Cadmium in PDB 1n8r: Structure of Large Ribosomal Subunit in Complex with Virginiamycin M

The structure of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M, PDB code: 1n8r was solved by J.L.Hansen, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.902, 300.474, 575.176, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.2

The structure of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M also contains other interesting chemical elements:

Magnesium	(Mg)	117 atoms
Potassium	(K)	1 atom
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 atoms

The binding sites of Cadmium atom in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M (pdb code 1n8r). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M, PDB code: 1n8r:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ P:Cd8405 b:0.2 occ:1.00 ND1 P:HIS40 2.7 24.3 1.0 O P:HOH5322 2.9 23.1 1.0 O P:HOH5650 3.1 35.0 1.0 CG P:HIS40 3.6 24.6 1.0 CE1 P:HIS40 3.7 24.6 1.0 CB P:HIS40 3.8 26.6 1.0 CG P:ARG37 4.3 38.5 1.0 O A:HOH4727 4.5 31.8 1.0 CZ P:ARG37 4.5 37.5 1.0 NH1 P:ARG37 4.6 36.9 1.0 CB P:ARG37 4.7 37.6 1.0 NE P:ARG37 4.7 37.8 1.0 CA P:ARG37 4.8 37.4 1.0 NH2 P:ARG37 4.8 35.0 1.0 CD2 P:HIS40 4.8 24.9 1.0 O P:ARG37 4.8 37.3 1.0 NE2 P:HIS40 4.8 25.6 1.0

Cadmium binding site 2 out of 5 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ V:Cd8401 b:0.8 occ:1.00 CB V:CYS9 3.1 65.0 1.0 SG V:CYS36 3.2 75.8 1.0 CB V:CYS36 3.3 70.5 1.0 SG V:CYS6 3.4 78.2 1.0 N V:CYS9 3.4 64.8 1.0 CB V:CYS6 3.7 75.8 1.0 SG V:CYS9 3.8 66.2 1.0 CA V:CYS9 3.9 65.5 1.0 SG V:CYS32 3.9 65.4 1.0 CB V:TYR8 4.2 63.5 1.0 CB V:CYS32 4.3 64.3 1.0 N V:CYS32 4.4 64.5 1.0 OG V:SER33 4.5 53.6 1.0 C V:TYR8 4.6 65.6 1.0 CD2 V:TYR8 4.6 61.4 1.0 OG1 V:THR11 4.6 63.1 1.0 N V:GLY10 4.6 64.9 1.0 C V:CYS9 4.8 65.2 1.0 CA V:TYR8 4.8 65.3 1.0 CA V:CYS36 4.9 68.0 1.0 N V:SER33 4.9 63.2 1.0 CA V:CYS32 4.9 64.8 1.0 CG V:TYR8 4.9 62.3 1.0

Cadmium binding site 3 out of 5 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8403 b:0.8 occ:1.00 CB 1:CYS42 3.3 79.1 1.0 SG 1:CYS39 3.3 78.2 1.0 CB 1:CYS57 3.6 75.6 1.0 CB 1:CYS60 3.6 68.5 1.0 CB 1:CYS39 3.6 75.7 1.0 N 1:CYS42 3.6 77.0 1.0 SG 1:CYS57 3.6 79.9 1.0 SG 1:CYS60 3.7 73.1 1.0 SG 1:CYS42 3.8 81.8 1.0 N 1:CYS60 4.0 67.6 1.0 CA 1:CYS42 4.1 78.8 1.0 CA 1:CYS60 4.3 68.0 1.0 CB 1:VAL41 4.4 71.8 1.0 CG1 1:VAL41 4.4 71.1 1.0 CB 1:TYR62 4.5 59.3 1.0 CD2 1:HIS59 4.6 69.3 1.0 CB 1:HIS59 4.6 68.2 1.0 C 1:CYS42 4.7 79.4 1.0 C 1:VAL41 4.8 75.4 1.0 CA 1:VAL41 5.0 73.5 1.0 CG 1:HIS59 5.0 70.0 1.0

Cadmium binding site 4 out of 5 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ 2:Cd8402 b:43.6 occ:1.00 SG 2:CYS37 2.3 21.9 1.0 SG 2:CYS22 2.4 26.6 1.0 SG 2:CYS34 2.5 29.8 1.0 SG 2:CYS19 2.7 24.6 1.0 CB 2:CYS34 3.1 26.1 1.0 CB 2:CYS19 3.1 23.1 1.0 CB 2:CYS22 3.2 25.1 1.0 CB 2:CYS37 3.3 20.7 1.0 N 2:CYS22 3.6 24.8 1.0 N 2:CYS37 3.7 21.0 1.0 CA 2:CYS22 4.0 26.7 1.0 CA 2:CYS37 4.0 22.4 1.0 CB 2:PHE39 4.4 27.1 1.0 O 2:HOH1020 4.4 19.0 1.0 CB 2:ARG21 4.5 25.4 1.0 CA 2:CYS34 4.6 27.0 1.0 CA 2:CYS19 4.7 25.3 1.0 C 2:CYS37 4.7 20.6 1.0 C 2:ARG21 4.7 27.3 1.0 C 2:CYS22 4.8 26.1 1.0 C 2:SER36 4.8 20.6 1.0 N 2:GLY38 4.9 21.3 1.0 N 2:PHE39 4.9 24.8 1.0 CB 2:SER36 4.9 20.6 1.0 N 2:GLY23 4.9 25.6 1.0 CA 2:ARG21 5.0 25.6 1.0 CD 2:ARG21 5.0 27.5 1.0 N 2:ARG21 5.0 25.5 1.0

Cadmium binding site 5 out of 5 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ 4:Cd8404 b:0.6 occ:1.00 N 4:CYS14 2.7 74.5 1.0 CB 4:CYS14 2.7 74.2 1.0 CA 4:CYS14 3.2 74.7 1.0 SG 4:CYS11 3.3 78.1 1.0 CB 4:CYS11 3.4 75.5 1.0 CB 4:CYS74 3.5 76.5 1.0 SG 4:CYS74 3.6 76.7 1.0 SG 4:CYS71 3.7 77.8 1.0 C 4:HIS13 3.8 74.3 1.0 CB 4:HIS13 3.8 71.8 1.0 CB 4:CYS71 3.9 74.9 1.0 SG 4:CYS14 4.0 75.2 1.0 O 4:HOH8561 4.0 86.0 1.0 CA 4:HIS13 4.2 74.3 1.0 O 4:CYS11 4.4 75.2 1.0 N 4:HIS13 4.4 72.7 1.0 C 4:CYS14 4.5 74.2 1.0 CA 4:CYS11 4.7 75.8 1.0 C 4:CYS11 4.7 74.1 1.0 N 4:ASN15 4.7 72.8 1.0 CG 4:HIS13 4.8 71.3 1.0 CA 4:CYS74 4.9 75.1 1.0 O 4:HIS13 4.9 74.5 1.0 N 4:CYS74 4.9 73.7 1.0

J.Hansen, P.B.Moore, T.A.Steitz. Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit J.Mol.Biol. V. 330 1061 2003.
ISSN: ISSN 0022-2836
PubMed: 12860128
DOI: 10.1016/S0022-2836(03)00668-5