Cadmium in PDB 1vqk: The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui

The structure of The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqk 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 (°)	211.873, 298.569, 575.390, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25

The structure of The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Strontium	(Sr)	114 atoms
Magnesium	(Mg)	93 atoms
Potassium	(K)	2 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	75 atoms

The binding sites of Cadmium atom in the The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vqk). 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 Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqk:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the 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 Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd9205 b:85.6 occ:1.00 O O:HOH5650 2.2 35.4 1.0 ND1 O:HIS40 2.3 36.4 1.0 O O:HOH5322 2.5 37.8 1.0 CE1 O:HIS40 3.2 36.5 1.0 CG O:HIS40 3.3 37.2 1.0 CB O:HIS40 3.6 39.5 1.0 NE2 O:HIS40 4.3 39.2 1.0 CD2 O:HIS40 4.4 37.1 1.0 O O:HOH3002 4.5 61.2 1.0 CG O:ARG37 4.6 46.9 1.0 CA O:ARG37 4.9 45.2 1.0 CZ O:ARG37 4.9 45.7 1.0 CB O:ARG37 4.9 45.4 1.0 NH1 O:ARG37 4.9 46.4 1.0

Cadmium binding site 2 out of 5 in the The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the 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 Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd9201 b:56.1 occ:1.00 SG U:CYS36 2.4 49.9 1.0 SG U:CYS9 2.5 51.4 1.0 SG U:CYS6 2.5 42.4 1.0 SG U:CYS32 2.6 38.6 1.0 CB U:CYS6 3.2 48.4 1.0 CB U:CYS9 3.3 47.1 1.0 CB U:CYS36 3.5 47.4 1.0 CB U:CYS32 3.6 40.5 1.0 N U:CYS9 3.8 47.6 1.0 N U:CYS32 4.1 41.6 1.0 CA U:CYS9 4.1 48.8 1.0 OG1 U:THR11 4.4 57.8 1.0 OG U:SER33 4.4 45.0 1.0 CA U:CYS32 4.4 42.6 1.0 CA U:CYS6 4.7 49.3 1.0 CB U:TYR8 4.7 47.3 1.0 N U:SER33 4.7 45.6 1.0 C U:TYR8 4.9 48.7 1.0 N U:GLY10 4.9 50.5 1.0 C U:CYS32 4.9 44.6 1.0 C U:CYS9 4.9 49.5 1.0 CA U:CYS36 4.9 47.1 1.0

Cadmium binding site 3 out of 5 in the The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the 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 Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd9203 b:75.8 occ:1.00 SG Z:CYS60 2.2 56.2 1.0 SG Z:CYS39 2.5 62.1 1.0 SG Z:CYS57 2.6 63.2 1.0 SG Z:CYS42 2.8 80.5 1.0 CB Z:CYS57 3.1 60.1 1.0 CB Z:CYS39 3.2 63.6 1.0 CB Z:CYS60 3.3 59.0 1.0 CB Z:CYS42 3.6 76.1 1.0 N Z:CYS42 3.7 74.7 1.0 N Z:CYS60 3.8 61.1 1.0 CA Z:CYS60 4.1 59.2 1.0 CB Z:ASN41 4.2 71.1 1.0 CA Z:CYS42 4.2 75.8 1.0 ND2 Z:ASN41 4.5 71.7 1.0 CB Z:TYR62 4.5 52.8 1.0 CA Z:CYS39 4.6 65.1 1.0 CA Z:CYS57 4.7 58.6 1.0 CB Z:TYR59 4.7 65.5 1.0 CD2 Z:TYR59 4.7 71.5 1.0 C Z:CYS60 4.8 58.8 1.0 C Z:ASN41 4.8 73.3 1.0 CG Z:ASN41 4.9 71.8 1.0 N Z:TYR62 4.9 56.2 1.0 C Z:CYS42 4.9 76.3 1.0 N Z:ASP61 4.9 58.4 1.0 CA Z:ASN41 4.9 71.6 1.0 C Z:TYR59 5.0 62.3 1.0

Cadmium binding site 4 out of 5 in the The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the 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 Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd9202 b:52.0 occ:1.00 SG 1:CYS22 2.4 27.5 1.0 SG 1:CYS34 2.4 31.7 1.0 SG 1:CYS19 2.5 28.3 1.0 SG 1:CYS37 2.5 32.8 1.0 CB 1:CYS19 3.1 29.7 1.0 CB 1:CYS34 3.2 25.8 1.0 CB 1:CYS37 3.3 26.5 1.0 CB 1:CYS22 3.3 30.4 1.0 N 1:CYS22 3.7 32.5 1.0 N 1:CYS37 3.8 28.7 1.0 CA 1:CYS37 4.1 28.5 1.0 CA 1:CYS22 4.1 30.8 1.0 CB 1:PHE39 4.3 29.6 1.0 CA 1:CYS19 4.6 33.1 1.0 CA 1:CYS34 4.6 29.0 1.0 CB 1:ARG21 4.7 33.5 1.0 C 1:CYS37 4.7 28.1 1.0 C 1:ARG21 4.7 33.4 1.0 N 1:PHE39 4.8 28.8 1.0 O 1:HOH9475 4.8 38.6 1.0 CB 1:SER36 4.8 25.8 1.0 C 1:CYS22 4.8 29.3 1.0 N 1:GLY38 4.9 28.6 1.0 C 1:SER36 4.9 31.3 1.0 N 1:GLY23 4.9 30.1 1.0

Cadmium binding site 5 out of 5 in the The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the 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 Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd9204 b:58.1 occ:1.00 SG 3:CYS71 2.3 59.7 1.0 SG 3:CYS11 2.4 52.9 1.0 SG 3:CYS14 2.5 64.4 1.0 SG 3:CYS74 2.5 59.6 1.0 CB 3:CYS71 3.0 61.3 1.0 CB 3:CYS74 3.3 61.1 1.0 CB 3:CYS14 3.3 60.0 1.0 CB 3:CYS11 3.5 51.8 1.0 N 3:CYS14 3.6 60.9 1.0 N 3:CYS74 4.0 63.2 1.0 CA 3:CYS14 4.0 60.5 1.0 OE1 3:GLN18 4.2 67.8 1.0 CA 3:CYS74 4.2 61.5 1.0 CB 3:HIS13 4.4 60.1 1.0 CA 3:CYS71 4.5 61.0 1.0 C 3:HIS13 4.7 61.1 1.0 CD 3:GLN18 4.9 65.1 1.0 O 3:HOH9493 4.9 83.0 1.0 CA 3:CYS11 4.9 52.7 1.0 CA 3:HIS13 5.0 59.9 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