Cadmium in PDB 1m1k: Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1m1k 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)	20.00 / 3.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	213.751, 301.566, 574.436, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25

The structure of Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui 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 Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1m1k). 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 Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1m1k:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Co-Crystal Structure of Azithromycin 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 Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ P:Cd8405 b:0.6 occ:1.00 ND1 P:HIS40 2.8 56.4 1.0 O P:HOH5322 2.9 27.7 1.0 O P:HOH5650 2.9 50.2 1.0 CG P:HIS40 3.6 54.9 1.0 CE1 P:HIS40 3.7 55.7 1.0 CB P:HIS40 3.8 53.3 1.0 CG P:ARG37 4.3 63.7 1.0 NH1 P:ARG37 4.7 67.2 1.0 O A:HOH3935 4.7 47.6 1.0 CZ P:ARG37 4.7 67.0 1.0 O P:ARG37 4.7 59.0 1.0 CD2 P:HIS40 4.7 54.7 1.0 NE2 P:HIS40 4.8 55.5 1.0 CA P:ARG37 4.8 59.9 1.0 CB P:ARG37 4.8 61.8 1.0 NE P:ARG37 4.9 67.3 1.0

Cadmium binding site 2 out of 5 in the Co-Crystal Structure of Azithromycin 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 Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ V:Cd8401 b:75.8 occ:1.00 SG V:CYS32 2.2 46.8 1.0 SG V:CYS36 2.3 57.2 1.0 SG V:CYS6 2.4 61.1 1.0 SG V:CYS9 2.6 62.7 1.0 CB V:CYS6 3.3 63.6 1.0 CB V:CYS9 3.4 63.1 1.0 CB V:CYS36 3.5 57.8 1.0 CB V:CYS32 3.6 52.8 1.0 N V:CYS9 3.8 63.4 1.0 N V:CYS32 4.1 54.1 1.0 CA V:CYS9 4.2 62.6 1.0 OG1 V:THR11 4.4 69.8 1.0 OG V:SER33 4.4 60.1 1.0 CA V:CYS32 4.4 54.5 1.0 CB V:TYR8 4.6 63.4 1.0 N V:SER33 4.7 58.4 1.0 CA V:CYS6 4.8 63.5 1.0 N V:GLY10 4.8 63.2 1.0 CA V:CYS36 4.9 58.1 1.0 C V:TYR8 4.9 64.1 1.0 C V:CYS9 4.9 62.7 1.0 C V:CYS32 5.0 56.2 1.0 CD2 V:TYR8 5.0 62.0 1.0

Cadmium binding site 3 out of 5 in the Co-Crystal Structure of Azithromycin 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 Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8403 b:77.5 occ:1.00 SG 1:CYS60 2.3 68.5 1.0 SG 1:CYS39 2.4 64.0 1.0 SG 1:CYS57 2.5 75.7 1.0 SG 1:CYS42 2.8 80.1 1.0 CB 1:CYS39 3.3 67.3 1.0 CB 1:CYS57 3.3 75.7 1.0 CB 1:CYS60 3.4 68.3 1.0 CB 1:CYS42 3.5 80.4 1.0 N 1:CYS42 3.7 81.2 1.0 N 1:CYS60 3.9 70.4 1.0 CA 1:CYS42 4.2 81.1 1.0 CA 1:CYS60 4.3 68.6 1.0 CB 1:VAL41 4.6 80.9 1.0 CB 1:TYR62 4.6 69.8 1.0 CB 1:HIS59 4.6 79.8 1.0 CD2 1:HIS59 4.7 84.1 1.0 CA 1:CYS39 4.7 71.3 1.0 CG1 1:VAL41 4.8 80.8 1.0 CA 1:CYS57 4.8 74.9 1.0 C 1:CYS42 4.9 81.3 1.0 C 1:VAL41 4.9 80.7 1.0

Cadmium binding site 4 out of 5 in the Co-Crystal Structure of Azithromycin 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 Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 2:Cd8402 b:70.2 occ:1.00 SG 2:CYS37 2.4 49.8 1.0 SG 2:CYS19 2.5 54.4 1.0 SG 2:CYS34 2.6 49.0 1.0 SG 2:CYS22 2.6 48.3 1.0 CB 2:CYS19 3.0 50.4 1.0 CB 2:CYS22 3.2 47.3 1.0 CB 2:CYS34 3.2 45.7 1.0 CB 2:CYS37 3.3 44.4 1.0 N 2:CYS22 3.6 46.6 1.0 N 2:CYS37 3.8 44.7 1.0 CA 2:CYS22 4.0 48.4 1.0 CA 2:CYS37 4.2 45.0 1.0 CB 2:PHE39 4.3 49.2 1.0 CA 2:CYS19 4.5 50.0 1.0 CB 2:ARG21 4.6 46.9 1.0 C 2:CYS22 4.7 47.2 1.0 CA 2:CYS34 4.7 47.2 1.0 C 2:ARG21 4.7 47.6 1.0 O 2:HOH8420 4.7 36.1 1.0 CB 2:SER36 4.7 43.9 1.0 N 2:GLY23 4.8 47.6 1.0 N 2:PHE39 4.8 46.8 1.0 C 2:CYS37 4.9 43.4 1.0 C 2:SER36 4.9 43.6 1.0 N 2:GLY38 4.9 43.9 1.0 C 2:CYS19 5.0 49.2 1.0 N 2:GLU24 5.0 49.2 1.0

Cadmium binding site 5 out of 5 in the Co-Crystal Structure of Azithromycin 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 Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 4:Cd8404 b:75.5 occ:1.00 SG 4:CYS71 2.3 54.0 1.0 SG 4:CYS74 2.5 72.7 1.0 SG 4:CYS14 2.5 79.9 1.0 SG 4:CYS11 2.6 72.2 1.0 CB 4:CYS14 3.0 76.7 1.0 CB 4:CYS71 3.1 59.3 1.0 O 4:HOH8561 3.1 0.8 1.0 CB 4:CYS74 3.5 71.5 1.0 CB 4:CYS11 3.5 70.4 1.0 N 4:CYS14 3.7 75.1 1.0 CA 4:CYS14 3.9 75.6 1.0 N 4:CYS74 4.1 73.2 1.0 CA 4:CYS74 4.3 72.0 1.0 CA 4:CYS71 4.5 62.6 1.0 OE1 4:GLN18 4.6 79.8 1.0 CB 4:HIS13 4.7 73.3 1.0 C 4:HIS13 4.9 75.8 1.0 CD 4:GLN18 5.0 77.7 1.0 CA 4:CYS11 5.0 70.7 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