Atomistry » Cadmium » PDB 3af7-3cme » 3ccl
Atomistry »
  Cadmium »
    PDB 3af7-3cme »
      3ccl »

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: Thu Jul 10 12:24:56 2025

Last articles

Cl in 2RAB
Cl in 2RA6
Cl in 2R9Z
Cl in 2R9H
Cl in 2R9V
Cl in 2R9F
Cl in 2R9K
Cl in 2R9C
Cl in 2R83
Cl in 2R8X
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy