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Cadmium in PDB 3cce: Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535A

Protein crystallography data

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535A, PDB code: 3cce 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) 49.33 / 2.75
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 (%) 18.3 / 23.2

Other elements in 3cce:

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535A 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 U2535A (pdb code 3cce). 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 U2535A, PDB code: 3cce:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3cce

Go back to Cadmium Binding Sites List in 3cce
Cadmium binding site 1 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535A


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 U2535A within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:81.1
occ:1.00
 ND1 O:HIS40 2.5 31.5 1.0
O 0:HOH6293 2.7 34.5 1.0
CE1 O:HIS40 3.5 33.0 1.0
CG O:HIS40 3.5 30.9 1.0
O O:HOH5322 3.8 46.2 1.0
CB O:HIS40 3.8 32.4 1.0
CG O:ARG37 4.5 43.5 1.0
O 0:HOH4365 4.6 46.0 1.0
NE2 O:HIS40 4.6 32.4 1.0
CD2 O:HIS40 4.7 31.7 1.0
NE O:ARG37 4.7 41.7 1.0
CZ O:ARG37 4.7 41.9 1.0
CB O:ARG37 4.8 43.7 1.0
NH2 O:ARG37 4.9 41.2 1.0
O 0:HOH3115 4.9 42.5 1.0
CA O:ARG37 5.0 42.6 1.0

Cadmium binding site 2 out of 5 in 3cce

Go back to Cadmium Binding Sites List in 3cce
Cadmium binding site 2 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535A


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 U2535A within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:60.9
occ:1.00
 SG U:CYS36 2.3 50.7 1.0
SG U:CYS6 2.4 50.5 1.0
SG U:CYS9 2.5 55.4 1.0
SG U:CYS32 2.5 38.8 1.0
CB U:CYS6 3.1 54.8 1.0
CB U:CYS9 3.3 52.7 1.0
CB U:CYS32 3.4 40.3 1.0
CB U:CYS36 3.5 51.6 1.0
N U:CYS9 3.7 50.5 1.0
N U:CYS32 3.8 40.6 1.0
CA U:CYS9 4.0 51.9 1.0
CA U:CYS32 4.2 42.4 1.0
OG1 U:THR11 4.3 59.2 1.0
CA U:CYS6 4.6 54.6 1.0
CB U:TYR8 4.6 48.6 1.0
N U:SER33 4.7 47.3 1.0
OG U:SER33 4.7 47.7 1.0
N U:GLY10 4.7 53.2 1.0
C U:CYS9 4.8 52.3 1.0
C U:TYR8 4.8 50.3 1.0
C U:CYS32 4.8 45.2 1.0
CA U:CYS36 4.9 50.4 1.0
CD2 U:TYR8 5.0 44.1 1.0
C U:PHE31 5.0 41.6 1.0

Cadmium binding site 3 out of 5 in 3cce

Go back to Cadmium Binding Sites List in 3cce
Cadmium binding site 3 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535A


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 U2535A within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:64.5
occ:1.00
 SG Z:CYS84 2.3 62.2 1.0
SG Z:CYS63 2.4 64.2 1.0
SG Z:CYS81 2.6 68.7 1.0
SG Z:CYS66 2.6 77.2 1.0
CB Z:CYS63 3.3 65.1 1.0
CB Z:CYS81 3.3 67.8 1.0
CB Z:CYS66 3.3 76.2 1.0
CB Z:CYS84 3.3 62.0 1.0
N Z:CYS66 3.5 75.0 1.0
N Z:CYS84 3.8 63.8 1.0
CB Z:ASN65 3.9 73.7 1.0
CA Z:CYS66 4.0 75.5 1.0
CA Z:CYS84 4.1 62.0 1.0
CD2 Z:TYR83 4.5 72.2 1.0
CB Z:TYR83 4.5 68.5 1.0
C Z:ASN65 4.6 74.8 1.0
CB Z:TYR86 4.6 57.1 1.0
CA Z:ASN65 4.7 73.8 1.0
CA Z:CYS63 4.7 66.3 1.0
N Z:ASN65 4.8 72.4 1.0
CA Z:CYS81 4.8 66.9 1.0
C Z:CYS84 4.8 61.1 1.0
N Z:GLY67 4.8 76.0 1.0
C Z:TYR83 4.9 65.6 1.0
C Z:CYS66 5.0 75.9 1.0
CG Z:TYR83 5.0 70.7 1.0
N Z:ASP85 5.0 60.8 1.0

Cadmium binding site 4 out of 5 in 3cce

Go back to Cadmium Binding Sites List in 3cce
Cadmium binding site 4 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535A


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 U2535A within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:53.1
occ:1.00
 SG 1:CYS22 2.3 27.6 1.0
SG 1:CYS37 2.3 28.0 1.0
SG 1:CYS34 2.4 29.2 1.0
SG 1:CYS19 2.5 28.6 1.0
CB 1:CYS34 3.1 24.6 1.0
CB 1:CYS19 3.2 26.8 1.0
CB 1:CYS22 3.2 30.1 1.0
CB 1:CYS37 3.4 20.8 1.0
N 1:CYS22 3.6 30.9 1.0
N 1:CYS37 3.8 19.5 1.0
CA 1:CYS22 4.0 30.5 1.0
CA 1:CYS37 4.1 20.9 1.0
CB 1:PHE39 4.1 29.6 1.0
CA 1:CYS34 4.5 25.8 1.0
CB 1:ARG21 4.6 28.0 1.0
N 1:PHE39 4.6 28.9 1.0
C 1:CYS37 4.6 20.0 1.0
CA 1:CYS19 4.6 29.1 1.0
C 1:ARG21 4.7 30.2 1.0
CB 1:SER36 4.8 21.7 1.0
N 1:GLY38 4.8 21.6 1.0
C 1:CYS22 4.8 30.1 1.0
N 1:GLY23 4.9 30.4 1.0
C 1:SER36 4.9 20.6 1.0
CD 1:ARG21 4.9 28.3 1.0
CA 1:ARG21 5.0 29.5 1.0

Cadmium binding site 5 out of 5 in 3cce

Go back to Cadmium Binding Sites List in 3cce
Cadmium binding site 5 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535A


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 U2535A within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:62.9
occ:1.00
 SG 3:CYS74 2.3 58.3 1.0
SG 3:CYS71 2.3 49.6 1.0
O 3:HOH9049 2.4 0.1 1.0
SG 3:CYS11 2.4 55.3 1.0
CB 3:CYS14 2.7 62.8 1.0
SG 3:CYS14 3.1 67.1 1.0
CB 3:CYS71 3.3 53.6 1.0
CB 3:CYS74 3.4 60.6 1.0
CB 3:CYS11 3.5 54.4 1.0
CA 3:CYS14 3.7 61.8 1.0
N 3:CYS14 3.8 61.7 1.0
N 3:CYS74 3.9 61.3 1.0
CG 3:GLN18 4.1 54.3 1.0
CA 3:CYS74 4.2 60.8 1.0
NE2 3:GLN18 4.7 55.8 1.0
CA 3:CYS71 4.7 53.5 1.0
CB 3:GLN18 4.8 53.1 1.0
C 3:HIS13 4.8 61.2 1.0
CA 3:CYS11 4.9 54.5 1.0
CD 3:GLN18 5.0 55.8 1.0
O 3:HOH9029 5.0 42.7 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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