Cadmium in PDB 1k9m: Co-Crystal Structure of Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Co-Crystal Structure of Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1k9m 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 (%)	21.9 / 26.2

The structure of Co-Crystal Structure of Tylosin 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 Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1k9m). 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 Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1k9m:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Co-Crystal Structure of Tylosin 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 Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ P:Cd8405 b:0.0 occ:1.00 O P:HOH5650 2.7 66.0 1.0 ND1 P:HIS40 2.9 36.3 1.0 O P:HOH5322 3.3 37.2 1.0 CE1 P:HIS40 3.6 36.2 1.0 CG P:ARG37 3.8 52.0 1.0 CG P:HIS40 3.8 36.4 1.0 CB P:HIS40 4.2 37.8 1.0 CZ P:ARG37 4.2 55.7 1.0 NH1 P:ARG37 4.3 54.7 1.0 NE P:ARG37 4.3 54.1 1.0 O A:HOH4330 4.4 66.5 1.0 CB P:ARG37 4.5 47.8 1.0 CD P:ARG37 4.5 53.5 1.0 CA P:ARG37 4.6 46.6 1.0 NH2 P:ARG37 4.7 56.2 1.0 NE2 P:HIS40 4.8 36.6 1.0 O P:ARG37 4.8 46.3 1.0 CD2 P:HIS40 4.9 35.9 1.0 CD2 P:LEU7 5.0 55.1 1.0

Cadmium binding site 2 out of 5 in the Co-Crystal Structure of Tylosin 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 Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ V:Cd8401 b:0.4 occ:1.00 CB V:CYS9 2.9 92.1 1.0 N V:CYS9 3.0 92.4 1.0 SG V:CYS36 3.1 92.3 1.0 SG V:CYS6 3.1 99.0 1.0 CB V:CYS36 3.3 87.9 1.0 SG V:CYS9 3.3 92.8 1.0 CB V:CYS6 3.4 97.0 1.0 CA V:CYS9 3.5 92.0 1.0 CB V:TYR8 3.8 92.7 1.0 C V:TYR8 4.1 92.5 1.0 SG V:CYS32 4.1 95.1 1.0 CD2 V:TYR8 4.2 92.4 1.0 CA V:TYR8 4.3 93.1 1.0 N V:GLY10 4.4 91.0 1.0 C V:CYS9 4.5 91.8 1.0 CG V:TYR8 4.5 92.7 1.0 N V:TYR8 4.6 93.8 1.0 CB V:CYS32 4.6 94.3 1.0 N V:CYS32 4.6 92.6 1.0 CA V:CYS36 4.8 87.5 1.0 CA V:CYS6 4.8 96.6 1.0 OG1 V:THR11 4.9 90.4 1.0 O V:CYS6 5.0 94.8 1.0

Cadmium binding site 3 out of 5 in the Co-Crystal Structure of Tylosin 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 Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8403 b:0.5 occ:1.00 SG 1:CYS39 3.2 97.2 1.0 CB 1:CYS42 3.3 98.0 1.0 CB 1:CYS60 3.3 92.9 1.0 SG 1:CYS60 3.4 92.5 1.0 N 1:CYS42 3.6 98.6 1.0 SG 1:CYS42 3.6 97.3 1.0 CB 1:CYS39 3.7 95.2 1.0 SG 1:CYS57 3.7 98.3 1.0 CB 1:CYS57 3.8 95.6 1.0 CA 1:CYS42 4.0 98.2 1.0 N 1:CYS60 4.0 93.6 1.0 CA 1:CYS60 4.3 92.5 1.0 CB 1:VAL41 4.3 99.0 1.0 CG1 1:VAL41 4.3 99.1 1.0 CB 1:TYR62 4.6 86.4 1.0 CD2 1:HIS59 4.6 0.6 1.0 C 1:VAL41 4.7 98.9 1.0 C 1:CYS42 4.7 98.0 1.0 CB 1:HIS59 4.8 97.5 1.0 CA 1:VAL41 5.0 98.6 1.0

Cadmium binding site 4 out of 5 in the Co-Crystal Structure of Tylosin 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 Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 2:Cd8402 b:52.3 occ:1.00 SG 2:CYS37 2.3 33.2 1.0 SG 2:CYS19 2.5 41.8 1.0 SG 2:CYS34 2.6 31.9 1.0 SG 2:CYS22 2.7 30.0 1.0 CB 2:CYS19 3.0 34.4 1.0 CB 2:CYS34 3.2 30.1 1.0 CB 2:CYS37 3.3 31.2 1.0 CB 2:CYS22 3.4 30.6 1.0 N 2:CYS22 3.7 33.8 1.0 N 2:CYS37 3.8 31.6 1.0 CA 2:CYS22 4.1 33.0 1.0 CA 2:CYS37 4.1 31.1 1.0 CB 2:PHE39 4.3 35.7 1.0 CA 2:CYS19 4.5 33.0 1.0 CB 2:ARG21 4.6 36.0 1.0 CA 2:CYS34 4.6 29.9 1.0 C 2:ARG21 4.7 33.6 1.0 C 2:CYS22 4.8 33.5 1.0 O 2:HOH1020 4.8 47.3 1.0 C 2:CYS37 4.8 30.9 1.0 N 2:PHE39 4.9 33.3 1.0 N 2:GLY38 4.9 29.7 1.0 N 2:GLY23 4.9 34.3 1.0 CB 2:SER36 4.9 29.6 1.0 C 2:SER36 4.9 30.7 1.0 CA 2:ARG21 5.0 35.5 1.0

Cadmium binding site 5 out of 5 in the Co-Crystal Structure of Tylosin 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 Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 4:Cd8404 b:0.7 occ:1.00 CB 4:CYS14 2.9 0.7 1.0 O 4:HOH8563 3.0 0.8 1.0 SG 4:CYS71 3.1 0.3 1.0 CB 4:CYS71 3.5 0.9 1.0 SG 4:CYS11 3.5 0.4 1.0 CB 4:CYS74 3.6 0.8 1.0 SG 4:CYS14 3.7 0.9 1.0 CB 4:CYS11 3.7 0.2 1.0 N 4:CYS14 3.8 0.8 1.0 CA 4:CYS14 3.9 0.4 1.0 OE1 4:GLN18 3.9 0.9 1.0 SG 4:CYS74 4.0 0.3 1.0 N 4:CYS74 4.1 0.9 1.0 CD 4:GLN18 4.3 0.5 1.0 NE2 4:GLN18 4.4 0.5 1.0 CA 4:CYS74 4.5 1.0 1.0 CB 4:GLN18 4.9 0.7 1.0 CA 4:CYS71 5.0 0.8 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