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Cadmium in PDB 3ccu: Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2482C

Protein crystallography data

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2482C, PDB code: 3ccu 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) 49.99 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.756, 299.274, 574.365, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2482C (pdb code 3ccu). 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 G2482C, PDB code: 3ccu:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3ccu

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Cadmium binding site 1 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2482C


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 G2482C within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:80.0
occ:1.00
ND1 O:HIS40 2.5 29.7 1.0
O 0:HOH6295 2.6 28.1 1.0
O O:HOH5322 2.9 33.4 1.0
CE1 O:HIS40 3.5 30.3 1.0
CG O:HIS40 3.5 29.3 1.0
CB O:HIS40 3.8 32.7 1.0
CG O:ARG37 4.5 46.0 1.0
O 0:HOH4363 4.5 50.1 1.0
NE2 O:HIS40 4.6 30.8 1.0
CD2 O:HIS40 4.7 30.5 1.0
CZ O:ARG37 4.8 47.0 1.0
NE O:ARG37 4.8 47.3 1.0
CB O:ARG37 4.9 42.4 1.0

Cadmium binding site 2 out of 5 in 3ccu

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Cadmium binding site 2 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2482C


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 G2482C within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:48.2
occ:1.00
SG U:CYS32 2.4 36.5 1.0
SG U:CYS9 2.4 47.6 1.0
SG U:CYS6 2.5 49.2 1.0
SG U:CYS36 2.5 49.6 1.0
CB U:CYS6 3.3 51.3 1.0
CB U:CYS9 3.4 48.2 1.0
CB U:CYS32 3.4 39.2 1.0
CB U:CYS36 3.6 47.5 1.0
N U:CYS9 3.8 49.6 1.0
N U:CYS32 3.9 38.8 1.0
CA U:CYS9 4.1 48.8 1.0
OG1 U:THR11 4.2 59.0 1.0
CA U:CYS32 4.2 39.4 1.0
OG U:SER33 4.6 44.8 1.0
CB U:TYR8 4.6 47.1 1.0
N U:SER33 4.7 43.6 1.0
CA U:CYS6 4.7 50.7 1.0
N U:GLY10 4.8 51.2 1.0
C U:CYS32 4.8 42.9 1.0
C U:TYR8 4.9 49.8 1.0
C U:CYS9 4.9 50.2 1.0
CA U:CYS36 5.0 46.1 1.0

Cadmium binding site 3 out of 5 in 3ccu

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Cadmium binding site 3 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2482C


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 G2482C within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:79.8
occ:1.00
SG Z:CYS84 2.3 71.7 1.0
SG Z:CYS63 2.5 76.5 1.0
SG Z:CYS81 2.6 76.3 1.0
SG Z:CYS66 2.9 80.9 1.0
CB Z:CYS81 3.3 73.2 1.0
CB Z:CYS63 3.3 76.0 1.0
CB Z:CYS84 3.4 70.7 1.0
N Z:CYS84 3.7 71.9 1.0
N Z:CYS66 3.8 79.7 1.0
CB Z:CYS66 3.9 79.9 1.0
CB Z:ASN65 3.9 78.3 1.0
CA Z:CYS84 4.1 71.2 1.0
CD2 Z:TYR83 4.3 77.6 1.0
CB Z:TYR83 4.4 74.7 1.0
CA Z:CYS66 4.4 79.7 1.0
CB Z:TYR86 4.7 62.4 1.0
CA Z:ASN65 4.7 79.1 1.0
CA Z:CYS81 4.8 71.6 1.0
CA Z:CYS63 4.8 76.5 1.0
C Z:ASN65 4.8 79.6 1.0
C Z:CYS84 4.9 71.0 1.0
N Z:ASN65 4.9 78.7 1.0
C Z:TYR83 4.9 73.3 1.0
CG Z:TYR83 4.9 76.9 1.0

Cadmium binding site 4 out of 5 in 3ccu

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Cadmium binding site 4 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2482C


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 G2482C within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:59.8
occ:1.00
SG 1:CYS34 2.4 24.3 1.0
SG 1:CYS22 2.4 29.4 1.0
SG 1:CYS37 2.4 29.5 1.0
SG 1:CYS19 2.5 28.1 1.0
CB 1:CYS19 3.1 30.0 1.0
CB 1:CYS22 3.1 29.1 1.0
CB 1:CYS34 3.2 21.0 1.0
CB 1:CYS37 3.3 25.0 1.0
N 1:CYS22 3.6 30.9 1.0
N 1:CYS37 3.8 23.4 1.0
CA 1:CYS22 3.9 29.9 1.0
CA 1:CYS37 4.1 24.6 1.0
CB 1:PHE39 4.2 30.4 1.0
CA 1:CYS19 4.6 31.9 1.0
CA 1:CYS34 4.6 23.3 1.0
CB 1:ARG21 4.7 27.5 1.0
C 1:ARG21 4.7 30.1 1.0
C 1:CYS22 4.7 29.2 1.0
C 1:CYS37 4.8 23.9 1.0
N 1:PHE39 4.8 26.8 1.0
N 1:GLY23 4.8 28.0 1.0
CB 1:SER36 4.8 21.0 1.0
CD 1:ARG21 4.9 27.5 1.0
N 1:GLY38 4.9 24.3 1.0
C 1:SER36 4.9 22.6 1.0

Cadmium binding site 5 out of 5 in 3ccu

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Cadmium binding site 5 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2482C


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 G2482C within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:66.5
occ:1.00
SG 3:CYS71 2.3 53.9 1.0
SG 3:CYS74 2.4 64.7 1.0
SG 3:CYS11 2.4 57.1 1.0
SG 3:CYS14 2.5 71.0 1.0
O 3:HOH9049 2.8 0.7 1.0
CB 3:CYS71 3.1 56.9 1.0
CB 3:CYS14 3.3 66.5 1.0
CB 3:CYS11 3.4 56.4 1.0
CB 3:CYS74 3.5 64.7 1.0
N 3:CYS14 3.7 67.3 1.0
CA 3:CYS14 4.1 66.9 1.0
N 3:CYS74 4.1 65.0 1.0
CG 3:GLN18 4.2 61.0 1.0
CA 3:CYS74 4.4 65.0 1.0
CB 3:HIS13 4.5 66.4 1.0
CA 3:CYS71 4.6 57.0 1.0
C 3:HIS13 4.7 67.7 1.0
O 3:HOH9028 4.8 30.9 1.0
CB 3:GLN18 4.8 59.8 1.0
CA 3:CYS11 4.9 56.7 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 Aug 28 13:28:43 2020
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