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Cadmium in PDB 3ccl: Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535C. Density For Anisomycin Is Visible But Not Included in Model.

Protein crystallography data

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535C. Density For Anisomycin Is Visible But Not Included in Model., PDB code: 3ccl 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) 49.98 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 213.161, 300.032, 576.127, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22

Other elements in 3ccl:

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535C. Density For Anisomycin Is Visible But Not Included in Model. 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 U2535C. Density For Anisomycin Is Visible But Not Included in Model. (pdb code 3ccl). 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 U2535C. Density For Anisomycin Is Visible But Not Included in Model., PDB code: 3ccl:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3ccl

Go back to Cadmium Binding Sites List in 3ccl
Cadmium binding site 1 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535C. Density For Anisomycin Is Visible But Not Included in Model.


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 U2535C. Density For Anisomycin Is Visible But Not Included in Model. within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:94.2
occ:1.00
 ND1 O:HIS40 2.6 42.0 1.0
O 0:HOH6282 2.7 55.5 1.0
O O:HOH5322 2.9 45.3 1.0
CE1 O:HIS40 3.4 42.0 1.0
CG O:HIS40 3.6 42.3 1.0
CB O:HIS40 3.9 44.6 1.0
O 0:HOH4374 4.3 49.8 1.0
CG O:ARG37 4.5 56.0 1.0
NE2 O:HIS40 4.6 42.9 1.0
CZ O:ARG37 4.7 55.2 1.0
CD2 O:HIS40 4.7 42.6 1.0
NE O:ARG37 4.8 55.4 1.0
NH1 O:ARG37 4.9 53.5 1.0
CB O:ARG37 4.9 54.4 1.0

Cadmium binding site 2 out of 5 in 3ccl

Go back to Cadmium Binding Sites List in 3ccl
Cadmium binding site 2 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535C. Density For Anisomycin Is Visible But Not Included in Model.


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 U2535C. Density For Anisomycin Is Visible But Not Included in Model. within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:72.1
occ:1.00
 SG U:CYS36 2.4 64.8 1.0
SG U:CYS32 2.4 46.9 1.0
SG U:CYS6 2.4 60.9 1.0
SG U:CYS9 2.5 62.4 1.0
CB U:CYS6 3.2 62.5 1.0
CB U:CYS32 3.4 48.4 1.0
CB U:CYS9 3.4 62.1 1.0
CB U:CYS36 3.6 59.5 1.0
N U:CYS9 3.8 60.3 1.0
N U:CYS32 4.0 48.0 1.0
CA U:CYS9 4.2 61.8 1.0
CA U:CYS32 4.2 49.0 1.0
OG1 U:THR11 4.4 69.0 1.0
OG U:SER33 4.6 52.5 1.0
CB U:TYR8 4.6 57.8 1.0
N U:SER33 4.6 52.1 1.0
CA U:CYS6 4.7 63.0 1.0
C U:CYS32 4.7 51.0 1.0
N U:GLY10 4.8 63.0 1.0
C U:CYS9 4.9 62.0 1.0
C U:TYR8 4.9 59.6 1.0
CA U:CYS36 4.9 58.3 1.0

Cadmium binding site 3 out of 5 in 3ccl

Go back to Cadmium Binding Sites List in 3ccl
Cadmium binding site 3 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535C. Density For Anisomycin Is Visible But Not Included in Model.


