Cadmium in PDB 1vqm: The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

The structure of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqm was solved by T.M.Schmeing, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.445, 298.564, 574.493, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 24.7

The structure of The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Strontium	(Sr)	114 atoms
Magnesium	(Mg)	94 atoms
Potassium	(K)	2 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	75 atoms

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

Cadmium binding site 1 out of 5 in the The Structure of the Transition State Analogue "Dan" Bound to the Large 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 The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd9205 b:0.6 occ:1.00 O O:HOH5650 2.4 74.7 1.0 ND1 O:HIS40 2.6 38.1 1.0 CE1 O:HIS40 3.5 37.4 1.0 CG O:HIS40 3.6 38.5 1.0 CB O:HIS40 3.9 41.2 1.0 O 0:HOH6551 4.3 73.8 1.0 CG O:ARG37 4.5 54.8 1.0 O O:HOH3002 4.6 71.8 1.0 NE2 O:HIS40 4.7 39.1 1.0 CD2 O:HIS40 4.7 39.0 1.0 NH1 O:ARG37 4.8 53.8 1.0 CZ O:ARG37 4.8 54.4 1.0

Cadmium binding site 2 out of 5 in the The Structure of the Transition State Analogue "Dan" Bound to the Large 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 The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd9201 b:60.5 occ:1.00 SG U:CYS36 2.4 57.0 1.0 SG U:CYS6 2.5 50.0 1.0 SG U:CYS32 2.5 41.8 1.0 SG U:CYS9 2.5 55.6 1.0 CB U:CYS6 3.2 54.9 1.0 CB U:CYS9 3.4 53.2 1.0 CB U:CYS36 3.5 54.7 1.0 CB U:CYS32 3.6 44.9 1.0 N U:CYS9 3.8 53.1 1.0 N U:CYS32 4.1 46.2 1.0 CA U:CYS9 4.2 54.8 1.0 OG1 U:THR11 4.3 63.9 1.0 CA U:CYS32 4.4 46.6 1.0 OG U:SER33 4.5 47.7 1.0 CB U:TYR8 4.7 50.6 1.0 CA U:CYS6 4.7 55.1 1.0 N U:SER33 4.8 49.7 1.0 CA U:CYS36 4.9 54.1 1.0 C U:TYR8 4.9 53.0 1.0 N U:GLY10 4.9 56.7 1.0 C U:CYS32 4.9 48.5 1.0 C U:CYS9 4.9 56.1 1.0

Cadmium binding site 3 out of 5 in the The Structure of the Transition State Analogue "Dan" Bound to the Large 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 The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd9203 b:93.5 occ:1.00 SG Z:CYS60 2.4 68.1 1.0 SG Z:CYS39 2.5 68.1 1.0 SG Z:CYS57 2.6 76.0 1.0 SG Z:CYS42 2.7 88.6 1.0 CB Z:CYS39 3.3 78.3 1.0 CB Z:CYS60 3.6 71.9 1.0 CB Z:CYS57 3.6 72.3 1.0 CD2 Z:TYR59 3.8 85.3 1.0 CB Z:CYS42 3.8 83.9 1.0 N Z:CYS60 3.9 75.0 1.0 CB Z:ASN41 4.1 81.4 1.0 CB Z:TYR59 4.1 80.2 1.0 C Z:ASN41 4.2 80.9 1.0 O Z:ASN41 4.2 78.8 1.0 ND2 Z:ASN41 4.2 82.3 1.0 CA Z:CYS60 4.4 72.5 1.0 N Z:CYS42 4.4 82.5 1.0 CG Z:TYR59 4.4 83.9 1.0 CA Z:ASN41 4.6 80.2 1.0 CB Z:GLU44 4.7 92.0 1.0 CA Z:CYS42 4.7 83.5 1.0 CE2 Z:TYR59 4.7 87.9 1.0 CA Z:CYS39 4.7 80.9 1.0 CG Z:ASN41 4.7 82.1 1.0 N Z:ASN41 4.8 78.8 1.0 C Z:TYR59 4.9 76.9 1.0

Cadmium binding site 4 out of 5 in the The Structure of the Transition State Analogue "Dan" Bound to the Large 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 The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd9202 b:55.4 occ:1.00 SG 1:CYS22 2.3 33.3 1.0 SG 1:CYS37 2.4 34.2 1.0 SG 1:CYS34 2.4 37.5 1.0 SG 1:CYS19 2.5 34.8 1.0 CB 1:CYS19 3.1 33.5 1.0 CB 1:CYS34 3.2 31.4 1.0 CB 1:CYS37 3.2 28.1 1.0 CB 1:CYS22 3.3 34.1 1.0 N 1:CYS37 3.7 31.2 1.0 N 1:CYS22 3.7 37.5 1.0 CA 1:CYS37 4.0 29.7 1.0 CA 1:CYS22 4.1 34.4 1.0 CB 1:PHE39 4.4 33.0 1.0 CA 1:CYS19 4.6 36.9 1.0 CA 1:CYS34 4.6 33.8 1.0 C 1:CYS37 4.7 29.6 1.0 CB 1:ARG21 4.7 36.3 1.0 C 1:ARG21 4.8 36.9 1.0 CB 1:SER36 4.8 30.6 1.0 C 1:SER36 4.8 34.7 1.0 N 1:PHE39 4.8 31.3 1.0 C 1:CYS22 4.8 33.6 1.0 N 1:GLY38 4.9 30.6 1.0 N 1:GLY23 4.9 34.9 1.0 O 1:HOH9477 4.9 48.7 1.0

Cadmium binding site 5 out of 5 in the The Structure of the Transition State Analogue "Dan" Bound to the Large 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 The Structure of the Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd9204 b:63.9 occ:1.00 SG 3:CYS71 2.3 62.7 1.0 SG 3:CYS11 2.4 57.6 1.0 SG 3:CYS74 2.5 66.4 1.0 SG 3:CYS14 2.6 68.1 1.0 CB 3:CYS71 3.1 65.7 1.0 CB 3:CYS14 3.2 65.8 1.0 CB 3:CYS74 3.3 67.0 1.0 CB 3:CYS11 3.5 57.3 1.0 N 3:CYS14 3.6 67.0 1.0 CA 3:CYS14 3.9 66.3 1.0 N 3:CYS74 4.0 69.0 1.0 OE1 3:GLN18 4.1 72.2 1.0 CA 3:CYS74 4.2 67.6 1.0 CB 3:HIS13 4.4 66.6 1.0 CA 3:CYS71 4.5 65.8 1.0 C 3:HIS13 4.7 67.0 1.0 CD 3:GLN18 4.7 69.6 1.0 CA 3:CYS11 4.9 58.0 1.0 C 3:CYS74 5.0 67.3 1.0 CA 3:HIS13 5.0 66.0 1.0

T.M.Schmeing, K.S.Huang, D.E.Kitchen, S.A.Strobel, T.A.Steitz. Structural Insights Into the Roles of Water and the 2' Hydroxyl of the P Site Trna in the Peptidyl Transferase Reaction. Mol.Cell V. 20 437 2005.
ISSN: ISSN 1097-2765
PubMed: 16285925
DOI: 10.1016/J.MOLCEL.2005.09.006