Deoxytedanolide and Girodazole. J.Mol.Biol. V. 367 1471 2007.
ISSN: ISSN 0022-2836
PubMed: 17321546
DOI: 10.1016/J.JMB.2007.01.081