Cadmium in PDB 1w2b: Trigger Factor Ribosome Binding Domain in Complex with 50S

The structure of Trigger Factor Ribosome Binding Domain in Complex with 50S, PDB code: 1w2b was solved by L.Ferbitz, T.Maier, H.Patzelt, B.Bukau, E.Deuerling, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	210.746, 298.871, 574.173, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 26.8

The structure of Trigger Factor Ribosome Binding Domain in Complex with 50S 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 Trigger Factor Ribosome Binding Domain in Complex with 50S (pdb code 1w2b). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Trigger Factor Ribosome Binding Domain in Complex with 50S, PDB code: 1w2b:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ 2:Cd101 b:42.6 occ:1.00 SG 2:CYS11 3.1 48.7 1.0 CB 2:CYS14 3.4 0.2 1.0 N 2:CYS14 3.4 0.4 1.0 CB 2:CYS74 3.5 73.2 1.0 CB 2:CYS11 3.5 49.7 1.0 CB 2:CYS71 3.6 0.1 1.0 CB 2:HIS13 3.7 0.3 1.0 SG 2:CYS71 3.8 0.4 1.0 CA 2:CYS14 4.0 0.5 1.0 SG 2:CYS74 4.0 75.1 1.0 C 2:HIS13 4.1 0.2 1.0 O 2:HOH237 4.1 26.6 1.0 N 2:HIS13 4.2 0.2 1.0 CA 2:HIS13 4.2 0.7 1.0 CD2 2:HIS13 4.3 0.2 1.0 O 2:HOH217 4.4 91.1 1.0 CG 2:HIS13 4.4 0.0 1.0 NE2 2:GLN18 4.5 0.9 1.0 O 2:LYS76 4.7 0.0 1.0 SG 2:CYS14 4.7 0.8 1.0 CA 2:CYS11 4.7 0.2 1.0 CB 2:LYS76 4.7 0.9 1.0 C 2:CYS11 4.8 0.1 1.0 CA 2:CYS74 4.8 0.4 1.0 O 2:CYS11 4.9 0.3 1.0 OE1 2:GLN18 4.9 0.1 1.0 CD 2:GLN18 4.9 0.2 1.0 O 2:HIS13 5.0 0.8 1.0

Cadmium binding site 2 out of 5 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ N:Cd201 b:66.8 occ:1.00 O N:HOH321 2.7 29.2 1.0 ND1 N:HIS40 2.9 17.6 1.0 CG N:HIS40 3.7 18.6 1.0 CB N:HIS40 3.8 20.0 1.0 CE1 N:HIS40 3.9 21.3 1.0 O N:HOH332 3.9 23.9 1.0 O 0:HOH4174 4.4 36.1 1.0 CG N:ARG37 4.5 20.0 1.0 NH1 N:ARG37 4.5 21.6 1.0 CZ N:ARG37 4.8 21.8 1.0 CD2 N:HIS40 4.9 21.1 1.0 NE2 N:HIS40 5.0 23.7 1.0

Cadmium binding site 3 out of 5 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ T:Cd101 b:44.4 occ:1.00 SG T:CYS6 3.0 70.6 1.0 SG T:CYS36 3.1 82.0 1.0 CB T:CYS9 3.2 78.8 1.0 CB T:CYS36 3.4 80.8 1.0 N T:CYS9 3.6 42.2 1.0 CB T:CYS6 3.8 70.8 1.0 SG T:CYS9 3.8 77.7 1.0 CB T:CYS32 3.8 58.2 1.0 SG T:CYS32 4.0 53.5 1.0 CA T:CYS9 4.0 41.5 1.0 N T:CYS32 4.0 40.2 1.0 OG1 T:THR11 4.0 73.6 1.0 CB T:TYR8 4.3 51.0 1.0 OG T:SER33 4.4 84.7 1.0 CA T:CYS32 4.5 41.4 1.0 N T:SER33 4.5 96.7 1.0 CD2 T:TYR8 4.5 44.0 1.0 N T:GLY10 4.7 78.3 1.0 C T:CYS9 4.7 42.3 1.0 C T:TYR8 4.8 0.0 1.0 CG T:TYR8 4.9 46.3 1.0 CA T:CYS36 4.9 65.5 1.0 C T:CYS32 5.0 43.3 1.0

