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Cadmium in PDB 3g4s: Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit

Protein crystallography data

The structure of Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit, PDB code: 3g4s 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) 49.84 / 3.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.270, 299.840, 574.137, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 29

Other elements in 3g4s:

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

Strontium (Sr) 108 atoms
Magnesium (Mg) 93 atoms
Potassium (K) 1 atom
Chlorine (Cl) 22 atoms
Sodium (Na) 75 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit (pdb code 3g4s). 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 Tiamulin Bound to the Large Ribosomal Subunit, PDB code: 3g4s:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3g4s

Go back to Cadmium Binding Sites List in 3g4s
Cadmium binding site 1 out of 5 in the Co-Crystal Structure of Tiamulin 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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:0.0
occ:1.00
 ND1 O:HIS40 2.6 62.5 1.0
O O:HOH5650 3.2 65.9 1.0
CE1 O:HIS40 3.3 61.0 1.0
CG O:HIS40 3.8 63.6 1.0
O O:HOH5322 3.8 56.5 1.0
O O:HOH3002 4.0 77.2 1.0
CB O:HIS40 4.2 66.7 1.0
NE2 O:HIS40 4.5 61.5 1.0
CZ O:ARG37 4.5 77.9 1.0
NH2 O:ARG37 4.6 79.3 1.0
CD2 O:HIS40 4.8 62.5 1.0
NE O:ARG37 4.8 77.5 1.0
NH1 O:ARG37 4.8 76.5 1.0
CD1 O:LEU7 4.9 82.9 1.0
CG O:ARG37 4.9 76.3 1.0
CD2 O:LEU7 5.0 84.3 1.0

Cadmium binding site 2 out of 5 in 3g4s

Go back to Cadmium Binding Sites List in 3g4s
Cadmium binding site 2 out of 5 in the Co-Crystal Structure of Tiamulin 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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:0.4
occ:1.00
 CB U:CYS9 2.9 0.3 1.0
OG1 U:THR11 3.0 0.8 1.0
SG U:CYS36 3.1 0.9 1.0
SG U:CYS6 3.1 0.8 1.0
SG U:CYS32 3.2 0.8 1.0
CB U:CYS32 3.5 0.8 1.0
N U:CYS32 3.6 0.1 1.0
CB U:CYS36 3.7 0.6 1.0
N U:CYS9 3.8 0.4 1.0
CB U:CYS6 4.0 0.5 1.0
SG U:CYS9 4.0 0.7 1.0
CA U:CYS9 4.0 0.9 1.0
CA U:CYS32 4.1 0.0 1.0
CB U:THR11 4.4 0.1 1.0
C U:PHE31 4.6 0.5 1.0
N U:SER33 4.7 0.2 1.0
CA U:PHE31 4.8 0.5 1.0
CB U:TYR8 4.8 0.3 1.0
C U:CYS9 4.8 0.7 1.0
CD2 U:TYR8 4.9 1.0 1.0
C U:CYS32 4.9 1.0 1.0
N U:GLY10 4.9 0.3 1.0
N U:THR11 5.0 0.7 1.0

Cadmium binding site 3 out of 5 in 3g4s

Go back to Cadmium Binding Sites List in 3g4s
Cadmium binding site 3 out of 5 in the Co-Crystal Structure of Tiamulin 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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:0.8
occ:1.00
 CB Z:CYS84 3.1 0.6 1.0
N Z:CYS84 3.2 0.3 1.0
CD2 Z:TYR83 3.3 0.9 1.0
CA Z:CYS84 3.5 0.3 1.0
C Z:CYS84 3.7 0.9 1.0
CB Z:ASN65 3.8 0.1 1.0
CB Z:TYR83 3.9 0.4 1.0
SG Z:CYS66 3.9 0.1 1.0
SG Z:CYS81 3.9 0.3 1.0
O Z:CYS84 4.1 0.8 1.0
CB Z:TYR86 4.1 0.3 1.0
CG Z:TYR83 4.1 0.1 1.0
ND2 Z:ASN65 4.1 0.3 1.0
SG Z:CYS84 4.2 0.6 1.0
N Z:ASP85 4.2 0.4 1.0
CE2 Z:TYR83 4.3 0.3 1.0
O Z:ASN65 4.3 1.0 1.0
N Z:TYR86 4.3 0.3 1.0
SG Z:CYS63 4.3 0.8 1.0
C Z:TYR83 4.4 1.0 1.0
C Z:ASN65 4.4 0.2 1.0
CB Z:CYS66 4.4 0.5 1.0
CG Z:ASN65 4.5 0.7 1.0
CB Z:CYS81 4.6 0.9 1.0
CA Z:ASN65 4.6 0.4 1.0
CA Z:TYR83 4.7 0.9 1.0
CA Z:TYR86 4.8 0.8 1.0
N Z:CYS66 4.8 0.9 1.0

Cadmium binding site 4 out of 5 in 3g4s

Go back to Cadmium Binding Sites List in 3g4s
Cadmium binding site 4 out of 5 in the Co-Crystal Structure of Tiamulin 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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:68.4
occ:1.00
 SG 1:CYS37 2.5 53.9 1.0
SG 1:CYS34 2.6 49.8 1.0
SG 1:CYS22 2.6 59.5 1.0
SG 1:CYS19 2.7 61.1 1.0
CB 1:CYS19 3.1 57.4 1.0
CB 1:CYS37 3.3 52.2 1.0
CB 1:CYS22 3.4 56.6 1.0
CB 1:CYS34 3.5 48.2 1.0
N 1:CYS22 3.7 57.7 1.0
N 1:CYS37 3.9 53.5 1.0
CA 1:CYS22 4.1 57.0 1.0
CA 1:CYS37 4.1 51.9 1.0
N 1:GLY23 4.5 55.3 1.0
CB 1:PHE39 4.6 59.5 1.0
CA 1:CYS19 4.6 55.8 1.0
CB 1:ARG21 4.7 53.6 1.0
C 1:CYS22 4.8 56.2 1.0
CB 1:SER36 4.8 51.0 1.0
C 1:ARG21 4.8 56.2 1.0
C 1:CYS37 4.8 50.4 1.0
N 1:GLY38 4.9 50.7 1.0
CA 1:CYS34 4.9 49.0 1.0
O 1:GLU24 5.0 53.1 1.0
C 1:SER36 5.0 51.9 1.0
N 1:GLU24 5.0 53.1 1.0

Cadmium binding site 5 out of 5 in 3g4s

Go back to Cadmium Binding Sites List in 3g4s
Cadmium binding site 5 out of 5 in the Co-Crystal Structure of Tiamulin 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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:0.3
occ:1.00
 CB 3:CYS11 3.1 0.4 1.0
CE1 3:HIS20 3.3 0.3 1.0
O 3:GLU16 3.5 0.3 1.0
CB 3:CYS14 3.5 0.1 1.0
SG 3:CYS14 3.7 0.1 1.0
N 3:GLN18 3.7 0.0 1.0
NE2 3:HIS20 3.8 0.3 1.0
CB 3:GLN18 3.8 0.9 1.0
OE1 3:GLN18 3.8 0.6 1.0
N 3:CYS11 3.9 0.2 1.0
O 3:THR9 4.0 0.4 1.0
SG 3:CYS11 4.1 0.1 1.0
C 3:GLU16 4.1 0.0 1.0
CA 3:CYS11 4.1 0.1 1.0
SG 3:CYS71 4.2 0.5 1.0
CD 3:GLN18 4.2 0.7 1.0
CA 3:GLN18 4.3 0.9 1.0
C 3:TYR10 4.3 0.3 1.0
CB 3:CYS71 4.4 0.4 1.0
ND1 3:HIS20 4.4 0.3 1.0
C 3:HIS17 4.5 0.2 1.0
O 3:CYS11 4.5 0.6 1.0
CG 3:GLN18 4.6 0.4 1.0
CA 3:HIS17 4.6 0.4 1.0
N 3:HIS17 4.6 0.9 1.0
O 3:GLN18 4.6 0.5 1.0
O 3:TYR10 4.7 0.3 1.0
N 3:GLU16 4.8 1.0 1.0
CA 3:TYR10 4.8 0.4 1.0
C 3:GLN18 4.8 0.5 1.0
C 3:CYS11 4.8 0.8 1.0
CA 3:CYS14 4.9 0.1 1.0
CG 3:GLU16 4.9 0.6 1.0
CA 3:GLU16 5.0 0.0 1.0

Reference:

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
Page generated: Thu Jul 10 12:37:44 2025

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