Cadmium in PDB 2otl: Girodazole Bound to the Large Subunit of Haloarcula Marismortui

The structure of Girodazole Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otl 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)	49.36 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	213.077, 300.598, 575.055, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.8

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

Magnesium	(Mg)	116 atoms
Potassium	(K)	2 atoms
Chlorine	(Cl)	23 atoms
Sodium	(Na)	85 atoms

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

Cadmium binding site 1 out of 5 in the Girodazole 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 Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd8605 b:93.4 occ:1.00 ND1 O:HIS40 2.6 37.6 1.0 O O:HOH5650 2.7 42.1 1.0 O O:HOH5322 2.8 39.4 1.0 CE1 O:HIS40 3.5 38.0 1.0 CG O:HIS40 3.6 38.1 1.0 CB O:HIS40 3.9 40.9 1.0 CG O:ARG37 4.3 51.5 1.0 NE2 O:HIS40 4.6 38.2 1.0 CZ O:ARG37 4.7 50.0 1.0 CB O:ARG37 4.7 49.4 1.0 CD2 O:HIS40 4.7 37.6 1.0 NH1 O:ARG37 4.7 49.5 1.0 O O:HOH3002 4.7 50.3 1.0 CA O:ARG37 4.8 48.2 1.0 NE O:ARG37 4.8 51.8 1.0 O O:ARG37 4.8 48.4 1.0

Cadmium binding site 2 out of 5 in the Girodazole 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 Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd8601 b:62.1 occ:1.00 SG U:CYS36 2.3 57.8 1.0 SG U:CYS6 2.5 58.5 1.0 SG U:CYS32 2.5 43.1 1.0 SG U:CYS9 2.6 61.2 1.0 CB U:CYS6 3.2 60.6 1.0 CB U:CYS9 3.5 60.2 1.0 CB U:CYS36 3.5 56.7 1.0 CB U:CYS32 3.5 46.7 1.0 N U:CYS9 3.8 59.7 1.0 N U:CYS32 4.0 46.5 1.0 CA U:CYS9 4.2 60.4 1.0 CA U:CYS32 4.3 47.6 1.0 OG1 U:THR11 4.4 68.2 1.0 OG U:SER33 4.4 51.6 1.0 CB U:TYR8 4.5 57.1 1.0 N U:SER33 4.6 50.1 1.0 CA U:CYS6 4.7 61.0 1.0 C U:CYS32 4.8 49.7 1.0 N U:GLY10 4.8 62.4 1.0 CA U:CYS36 4.9 55.2 1.0 C U:TYR8 4.9 59.4 1.0

Cadmium binding site 3 out of 5 in the Girodazole 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 Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd8603 b:98.8 occ:1.00 SG Z:CYS60 2.5 90.2 1.0 SG Z:CYS39 2.6 80.1 1.0 SG Z:CYS57 2.7 87.1 1.0 CB Z:CYS60 2.9 89.7 1.0 SG Z:CYS42 3.0 0.7 1.0 C Z:ASN41 3.0 97.8 1.0 CB Z:CYS42 3.1 0.9 1.0 O Z:ASN41 3.1 97.8 1.0 N Z:CYS42 3.2 99.5 1.0 CB Z:ASN41 3.2 94.9 1.0 CB Z:CYS57 3.3 89.1 1.0 N Z:CYS60 3.5 91.4 1.0 CA Z:ASN41 3.5 96.2 1.0 CA Z:CYS60 3.7 89.1 1.0 CA Z:CYS42 3.7 0.1 1.0 CB Z:CYS39 3.9 87.9 1.0 N Z:ASN41 3.9 95.9 1.0 ND2 Z:ASN41 4.3 92.9 1.0 CG Z:ASN41 4.3 93.6 1.0 O Z:CYS42 4.4 0.9 1.0 CB Z:TYR62 4.4 77.2 1.0 C Z:CYS60 4.5 87.8 1.0 CD2 Z:TYR59 4.5 0.3 1.0 CB Z:TYR59 4.5 98.7 1.0 C Z:CYS42 4.6 0.7 1.0 C Z:TYR59 4.7 94.2 1.0 CA Z:CYS57 4.8 88.5 1.0 CG Z:TYR59 4.9 0.6 1.0 O Z:CYS57 4.9 90.0 1.0 N Z:ASP61 4.9 86.6 1.0 C Z:PRO40 5.0 95.7 1.0 N Z:TYR62 5.0 82.0 1.0

Cadmium binding site 4 out of 5 in the Girodazole 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 Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8602 b:63.6 occ:1.00 SG 1:CYS37 2.3 38.0 1.0 SG 1:CYS34 2.4 38.5 1.0 SG 1:CYS22 2.4 36.4 1.0 SG 1:CYS19 2.5 42.4 1.0 CB 1:CYS19 3.0 38.2 1.0 CB 1:CYS34 3.1 33.4 1.0 CB 1:CYS22 3.1 34.1 1.0 CB 1:CYS37 3.4 32.6 1.0 N 1:CYS22 3.6 36.2 1.0 N 1:CYS37 3.8 32.8 1.0 CA 1:CYS22 3.9 35.3 1.0 CA 1:CYS37 4.1 31.9 1.0 CB 1:PHE39 4.3 38.0 1.0 CA 1:CYS19 4.5 40.4 1.0 CA 1:CYS34 4.6 33.6 1.0 CB 1:ARG21 4.7 35.0 1.0 C 1:ARG21 4.7 37.0 1.0 CB 1:SER36 4.8 34.3 1.0 O 1:HOH1020 4.8 37.6 1.0 C 1:CYS22 4.8 36.1 1.0 C 1:CYS37 4.8 32.4 1.0 C 1:SER36 4.9 34.8 1.0 N 1:PHE39 4.9 36.8 1.0 N 1:GLY23 5.0 35.9 1.0 N 1:GLY38 5.0 34.2 1.0

Cadmium binding site 5 out of 5 in the Girodazole 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 Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd8604 b:68.2 occ:1.00 SG 3:CYS71 2.3 53.2 1.0 O 3:HOH8757 2.3 0.9 1.0 SG 3:CYS11 2.5 68.3 1.0 SG 3:CYS74 2.5 68.9 1.0 CB 3:CYS14 2.9 73.4 1.0 SG 3:CYS14 3.1 77.1 1.0 CB 3:CYS71 3.3 59.3 1.0 CB 3:CYS74 3.6 70.6 1.0 CB 3:CYS11 3.6 65.7 1.0 N 3:CYS14 3.8 73.3 1.0 CA 3:CYS14 3.9 73.3 1.0 N 3:CYS74 4.0 71.9 1.0 CA 3:CYS74 4.3 71.0 1.0 CA 3:CYS71 4.7 60.9 1.0 CB 3:HIS13 4.8 71.1 1.0 O 3:HOH8733 4.8 50.9 1.0 C 3:HIS13 4.9 72.6 1.0 NE2 3:GLN18 5.0 78.9 1.0 CA 3:CYS11 5.0 65.3 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