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

Cadmium in PDB 3ccv: Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A

Protein crystallography data

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A, PDB code: 3ccv 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 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.752, 299.012, 574.480, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.5

Other elements in 3ccv:

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A 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 G2616A (pdb code 3ccv). 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 G2616A, PDB code: 3ccv:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3ccv

Go back to Cadmium Binding Sites List in 3ccv
Cadmium binding site 1 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


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 G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:84.2
occ:1.00
 ND1 O:HIS40 2.6 30.2 1.0
O 0:HOH6276 2.8 40.7 1.0
O 0:HOH6040 3.4 43.2 1.0
CE1 O:HIS40 3.4 31.4 1.0
CG O:HIS40 3.6 29.9 1.0
CB O:HIS40 3.9 33.3 1.0
O 0:HOH4360 4.3 40.1 1.0
CG O:ARG37 4.5 48.2 1.0
NE2 O:HIS40 4.6 32.0 1.0
CD2 O:HIS40 4.7 30.9 1.0
CZ O:ARG37 4.7 46.9 1.0
NE O:ARG37 4.8 48.4 1.0
CB O:ARG37 4.9 45.6 1.0

Cadmium binding site 2 out of 5 in 3ccv

Go back to Cadmium Binding Sites List in 3ccv
Cadmium binding site 2 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


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 G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:62.3
occ:1.00
 SG U:CYS9 2.3 54.2 1.0
SG U:CYS36 2.4 57.8 1.0
SG U:CYS6 2.4 54.2 1.0
SG U:CYS32 2.4 43.1 1.0
CB U:CYS9 3.2 52.7 1.0
CB U:CYS6 3.2 56.4 1.0
CB U:CYS32 3.4 44.6 1.0
CB U:CYS36 3.5 55.2 1.0
N U:CYS9 3.7 53.4 1.0
N U:CYS32 3.9 44.1 1.0
CA U:CYS9 4.0 52.7 1.0
CA U:CYS32 4.2 45.3 1.0
OG1 U:THR11 4.4 63.0 1.0
OG U:SER33 4.6 53.4 1.0
CB U:TYR8 4.6 52.8 1.0
N U:SER33 4.6 49.4 1.0
CA U:CYS6 4.7 56.8 1.0
N U:GLY10 4.7 53.2 1.0
C U:CYS32 4.8 47.9 1.0
C U:TYR8 4.9 53.4 1.0
C U:CYS9 4.9 52.8 1.0
CA U:CYS36 5.0 54.4 1.0

Cadmium binding site 3 out of 5 in 3ccv

Go back to Cadmium Binding Sites List in 3ccv
Cadmium binding site 3 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


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 G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:83.5
occ:1.00
 SG Z:CYS84 2.3 70.2 1.0
SG Z:CYS63 2.4 78.0 1.0
SG Z:CYS81 2.5 76.4 1.0
SG Z:CYS66 2.9 88.9 1.0
CB Z:CYS81 3.2 73.7 1.0
CB Z:CYS84 3.4 68.6 1.0
CB Z:CYS63 3.4 79.6 1.0
N Z:CYS66 3.5 88.0 1.0
CB Z:ASN65 3.6 85.2 1.0
CB Z:CYS66 3.6 88.1 1.0
N Z:CYS84 3.8 70.5 1.0
CA Z:CYS84 4.1 69.2 1.0
CA Z:CYS66 4.2 88.2 1.0
CD2 Z:TYR83 4.3 78.2 1.0
CB Z:TYR83 4.4 74.8 1.0
C Z:ASN65 4.5 87.5 1.0
ND2 Z:ASN65 4.5 84.5 1.0
CA Z:ASN65 4.5 86.2 1.0
CG Z:ASN65 4.6 84.9 1.0
CB Z:TYR86 4.6 63.1 1.0
N Z:ASN65 4.7 85.3 1.0
CA Z:CYS81 4.7 72.9 1.0
CA Z:CYS63 4.8 80.7 1.0
CG Z:TYR83 4.8 77.0 1.0
C Z:CYS84 4.8 68.5 1.0
C Z:TYR83 4.9 72.5 1.0
C Z:CYS66 5.0 88.8 1.0

Cadmium binding site 4 out of 5 in 3ccv

Go back to Cadmium Binding Sites List in 3ccv
Cadmium binding site 4 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


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 G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:60.5
occ:1.00
 SG 1:CYS22 2.4 28.5 1.0
SG 1:CYS34 2.4 35.8 1.0
SG 1:CYS37 2.4 30.9 1.0
SG 1:CYS19 2.5 29.6 1.0
CB 1:CYS19 3.1 30.6 1.0
CB 1:CYS22 3.1 30.5 1.0
CB 1:CYS34 3.2 28.7 1.0
CB 1:CYS37 3.3 27.8 1.0
N 1:CYS22 3.6 30.5 1.0
N 1:CYS37 3.8 26.8 1.0
CA 1:CYS22 3.9 30.3 1.0
CB 1:PHE39 4.1 31.6 1.0
CA 1:CYS37 4.1 26.8 1.0
CA 1:CYS19 4.6 31.1 1.0
CA 1:CYS34 4.6 29.2 1.0
CB 1:ARG21 4.7 29.0 1.0
C 1:CYS22 4.7 30.0 1.0
C 1:ARG21 4.7 30.8 1.0
N 1:GLY23 4.7 29.8 1.0
N 1:PHE39 4.7 29.3 1.0
C 1:CYS37 4.8 25.1 1.0
N 1:GLY38 4.9 25.4 1.0
CB 1:SER36 4.9 25.0 1.0
CD 1:ARG21 4.9 29.1 1.0
C 1:SER36 5.0 27.5 1.0
CA 1:ARG21 5.0 30.4 1.0
O 1:HOH8968 5.0 32.4 1.0
N 1:ARG21 5.0 30.5 1.0

Cadmium binding site 5 out of 5 in 3ccv

Go back to Cadmium Binding Sites List in 3ccv
Cadmium binding site 5 out of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


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 G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:76.5
occ:1.00
 SG 3:CYS71 2.3 64.5 1.0
SG 3:CYS74 2.4 76.9 1.0
SG 3:CYS11 2.4 64.0 1.0
SG 3:CYS14 2.4 79.6 1.0
CB 3:CYS71 3.1 63.6 1.0
CB 3:CYS14 3.4 75.6 1.0
CB 3:CYS11 3.6 63.6 1.0
CB 3:CYS74 3.6 75.1 1.0
N 3:CYS14 3.8 75.7 1.0
N 3:CYS74 4.1 73.9 1.0
CA 3:CYS14 4.2 76.0 1.0
CG 3:GLN18 4.3 69.6 1.0
CA 3:CYS74 4.4 74.6 1.0
CB 3:HIS13 4.5 74.1 1.0
CA 3:CYS71 4.6 63.3 1.0
O 3:HOH8963 4.6 28.0 1.0
C 3:HIS13 4.8 75.2 1.0
O 3:HOH8985 4.8 0.9 1.0
CB 3:GLN18 4.9 67.6 1.0
NE2 3:GLN18 4.9 71.5 1.0
CA 3:CYS11 4.9 64.5 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 12:26:36 2025

Last articles

F in 3ZSH
F in 3ZSE
F in 3ZS5
F in 3ZNS
F in 3ZS0
F in 3ZOS
F in 3ZRA
F in 3ZOZ
F in 3ZOV
F in 3ZNR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy