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Cadmium in PDB 3ccj: Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U

Protein crystallography data

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U, PDB code: 3ccj was solved by G.Blaha, G.Gurel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.010, 299.254, 573.808, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 28.7

Other elements in 3ccj:

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U 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

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U (pdb code 3ccj). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U, PDB code: 3ccj:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3ccj

Go back to Cadmium Binding Sites List in 3ccj
Cadmium binding site 1 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:0.8
occ:1.00
 ND1 O:HIS40 2.6 55.8 1.0
O 0:HOH6199 2.7 54.1 1.0
O 0:HOH5962 3.5 53.4 1.0
CE1 O:HIS40 3.5 56.0 1.0
CG O:HIS40 3.6 56.0 1.0
O 0:HOH4326 3.7 54.7 1.0
CB O:HIS40 3.9 57.2 1.0
CZ O:ARG37 4.3 62.2 1.0
NE O:ARG37 4.3 62.8 1.0
NH2 O:ARG37 4.4 61.4 1.0
CG O:ARG37 4.5 63.4 1.0
NE2 O:HIS40 4.7 56.2 1.0
CD2 O:HIS40 4.8 55.7 1.0
CB O:ARG37 4.8 61.5 1.0
NH1 O:ARG37 4.8 60.9 1.0
CD O:ARG37 5.0 63.8 1.0

Cadmium binding site 2 out of 5 in 3ccj

Go back to Cadmium Binding Sites List in 3ccj
Cadmium binding site 2 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:0.5
occ:1.00
 CB U:CYS36 2.8 0.3 1.0
CB U:TYR8 3.3 0.6 1.0
CD2 U:PHE31 3.3 0.9 1.0
CG U:TYR8 3.5 0.0 1.0
CD2 U:TYR8 3.5 0.3 1.0
SG U:CYS6 3.6 0.4 1.0
O U:SER33 3.7 0.5 1.0
C U:CYS36 3.7 0.3 1.0
CA U:CYS36 3.8 0.5 1.0
N U:GLU37 3.8 0.6 1.0
N U:CYS32 3.9 0.5 1.0
CA U:PHE31 3.9 0.6 1.0
CB U:PHE31 4.0 0.8 1.0
SG U:CYS36 4.0 0.3 1.0
SG U:CYS32 4.0 0.2 1.0
CG U:PHE31 4.1 1.0 1.0
O U:CYS36 4.2 0.1 1.0
CE2 U:PHE31 4.2 0.8 1.0
N U:SER33 4.4 0.9 1.0
N U:CYS36 4.4 1.0 1.0
C U:PHE31 4.4 0.6 1.0
CD1 U:TYR8 4.4 0.3 1.0
CE2 U:TYR8 4.5 0.3 1.0
CA U:GLU37 4.5 0.1 1.0
N U:CYS9 4.5 0.6 1.0
CA U:TYR8 4.7 0.3 1.0
C U:SER33 4.8 0.6 1.0
CG U:GLU37 4.8 0.4 1.0
OG U:SER33 4.8 0.6 1.0
O U:HIS30 4.8 0.6 1.0
CA U:CYS32 4.9 0.6 1.0
SG U:CYS9 4.9 0.3 1.0

Cadmium binding site 3 out of 5 in 3ccj

Go back to Cadmium Binding Sites List in 3ccj
Cadmium binding site 3 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:0.3
occ:1.00
 SG Z:CYS84 2.7 0.7 1.0
CD2 Z:TYR83 3.1 0.6 1.0
SG Z:CYS81 3.4 0.0 1.0
SG Z:CYS66 3.4 0.4 1.0
CB Z:CYS84 3.6 1.0 1.0
CB Z:GLU68 3.7 0.5 1.0
O Z:CYS66 3.8 0.3 1.0
N Z:CYS66 3.8 0.7 1.0
CE2 Z:TYR83 3.9 0.5 1.0
N Z:CYS84 3.9 0.8 1.0
CB Z:ASN65 4.0 1.0 1.0
CB Z:CYS63 4.0 0.7 1.0
CG Z:TYR83 4.0 0.4 1.0
OE1 Z:GLU68 4.1 0.5 1.0
CB Z:TYR83 4.1 0.7 1.0
CG Z:GLU68 4.1 0.1 1.0
CB Z:CYS66 4.4 0.0 1.0
CA Z:CYS84 4.4 0.2 1.0
CA Z:CYS66 4.4 0.2 1.0
C Z:CYS66 4.4 0.2 1.0
SG Z:CYS63 4.6 0.0 1.0
CD Z:GLU68 4.6 0.4 1.0
CB Z:CYS81 4.6 0.4 1.0
C Z:ASN65 4.8 0.3 1.0
CA Z:ASN65 4.8 0.8 1.0
N Z:GLU68 4.8 0.0 1.0
CA Z:GLU68 4.8 0.9 1.0
N Z:ASN65 4.9 0.1 1.0

Cadmium binding site 4 out of 5 in 3ccj

Go back to Cadmium Binding Sites List in 3ccj
Cadmium binding site 4 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:78.3
occ:1.00
 SG 1:CYS22 2.2 39.9 1.0
SG 1:CYS34 2.3 38.6 1.0
SG 1:CYS19 2.4 48.9 1.0
SG 1:CYS37 2.4 44.8 1.0
CB 1:CYS19 2.9 49.1 1.0
CB 1:CYS34 3.0 39.3 1.0
CB 1:CYS22 3.2 43.5 1.0
CB 1:CYS37 3.4 46.8 1.0
N 1:CYS22 3.6 45.3 1.0
CA 1:CYS22 4.0 45.0 1.0
N 1:CYS37 4.0 47.7 1.0
CB 1:PHE39 4.1 54.2 1.0
CA 1:CYS37 4.2 46.0 1.0
CA 1:CYS34 4.4 41.0 1.0
CA 1:CYS19 4.4 49.1 1.0
CB 1:ARG21 4.6 44.3 1.0
N 1:GLY23 4.6 47.8 1.0
C 1:ARG21 4.7 45.6 1.0
C 1:CYS22 4.7 46.0 1.0
N 1:PHE39 4.7 52.3 1.0
C 1:CYS37 4.8 45.5 1.0
N 1:ARG21 4.9 45.7 1.0
C 1:CYS19 4.9 48.6 1.0
CA 1:ARG21 4.9 45.5 1.0
N 1:GLY38 5.0 45.9 1.0
O 1:GLU24 5.0 52.4 1.0

Cadmium binding site 5 out of 5 in 3ccj

Go back to Cadmium Binding Sites List in 3ccj
Cadmium binding site 5 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2534U within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:0.3
occ:1.00
 CB 3:CYS11 2.5 0.6 1.0
CB 3:CYS14 3.2 0.1 1.0
CB 3:GLN18 3.6 0.4 1.0
SG 3:CYS11 3.6 0.6 1.0
O 3:CYS11 3.6 0.2 1.0
CA 3:CYS11 3.7 0.8 1.0
CB 3:CYS74 3.8 1.0 1.0
O 3:GLU16 3.8 0.7 1.0
N 3:GLN18 3.9 0.5 1.0
SG 3:CYS71 3.9 0.2 1.0
CG 3:GLN18 4.0 0.8 1.0
OE1 3:GLN18 4.0 0.9 1.0
N 3:CYS11 4.0 0.1 1.0
N 3:CYS14 4.0 0.6 1.0
SG 3:CYS74 4.0 0.4 1.0
SG 3:CYS14 4.1 0.7 1.0
C 3:CYS11 4.1 0.4 1.0
CD 3:GLN18 4.1 0.7 1.0
CA 3:CYS14 4.2 0.0 1.0
CG 3:GLU16 4.2 0.9 1.0
CA 3:GLN18 4.3 0.4 1.0
C 3:GLU16 4.3 0.2 1.0
N 3:GLU16 4.6 0.1 1.0
O 3:GLN18 4.7 0.5 1.0
CE1 3:HIS20 4.8 0.9 1.0
C 3:CYS14 4.8 0.3 1.0
C 3:HIS17 4.8 0.2 1.0
N 3:HIS17 4.9 0.7 1.0
N 3:ASN15 4.9 0.7 1.0
CA 3:GLU16 4.9 0.8 1.0
C 3:GLN18 4.9 1.0 1.0
NE2 3:GLN18 5.0 0.3 1.0
NE2 3:HIS20 5.0 0.4 1.0

Reference:

G.Blaha, G.Gurel, S.J.Schroeder, P.B.Moore, T.A.Steitz. Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant. J.Mol.Biol. V. 379 505 2008.
ISSN: ISSN 0022-2836
PubMed: 18455733
DOI: 10.1016/J.JMB.2008.03.075
Page generated: Fri Jul 19 15:41:30 2024

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