Cadmium in PDB 1kd1: Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1kd1 was solved by J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, 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)	19.99 / 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 (%)	22 / 26.9

The structure of Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium	(Mg)	119 atoms
Potassium	(K)	3 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	85 atoms

The binding sites of Cadmium atom in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1kd1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1kd1:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Co-Crystal Structure of Spiramycin Bound to the 50S 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ P:Cd8405 b:0.7 occ:1.00 O P:HOH5650 2.7 82.3 1.0 ND1 P:HIS40 2.9 47.5 1.0 O P:HOH5322 3.7 36.1 1.0 CE1 P:HIS40 3.7 48.1 1.0 CG P:HIS40 4.0 47.6 1.0 CB P:HIS40 4.3 47.9 1.0 CG P:ARG37 4.4 57.3 1.0 NH1 P:ARG37 4.6 59.2 1.0 O A:HOH4332 4.7 70.7 1.0 CZ P:ARG37 4.8 59.7 1.0 CD2 P:LEU7 4.9 55.1 1.0 NE2 P:HIS40 4.9 48.8 1.0 CG1 P:VAL79 4.9 54.5 1.0 CD1 P:LEU7 5.0 51.7 1.0

Cadmium binding site 2 out of 5 in the Co-Crystal Structure of Spiramycin Bound to the 50S 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ V:Cd8401 b:0.0 occ:1.00 CB V:CYS9 2.8 95.8 1.0 SG V:CYS36 3.0 0.4 1.0 N V:CYS9 3.0 95.5 1.0 SG V:CYS6 3.1 0.7 1.0 CB V:CYS36 3.4 95.5 1.0 CA V:CYS9 3.5 95.3 1.0 SG V:CYS9 3.5 96.8 1.0 CB V:CYS6 3.5 0.2 1.0 CB V:TYR8 3.9 95.4 1.0 SG V:CYS32 4.0 95.5 1.0 C V:TYR8 4.2 95.5 1.0 CD2 V:TYR8 4.2 95.7 1.0 N V:GLY10 4.3 94.3 1.0 C V:CYS9 4.4 94.9 1.0 CA V:TYR8 4.5 95.8 1.0 CG V:TYR8 4.6 95.6 1.0 CB V:CYS32 4.6 93.7 1.0 N V:CYS32 4.7 91.8 1.0 N V:TYR8 4.7 96.0 1.0 OG1 V:THR11 4.8 95.5 1.0 CA V:CYS36 4.9 94.6 1.0 CA V:CYS6 5.0 0.1 1.0

Cadmium binding site 3 out of 5 in the Co-Crystal Structure of Spiramycin Bound to the 50S 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8403 b:0.9 occ:1.00 CB 1:CYS42 2.9 0.3 1.0 N 1:CYS42 3.1 0.5 1.0 SG 1:CYS42 3.4 0.3 1.0 SG 1:CYS39 3.5 0.1 1.0 SG 1:CYS60 3.5 0.2 1.0 CA 1:CYS42 3.6 0.1 1.0 CB 1:CYS60 3.6 98.5 1.0 CB 1:CYS39 3.7 0.3 1.0 SG 1:CYS57 4.1 0.8 1.0 CB 1:VAL41 4.1 0.2 1.0 CB 1:CYS57 4.2 0.7 1.0 CG1 1:VAL41 4.2 0.6 1.0 C 1:VAL41 4.3 0.3 1.0 C 1:CYS42 4.3 0.6 1.0 N 1:CYS60 4.4 99.0 1.0 CA 1:CYS60 4.6 97.9 1.0 CD2 1:HIS59 4.6 0.8 1.0 CA 1:VAL41 4.7 0.1 1.0 O 1:CYS42 4.7 0.3 1.0 CB 1:TYR62 4.9 91.3 1.0 N 1:VAL41 4.9 0.8 1.0

Cadmium binding site 4 out of 5 in the Co-Crystal Structure of Spiramycin Bound to the 50S 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 2:Cd8402 b:59.9 occ:1.00 SG 2:CYS34 2.5 42.6 1.0 SG 2:CYS37 2.5 41.4 1.0 SG 2:CYS19 2.6 44.5 1.0 SG 2:CYS22 2.7 37.0 1.0 CB 2:CYS19 3.0 40.0 1.0 CB 2:CYS22 3.2 38.6 1.0 CB 2:CYS37 3.2 35.0 1.0 CB 2:CYS34 3.2 38.9 1.0 N 2:CYS22 3.6 40.3 1.0 N 2:CYS37 3.9 34.7 1.0 CA 2:CYS22 4.0 39.7 1.0 CA 2:CYS37 4.1 35.2 1.0 CB 2:PHE39 4.3 43.6 1.0 CA 2:CYS19 4.5 39.9 1.0 O 2:HOH8421 4.5 35.2 1.0 CB 2:ARG21 4.6 42.1 1.0 C 2:ARG21 4.6 39.7 1.0 CA 2:CYS34 4.7 37.9 1.0 C 2:CYS22 4.7 39.9 1.0 C 2:CYS37 4.8 35.3 1.0 N 2:GLY23 4.8 40.0 1.0 N 2:PHE39 4.9 40.6 1.0 CA 2:ARG21 4.9 41.6 1.0 CD 2:ARG21 5.0 40.8 1.0 C 2:SER36 5.0 34.2 1.0 C 2:CYS19 5.0 40.9 1.0 CB 2:SER36 5.0 34.6 1.0

Cadmium binding site 5 out of 5 in the Co-Crystal Structure of Spiramycin Bound to the 50S 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 4:Cd8404 b:0.9 occ:1.00 CB 4:CYS14 2.7 0.0 1.0 SG 4:CYS71 3.1 0.1 1.0 CB 4:CYS11 3.2 0.1 1.0 SG 4:CYS11 3.2 0.7 1.0 O 4:HOH8564 3.4 0.8 1.0 CB 4:CYS71 3.5 0.5 1.0 SG 4:CYS14 3.5 0.8 1.0 N 4:CYS14 3.7 0.9 1.0 CA 4:CYS14 3.8 0.4 1.0 OE1 4:GLN18 4.0 0.3 1.0 CD 4:GLN18 4.1 0.9 1.0 NE2 4:GLN18 4.1 0.4 1.0 CB 4:CYS74 4.2 0.4 1.0 SG 4:CYS74 4.4 0.6 1.0 CB 4:GLN18 4.6 0.2 1.0 O 4:GLU16 4.6 0.9 1.0 CA 4:CYS11 4.6 0.4 1.0 N 4:CYS74 4.7 0.8 1.0 C 4:CYS14 4.9 0.3 1.0 CG 4:GLN18 4.9 1.0 1.0 C 4:HIS13 4.9 0.3 1.0 O 4:CYS11 4.9 0.7 1.0 CA 4:CYS71 5.0 0.3 1.0

J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, T.A.Steitz. The Structures of Four Macrolide Antibiotics Bound to the Large Ribosomal Subunit. Mol.Cell V. 10 117 2002.
ISSN: ISSN 1097-2765
PubMed: 12150912
DOI: 10.1016/S1097-2765(02)00570-1