Cadmium binding site 4 out of 5 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ Y:Cd101 b:44.7 occ:1.00 CB Y:CYS60 2.9 0.5 1.0 CB Y:CYS42 3.4 0.7 1.0 N Y:CYS60 3.6 77.7 1.0 SG Y:CYS39 3.6 47.0 1.0 CB Y:CYS57 3.7 64.0 1.0 N Y:CYS42 3.7 63.1 1.0 SG Y:CYS57 3.7 62.0 1.0 CA Y:CYS60 3.8 76.5 1.0 CB Y:CYS39 4.0 48.9 1.0 CB Y:TYR62 4.1 0.1 1.0 CA Y:CYS42 4.1 62.7 1.0 SG Y:CYS60 4.1 0.3 1.0 CB Y:VAL41 4.1 78.7 1.0 CD2 Y:HIS59 4.2 0.7 1.0 CG1 Y:VAL41 4.3 80.1 1.0 CB Y:HIS59 4.4 0.8 1.0 C Y:CYS60 4.6 76.2 1.0 N Y:TYR62 4.7 96.9 1.0 N Y:GLY61 4.7 0.5 1.0 CG Y:HIS59 4.7 0.7 1.0 O Y:CYS57 4.7 0.4 1.0 C Y:HIS59 4.8 0.9 1.0 C Y:VAL41 4.8 0.4 1.0 O Y:CYS42 4.8 63.8 1.0 SG Y:CYS42 4.8 0.5 1.0 C Y:CYS42 4.8 62.3 1.0 CA Y:VAL41 4.9 0.4 1.0

Cadmium binding site 5 out of 5 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd101 b:32.7 occ:1.00 SG Z:CYS34 2.4 15.0 1.0 SG Z:CYS19 2.7 15.0 1.0 SG Z:CYS37 2.8 16.4 1.0 SG Z:CYS22 2.8 37.5 1.0 CB Z:CYS22 2.8 37.1 1.0 CB Z:CYS37 3.0 15.1 1.0 CB Z:CYS19 3.2 15.0 1.0 N Z:CYS22 3.5 17.2 1.0 CB Z:CYS34 3.6 15.0 1.0 N Z:CYS37 3.7 19.3 1.0 CA Z:CYS22 3.7 15.1 1.0 CA Z:CYS37 3.9 18.0 1.0 C Z:ARG21 4.4 16.0 1.0 CB Z:SER36 4.4 15.9 1.0 CB Z:ARG21 4.5 15.0 1.0 C Z:SER36 4.6 20.2 1.0 CA Z:CYS19 4.6 21.3 1.0 N Z:GLY23 4.7 15.0 1.0 O Z:HOH234 4.7 19.4 1.0 C Z:CYS22 4.7 15.1 1.0 CB Z:PHE39 4.8 28.9 1.0 CA Z:ARG21 4.8 16.2 1.0 CD Z:ARG21 4.8 15.0 1.0 C Z:CYS37 4.9 18.6 1.0 CA Z:CYS34 4.9 15.8 1.0 CA Z:SER36 4.9 18.3 1.0 N Z:ARG21 5.0 16.2 1.0

L.Ferbitz, T.Maier, H.Patzelt, B.Bukau, E.Deuerling, N.Ban. Trigger Factor in Complex with the Ribosome Forms A Molecular Cradle For Nascent Proteins Nature V. 431 590 2004.
ISSN: ISSN 0028-0836
PubMed: 15334087
DOI: 10.1038/NATURE02899