Cadmium in PDB 3g6e: Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit

The structure of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit, PDB code: 3g6e was solved by G.Gurel, G.Blaha, 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)	49.90 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.863, 299.418, 574.087, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.9

The structure of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit also contains other interesting chemical elements:

Strontium	(Sr)	108 atoms
Magnesium	(Mg)	93 atoms
Potassium	(K)	2 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	75 atoms

The binding sites of Cadmium atom in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit (pdb code 3g6e). 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 Homoharringtonine Bound to the Large Ribosomal Subunit, PDB code: 3g6e:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd8705 b:99.8 occ:1.00 O O:HOH5650 2.6 46.1 1.0 ND1 O:HIS40 2.6 39.1 1.0 O 0:HOH5322 2.9 40.7 1.0 CE1 O:HIS40 3.5 39.8 1.0 CG O:HIS40 3.6 38.0 1.0 CB O:HIS40 3.9 41.6 1.0 O 0:HOH3002 4.5 54.5 1.0 CG O:ARG37 4.5 52.2 1.0 NE2 O:HIS40 4.7 39.2 1.0 CZ O:ARG37 4.8 52.9 1.0 CD2 O:HIS40 4.8 38.6 1.0 NE O:ARG37 4.8 53.8 1.0 CB O:ARG37 5.0 50.0 1.0

Cadmium binding site 2 out of 5 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ U:Cd8701 b:72.5 occ:1.00 SG U:CYS36 2.6 60.8 1.0 SG U:CYS9 2.6 61.3 1.0 SG U:CYS32 2.6 48.1 1.0 SG U:CYS6 2.6 59.9 1.0 CB U:CYS9 3.3 60.6 1.0 CB U:CYS6 3.4 62.3 1.0 CB U:CYS36 3.5 59.6 1.0 CB U:CYS32 3.5 51.0 1.0 N U:CYS9 3.8 60.9 1.0 N U:CYS32 4.0 50.9 1.0 CA U:CYS9 4.2 62.0 1.0 CA U:CYS32 4.3 53.1 1.0 OG1 U:THR11 4.3 72.3 1.0 OG U:SER33 4.5 57.5 1.0 N U:SER33 4.7 56.0 1.0 CB U:TYR8 4.7 57.7 1.0 N U:GLY10 4.9 64.2 1.0 C U:CYS32 4.9 54.9 1.0 CA U:CYS6 4.9 63.0 1.0 CA U:CYS36 4.9 59.5 1.0

Cadmium binding site 3 out of 5 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ Z:Cd8703 b:98.7 occ:1.00 SG Z:CYS84 2.6 91.3 1.0 SG Z:CYS63 2.7 0.2 1.0 SG Z:CYS81 2.9 96.0 1.0 SG Z:CYS66 3.0 0.7 1.0 CB Z:CYS81 3.5 93.5 1.0 CB Z:CYS63 3.5 0.5 1.0 CB Z:CYS84 3.7 91.0 1.0 N Z:CYS84 3.9 92.2 1.0 CB Z:ASN65 3.9 0.7 1.0 N Z:CYS66 4.0 0.3 1.0 CB Z:CYS66 4.0 0.1 1.0 CD2 Z:TYR83 4.3 98.5 1.0 CA Z:CYS84 4.3 91.4 1.0 CB Z:TYR83 4.3 95.5 1.0 CB Z:TYR86 4.6 79.8 1.0 CA Z:CYS66 4.6 0.4 1.0 CA Z:ASN65 4.8 0.6 1.0 CG Z:TYR83 4.9 97.6 1.0 C Z:ASN65 4.9 0.1 1.0 N Z:ASN65 4.9 0.4 1.0 C Z:TYR83 4.9 93.6 1.0 CA Z:CYS81 4.9 92.5 1.0 CA Z:CYS63 5.0 0.8 1.0

Cadmium binding site 4 out of 5 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8702 b:57.8 occ:1.00 SG 1:CYS37 2.5 43.1 1.0 SG 1:CYS22 2.5 42.7 1.0 SG 1:CYS34 2.5 43.5 1.0 SG 1:CYS19 2.7 43.6 1.0 CB 1:CYS19 3.2 35.9 1.0 CB 1:CYS34 3.2 32.6 1.0 CB 1:CYS37 3.3 31.9 1.0 CB 1:CYS22 3.3 38.5 1.0 N 1:CYS37 3.8 30.9 1.0 N 1:CYS22 3.8 38.9 1.0 CA 1:CYS37 4.1 30.9 1.0 CA 1:CYS22 4.1 38.5 1.0 CB 1:PHE39 4.4 35.8 1.0 CB 1:ARG21 4.7 37.6 1.0 CA 1:CYS19 4.7 37.7 1.0 CA 1:CYS34 4.7 33.8 1.0 C 1:CYS37 4.7 30.5 1.0 CB 1:SER36 4.8 32.1 1.0 O 1:HOH1020 4.8 34.5 1.0 C 1:ARG21 4.8 39.1 1.0 N 1:GLY38 4.9 31.1 1.0 C 1:SER36 4.9 32.2 1.0 C 1:CYS22 4.9 38.8 1.0 N 1:PHE39 4.9 32.6 1.0 N 1:GLY23 4.9 38.5 1.0

Cadmium binding site 5 out of 5 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


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 Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 3:Cd8704 b:76.4 occ:1.00 SG 3:CYS71 2.6 66.9 1.0 SG 3:CYS11 2.6 73.8 1.0 SG 3:CYS74 2.7 85.2 1.0 O 3:HOH6741 2.8 0.3 1.0 CB 3:CYS14 2.9 82.3 1.0 CB 3:CYS74 3.4 81.6 1.0 CB 3:CYS71 3.4 70.2 1.0 SG 3:CYS14 3.6 87.2 1.0 CB 3:CYS11 3.6 71.2 1.0 N 3:CYS14 3.8 82.0 1.0 CA 3:CYS14 4.0 82.1 1.0 N 3:CYS74 4.1 80.5 1.0 CA 3:CYS74 4.3 80.9 1.0 CB 3:HIS13 4.8 79.6 1.0 O 3:HOH3785 4.8 47.5 1.0 C 3:HIS13 4.9 81.5 1.0 CA 3:CYS71 4.9 71.3 1.0 OE1 3:GLN18 4.9 80.6 1.0 CB 3:GLN18 5.0 75.1 1.0 CG 3:GLN18 5.0 77.6 1.0

G.Gurel, G.Blaha, P.B.Moore, T.A.Steitz. U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: the Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome. J.Mol.Biol. V. 389 146 2009.
ISSN: ISSN 0022-2836
PubMed: 19362093
DOI: 10.1016/J.JMB.2009.04.005