Cadmium in PDB 2qa4: A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit

The structure of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit, PDB code: 2qa4 was solved by T.A.Steitz, J.M.Kavran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	214.490, 302.432, 578.056, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 28.8

The structure of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit 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 A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit (pdb code 2qa4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit, PDB code: 2qa4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S 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 A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd67 b:0.3 occ:1.00 SG U:CYS36 2.7 0.7 1.0 CB U:CYS9 2.8 0.2 1.0 SG U:CYS6 3.0 0.2 1.0 SG U:CYS32 3.0 0.4 1.0 CB U:CYS6 3.6 0.1 1.0 N U:CYS9 3.7 0.1 1.0 CB U:CYS36 3.8 0.4 1.0 CA U:CYS9 3.8 0.5 1.0 SG U:CYS9 4.0 0.5 1.0 OG1 U:THR11 4.0 0.8 1.0 CB U:CYS32 4.2 0.6 1.0 N U:CYS32 4.3 0.4 1.0 C U:CYS9 4.7 0.1 1.0 N U:GLY10 4.7 0.1 1.0 CB U:TYR8 4.7 0.4 1.0 OG U:SER33 4.8 0.5 1.0 CD2 U:TYR8 4.8 0.9 1.0 CA U:CYS32 4.8 0.3 1.0 C U:TYR8 4.9 0.8 1.0

Cadmium binding site 2 out of 5 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S 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 A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd57 b:76.1 occ:1.00 SG 1:CYS22 2.1 43.9 1.0 SG 1:CYS19 2.2 54.9 1.0 SG 1:CYS37 2.5 44.6 1.0 SG 1:CYS34 2.7 50.8 1.0 CB 1:CYS19 2.7 47.6 1.0 CB 1:CYS22 3.1 42.9 1.0 CB 1:CYS37 3.1 39.3 1.0 N 1:CYS22 3.4 43.6 1.0 CB 1:CYS34 3.4 44.1 1.0 CA 1:CYS22 3.7 43.5 1.0 N 1:CYS37 3.9 38.9 1.0 CA 1:CYS37 4.1 39.1 1.0 CA 1:CYS19 4.2 45.2 1.0 N 1:GLY23 4.4 43.6 1.0 CB 1:PHE39 4.4 54.0 1.0 C 1:CYS22 4.5 43.7 1.0 C 1:ARG21 4.5 44.4 1.0 CB 1:ARG21 4.6 44.9 1.0 C 1:CYS19 4.6 46.5 1.0 O 1:CYS19 4.6 47.4 1.0 C 1:CYS37 4.8 38.8 1.0 N 1:GLU24 4.8 45.8 1.0 CA 1:ARG21 4.8 44.0 1.0 N 1:ARG21 4.8 44.3 1.0 CA 1:CYS34 4.9 42.4 1.0 N 1:GLY38 4.9 40.2 1.0 CB 1:SER36 4.9 38.6 1.0 N 1:PHE39 5.0 46.6 1.0 CB 1:GLU24 5.0 47.4 1.0 CD 1:ARG21 5.0 45.4 1.0

Cadmium binding site 3 out of 5 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S 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 A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd93 b:0.0 occ:1.00 SG Z:CYS42 3.1 0.1 1.0 CB Z:CYS60 3.4 0.3 1.0 SG Z:CYS39 3.6 0.9 1.0 CB Z:CYS39 3.9 0.2 1.0 SG Z:CYS57 3.9 0.5 1.0 CB Z:CYS57 4.1 0.3 1.0 N Z:CYS60 4.2 0.7 1.0 N Z:CYS42 4.2 0.2 1.0 CB Z:CYS42 4.2 0.9 1.0 CD2 Z:TYR59 4.2 0.5 1.0 CB Z:ASN41 4.3 0.5 1.0 CA Z:CYS60 4.4 0.1 1.0 SG Z:CYS60 4.6 0.3 1.0 CB Z:TYR62 4.7 0.2 1.0 CA Z:CYS42 4.7 0.9 1.0 CB Z:TYR59 4.8 0.3 1.0 CB Z:GLU44 4.8 0.3 1.0 N Z:GLU44 5.0 0.8 1.0

Cadmium binding site 4 out of 5 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S 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 A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd94 b:0.0 occ:1.00 CB 3:CYS74 3.5 0.4 1.0 SG 3:CYS11 3.8 0.6 1.0 CB 3:CYS71 3.8 0.9 1.0 N 3:CYS14 3.9 0.6 1.0 CB 3:CYS14 3.9 0.9 1.0 CB 3:HIS13 3.9 0.9 1.0 CB 3:CYS11 4.1 0.7 1.0 SG 3:CYS71 4.3 0.3 1.0 CA 3:CYS14 4.5 0.1 1.0 SG 3:CYS74 4.6 1.0 1.0 N 3:CYS74 4.6 0.5 1.0 CA 3:CYS74 4.6 0.7 1.0 CG 3:HIS13 4.7 0.7 1.0 CB 3:LYS76 4.7 0.0 1.0 C 3:HIS13 4.7 0.1 1.0 CA 3:HIS13 4.8 0.8 1.0 CD2 3:HIS13 4.8 0.1 1.0 O 3:LYS76 4.8 0.4 1.0 N 3:LYS76 4.9 0.6 1.0

Cadmium binding site 5 out of 5 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S 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 A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd116 b:0.0 occ:1.00 ND1 O:HIS40 3.0 45.2 1.0 CG O:HIS40 3.9 46.8 1.0 CB O:HIS40 3.9 49.3 1.0 CE1 O:HIS40 4.0 44.6 1.0 CG O:ARG37 4.3 61.7 1.0 NE O:ARG37 4.5 65.6 1.0 CB O:ARG37 4.8 60.1 1.0 CZ O:ARG37 4.8 66.9 1.0 O O:ARG37 4.8 59.5 1.0 CD O:ARG37 4.9 64.4 1.0

J.M.Kavran, T.A.Steitz. Structure of the Base of the L7/L12 Stalk of the Haloarcula Marismortui Large Ribosomal Subunit: Analysis of L11 Movements J.Mol.Biol. V. 371 1047 2007.
ISSN: ISSN 0022-2836
PubMed: 17599351
DOI: 10.1016/J.JMB.2007.05.091