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Cadmium in PDB 3cc2: The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins

Protein crystallography data

The structure of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins, PDB code: 3cc2 was solved by G.Gurel, G.Blaha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.95 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.646, 299.672, 573.773, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins (pdb code 3cc2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins, PDB code: 3cc2:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3cc2

Go back to Cadmium Binding Sites List in 3cc2
Cadmium binding site 1 out of 5 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8405

b:72.0
occ:1.00
O 0:HOH5821 2.4 30.6 1.0
ND1 O:HIS40 2.6 26.3 1.0
O 0:HOH5587 2.9 33.5 1.0
CE1 O:HIS40 3.5 29.1 1.0
CG O:HIS40 3.6 27.2 1.0
CB O:HIS40 3.8 29.1 1.0
CG O:ARG37 4.4 39.6 1.0
O 0:HOH3902 4.5 50.5 1.0
NE2 O:HIS40 4.6 30.8 1.0
CD2 O:HIS40 4.7 29.6 1.0
NH1 O:ARG37 4.7 42.2 1.0
CZ O:ARG37 4.7 42.7 1.0
CB O:ARG37 4.9 36.6 1.0
NE O:ARG37 4.9 41.6 1.0
CA O:ARG37 4.9 34.6 1.0
O O:ARG37 5.0 35.9 1.0

Cadmium binding site 2 out of 5 in 3cc2

Go back to Cadmium Binding Sites List in 3cc2
Cadmium binding site 2 out of 5 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8401

b:48.5
occ:1.00
SG U:CYS32 2.4 28.6 1.0
SG U:CYS36 2.4 45.3 1.0
SG U:CYS6 2.5 46.2 1.0
SG U:CYS9 2.5 42.5 1.0
CB U:CYS6 3.3 46.3 1.0
CB U:CYS9 3.3 43.7 1.0
CB U:CYS36 3.4 42.9 1.0
CB U:CYS32 3.6 34.2 1.0
N U:CYS9 3.7 46.0 1.0
N U:CYS32 4.0 35.7 1.0
CA U:CYS9 4.1 45.5 1.0
CA U:CYS32 4.3 36.9 1.0
OG1 U:THR11 4.4 53.9 1.0
CB U:TYR8 4.5 44.4 1.0
OG U:SER33 4.6 40.5 1.0
N U:SER33 4.8 40.3 1.0
N U:GLY10 4.8 47.7 1.0
CA U:CYS6 4.8 48.1 1.0
C U:TYR8 4.8 46.5 1.0
CA U:CYS36 4.9 42.6 1.0
C U:CYS9 4.9 46.8 1.0
C U:CYS32 4.9 39.3 1.0

Cadmium binding site 3 out of 5 in 3cc2

Go back to Cadmium Binding Sites List in 3cc2
Cadmium binding site 3 out of 5 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8403

b:43.8
occ:1.00
SG Z:CYS84 2.1 45.6 1.0
SG Z:CYS81 2.4 44.7 1.0
SG Z:CYS63 2.4 49.6 1.0
SG Z:CYS66 2.5 62.7 1.0
CB Z:CYS63 3.1 53.0 1.0
CB Z:CYS81 3.2 46.3 1.0
CB Z:CYS84 3.4 47.5 1.0
CB Z:CYS66 3.6 61.5 1.0
N Z:CYS66 3.7 61.6 1.0
N Z:CYS84 3.8 50.0 1.0
CB Z:ASN65 4.1 62.8 1.0
CA Z:CYS84 4.1 48.4 1.0
CA Z:CYS66 4.3 61.6 1.0
CB Z:TYR83 4.6 53.8 1.0
CD2 Z:TYR83 4.6 58.1 1.0
CA Z:CYS63 4.6 54.5 1.0
CB Z:TYR86 4.6 44.4 1.0
CA Z:CYS81 4.7 45.9 1.0
C Z:ASN65 4.8 61.9 1.0
CA Z:ASN65 4.9 61.6 1.0
C Z:CYS84 4.9 48.7 1.0
C Z:TYR83 4.9 51.4 1.0
ND2 Z:ASN65 5.0 64.4 1.0
C Z:CYS66 5.0 61.6 1.0
N Z:ASN65 5.0 60.7 1.0

Cadmium binding site 4 out of 5 in 3cc2

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Cadmium binding site 4 out of 5 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8402

b:45.9
occ:1.00
SG 1:CYS37 2.4 22.4 1.0
SG 1:CYS22 2.4 21.8 1.0
SG 1:CYS34 2.5 23.5 1.0
SG 1:CYS19 2.5 20.3 1.0
CB 1:CYS19 3.1 19.0 1.0
CB 1:CYS34 3.2 20.2 1.0
CB 1:CYS37 3.3 21.1 1.0
CB 1:CYS22 3.3 23.3 1.0
N 1:CYS22 3.7 27.6 1.0
N 1:CYS37 3.8 22.2 1.0
CA 1:CYS22 4.0 24.5 1.0
CA 1:CYS37 4.1 20.3 1.0
CB 1:PHE39 4.3 24.3 1.0
CA 1:CYS19 4.6 22.2 1.0
CA 1:CYS34 4.6 21.4 1.0
C 1:ARG21 4.7 27.0 1.0
CB 1:ARG21 4.7 27.4 1.0
C 1:CYS37 4.8 21.8 1.0
CB 1:SER36 4.8 22.3 1.0
C 1:CYS22 4.8 24.5 1.0
O 1:HOH8420 4.9 30.3 1.0
N 1:PHE39 4.9 23.4 1.0
C 1:SER36 4.9 23.2 1.0
N 1:GLY38 4.9 22.7 1.0
N 1:GLY23 4.9 25.3 1.0
CA 1:ARG21 5.0 27.1 1.0

Cadmium binding site 5 out of 5 in 3cc2

Go back to Cadmium Binding Sites List in 3cc2
Cadmium binding site 5 out of 5 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8404

b:45.9
occ:1.00
SG 3:CYS71 2.3 45.1 1.0
SG 3:CYS11 2.4 41.8 1.0
SG 3:CYS74 2.4 53.3 1.0
SG 3:CYS14 2.6 56.2 1.0
O 3:HOH8559 3.0 1.0 1.0
CB 3:CYS71 3.1 47.9 1.0
CB 3:CYS14 3.1 53.8 1.0
CB 3:CYS74 3.4 52.2 1.0
N 3:CYS14 3.5 53.3 1.0
CB 3:CYS11 3.6 42.2 1.0
CA 3:CYS14 3.9 54.1 1.0
N 3:CYS74 4.2 53.5 1.0
CA 3:CYS74 4.4 51.9 1.0
CB 3:HIS13 4.5 51.7 1.0
CA 3:CYS71 4.6 47.8 1.0
OE1 3:GLN18 4.6 59.5 1.0
C 3:HIS13 4.6 52.5 1.0
CA 3:CYS11 5.0 42.4 1.0
CA 3:HIS13 5.0 51.1 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 13:24:40 2020
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