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Cadmium in PDB 3cc7: Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2487U

Protein crystallography data

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2487U, PDB code: 3cc7 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) 49.83 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.832, 299.896, 576.013, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.6

Other elements in 3cc7:

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2487U 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 C2487U (pdb code 3cc7). 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 C2487U, PDB code: 3cc7:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3cc7

Go back to Cadmium Binding Sites List in 3cc7
Cadmium binding site 1 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2487U


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 C2487U within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:83.5
occ:1.00
O 0:HOH6308 2.5 35.6 1.0
ND1 O:HIS40 2.6 34.5 1.0
O O:HOH5322 2.7 32.0 1.0
CE1 O:HIS40 3.5 33.4 1.0
CG O:HIS40 3.5 32.5 1.0
CB O:HIS40 3.8 34.9 1.0
O 0:HOH4388 4.4 50.5 1.0
CZ O:ARG37 4.6 46.2 1.0
CG O:ARG37 4.6 47.5 1.0
NE2 O:HIS40 4.6 33.4 1.0
CD2 O:HIS40 4.7 32.6 1.0
NE O:ARG37 4.8 46.3 1.0
NH2 O:ARG37 4.8 44.3 1.0
CB O:ARG37 4.9 44.8 1.0
NH1 O:ARG37 4.9 46.3 1.0
CA O:ARG37 5.0 43.3 1.0
O O:ARG37 5.0 43.8 1.0

Cadmium binding site 2 out of 5 in 3cc7

Go back to Cadmium Binding Sites List in 3cc7
Cadmium binding site 2 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2487U


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 C2487U within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:52.0
occ:1.00
SG U:CYS36 2.4 49.9 1.0
SG U:CYS32 2.4 40.7 1.0
SG U:CYS9 2.5 53.7 1.0
SG U:CYS6 2.5 49.8 1.0
CB U:CYS9 3.2 51.7 1.0
CB U:CYS6 3.2 54.0 1.0
CB U:CYS36 3.5 51.0 1.0
CB U:CYS32 3.5 43.0 1.0
N U:CYS9 3.7 51.9 1.0
N U:CYS32 4.0 43.3 1.0
CA U:CYS9 4.1 52.0 1.0
CA U:CYS32 4.3 44.0 1.0
OG U:SER33 4.4 42.3 1.0
OG1 U:THR11 4.6 63.8 1.0
N U:GLY10 4.7 53.7 1.0
CB U:TYR8 4.7 48.0 1.0
CA U:CYS6 4.7 53.7 1.0
N U:SER33 4.7 47.2 1.0
C U:CYS32 4.8 46.9 1.0
C U:CYS9 4.9 52.8 1.0
CA U:CYS36 4.9 49.9 1.0
C U:TYR8 4.9 50.8 1.0

Cadmium binding site 3 out of 5 in 3cc7

Go back to Cadmium Binding Sites List in 3cc7
Cadmium binding site 3 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2487U


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 C2487U within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:71.6
occ:1.00
SG Z:CYS84 2.3 64.4 1.0
SG Z:CYS63 2.3 66.8 1.0
SG Z:CYS81 2.5 66.4 1.0
SG Z:CYS66 2.8 78.8 1.0
CB Z:CYS81 3.1 66.7 1.0
CB Z:CYS84 3.2 64.9 1.0
CB Z:CYS63 3.3 69.8 1.0
N Z:CYS66 3.5 78.3 1.0
CB Z:CYS66 3.5 78.3 1.0
N Z:CYS84 3.7 66.4 1.0
CB Z:ASN65 3.8 75.5 1.0
CA Z:CYS84 4.0 65.5 1.0
CA Z:CYS66 4.1 78.9 1.0
CD2 Z:TYR83 4.5 75.8 1.0
CB Z:TYR83 4.5 71.2 1.0
C Z:ASN65 4.5 77.6 1.0
CB Z:TYR86 4.6 56.5 1.0
CA Z:ASN65 4.6 76.8 1.0
CA Z:CYS81 4.7 65.5 1.0
C Z:CYS84 4.7 65.4 1.0
CA Z:CYS63 4.7 71.1 1.0
N Z:ASN65 4.8 76.5 1.0
C Z:TYR83 4.8 68.0 1.0
N Z:ASP85 4.9 65.9 1.0
C Z:CYS66 4.9 79.3 1.0
CG Z:ASN65 5.0 75.3 1.0
CG Z:TYR83 5.0 74.2 1.0
N Z:TYR86 5.0 62.9 1.0

Cadmium binding site 4 out of 5 in 3cc7

Go back to Cadmium Binding Sites List in 3cc7
Cadmium binding site 4 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2487U


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 C2487U within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:53.7
occ:1.00
SG 1:CYS34 2.4 31.4 1.0
SG 1:CYS37 2.4 30.9 1.0
SG 1:CYS22 2.5 30.6 1.0
SG 1:CYS19 2.5 29.5 1.0
CB 1:CYS19 3.0 27.6 1.0
CB 1:CYS22 3.1 27.0 1.0
CB 1:CYS34 3.1 27.7 1.0
CB 1:CYS37 3.4 29.1 1.0
N 1:CYS22 3.6 30.9 1.0
N 1:CYS37 3.9 29.8 1.0
CA 1:CYS22 3.9 28.5 1.0
CA 1:CYS37 4.2 27.8 1.0
CB 1:PHE39 4.3 30.8 1.0
CA 1:CYS19 4.5 29.4 1.0
CA 1:CYS34 4.6 28.2 1.0
C 1:ARG21 4.7 31.9 1.0
CB 1:ARG21 4.7 31.1 1.0
C 1:CYS22 4.7 29.5 1.0
CB 1:SER36 4.7 29.7 1.0
O 1:HOH1020 4.8 31.0 1.0
N 1:GLY23 4.8 30.2 1.0
C 1:CYS37 4.8 28.8 1.0
N 1:PHE39 4.9 28.9 1.0
C 1:SER36 4.9 30.6 1.0
N 1:GLY38 5.0 28.3 1.0

Cadmium binding site 5 out of 5 in 3cc7

Go back to Cadmium Binding Sites List in 3cc7
Cadmium binding site 5 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation C2487U


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 C2487U within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:64.0
occ:1.00
SG 3:CYS71 2.3 53.1 1.0
SG 3:CYS11 2.4 60.0 1.0
SG 3:CYS74 2.4 68.4 1.0
SG 3:CYS14 2.4 67.9 1.0
O 3:HOH9053 2.9 0.1 1.0
CB 3:CYS71 3.2 55.6 1.0
CB 3:CYS74 3.4 66.2 1.0
CB 3:CYS14 3.4 65.3 1.0
CB 3:CYS11 3.5 57.7 1.0
N 3:CYS14 3.9 65.3 1.0
N 3:CYS74 4.0 66.2 1.0
CA 3:CYS14 4.2 65.5 1.0
CA 3:CYS74 4.2 65.8 1.0
CB 3:HIS13 4.5 64.3 1.0
O 3:HOH9031 4.6 42.9 1.0
CA 3:CYS71 4.7 56.2 1.0
C 3:HIS13 4.8 65.1 1.0
CA 3:CYS11 4.9 56.5 1.0
CG 3:GLN18 5.0 62.8 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: Sun Jan 24 09:44:22 2021

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