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 U2535C. Density For Anisomycin Is Visible But Not Included in Model. within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:91.9
occ:1.00
 SG Z:CYS63 2.3 87.4 1.0
SG Z:CYS84 2.3 80.4 1.0
SG Z:CYS81 2.5 83.6 1.0
SG Z:CYS66 2.9 0.6 1.0
CB Z:CYS81 3.3 81.9 1.0
CB Z:CYS84 3.3 79.6 1.0
CB Z:CYS63 3.3 88.7 1.0
CB Z:ASN65 3.5 94.3 1.0
N Z:CYS66 3.5 98.0 1.0
CB Z:CYS66 3.8 99.0 1.0
N Z:CYS84 3.8 81.2 1.0
CA Z:CYS84 4.1 80.3 1.0
CA Z:CYS66 4.2 98.8 1.0
CA Z:ASN65 4.4 95.7 1.0
C Z:ASN65 4.5 97.0 1.0
ND2 Z:ASN65 4.6 92.8 1.0
CD2 Z:TYR83 4.6 87.7 1.0
CG Z:ASN65 4.6 93.7 1.0
CB Z:TYR83 4.6 84.6 1.0
N Z:ASN65 4.6 95.2 1.0
CB Z:TYR86 4.7 70.3 1.0
CA Z:CYS63 4.7 90.2 1.0
CA Z:CYS81 4.8 80.8 1.0
C Z:CYS84 4.8 80.0 1.0
C Z:CYS66 5.0 99.0 1.0
C Z:TYR83 5.0 83.0 1.0

Cadmium binding site 4 out of 5 in 3ccl

Go back to Cadmium Binding Sites List in 3ccl
Cadmium binding site 4 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535C. Density For Anisomycin Is Visible But Not Included in Model.


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 U2535C. Density For Anisomycin Is Visible But Not Included in Model. within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:65.7
occ:1.00
 SG 1:CYS22 2.3 38.8 1.0
SG 1:CYS34 2.3 39.5 1.0
SG 1:CYS37 2.4 37.9 1.0
SG 1:CYS19 2.5 37.7 1.0
CB 1:CYS19 3.0 40.0 1.0
CB 1:CYS34 3.2 36.1 1.0
CB 1:CYS22 3.3 39.3 1.0
CB 1:CYS37 3.4 36.0 1.0
N 1:CYS22 3.7 40.4 1.0
N 1:CYS37 3.9 35.4 1.0
CA 1:CYS22 4.1 40.4 1.0
CB 1:PHE39 4.2 41.1 1.0
CA 1:CYS37 4.2 35.8 1.0
CA 1:CYS19 4.5 41.0 1.0
CA 1:CYS34 4.6 36.8 1.0
CB 1:ARG21 4.6 40.5 1.0
C 1:ARG21 4.8 40.1 1.0
N 1:PHE39 4.8 38.0 1.0
C 1:CYS22 4.8 40.4 1.0
C 1:CYS37 4.8 36.0 1.0
N 1:GLY23 4.9 40.0 1.0
CB 1:SER36 4.9 34.1 1.0
CD 1:ARG21 4.9 42.3 1.0
N 1:GLY38 4.9 35.6 1.0

Cadmium binding site 5 out of 5 in 3ccl

Go back to Cadmium Binding Sites List in 3ccl
Cadmium binding site 5 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation U2535C. Density For Anisomycin Is Visible But Not Included in Model.


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 U2535C. Density For Anisomycin Is Visible But Not Included in Model. within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:81.9
occ:1.00
 SG 3:CYS11 2.4 74.4 1.0
SG 3:CYS14 2.4 82.5 1.0
SG 3:CYS74 2.4 78.5 1.0
SG 3:CYS71 2.4 65.2 1.0
O 3:HOH9049 3.0 0.1 1.0
CB 3:CYS71 3.3 68.2 1.0
CB 3:CYS74 3.4 78.0 1.0
CB 3:CYS14 3.5 79.2 1.0
CB 3:CYS11 3.5 70.9 1.0
N 3:CYS14 3.8 79.7 1.0
N 3:CYS74 4.1 77.8 1.0
CA 3:CYS14 4.2 79.3 1.0
CA 3:CYS74 4.3 78.0 1.0
CG 3:GLN18 4.4 76.3 1.0
CB 3:HIS13 4.4 79.6 1.0
O 3:HOH9030 4.5 42.5 1.0
CA 3:CYS71 4.7 68.9 1.0
C 3:HIS13 4.8 79.8 1.0
CA 3:CYS11 4.9 70.5 1.0
CB 3:GLN18 5.0 73.8 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: Fri Jul 19 15:42:13 2024

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