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Cadmium in PDB 1yj9: Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22

Protein crystallography data

The structure of Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22, PDB code: 1yj9 was solved by D.Tu, G.Blaha, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 213.076, 300.750, 575.478, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 24.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22 (pdb code 1yj9). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22, PDB code: 1yj9:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1yj9

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Cadmium binding site 1 out of 5 in the Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22 within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:98.1
occ:1.00
ND1 O:HIS40 2.6 44.3 1.0
O O:HOH5650 2.9 44.6 1.0
O 0:HOH5824 3.2 25.0 1.0
CE1 O:HIS40 3.5 43.5 1.0
CG O:HIS40 3.6 44.3 1.0
CB O:HIS40 3.9 46.6 1.0
CG O:ARG37 4.3 59.7 1.0
NH1 O:ARG37 4.5 61.8 1.0
CZ O:ARG37 4.5 62.4 1.0
NE2 O:HIS40 4.6 43.5 1.0
CB O:ARG37 4.7 57.1 1.0
CD2 O:HIS40 4.7 43.3 1.0
NE O:ARG37 4.7 62.6 1.0
O O:HOH3002 4.8 57.7 1.0
CA O:ARG37 4.8 56.2 1.0
NH2 O:ARG37 4.9 60.4 1.0
O O:ARG37 4.9 56.8 1.0
O 0:HOH9906 5.0 45.3 1.0

Cadmium binding site 2 out of 5 in 1yj9

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Cadmium binding site 2 out of 5 in the Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22 within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:76.4
occ:1.00
SG U:CYS36 2.3 68.7 1.0
SG U:CYS32 2.3 45.8 1.0
SG U:CYS9 2.5 66.1 1.0
SG U:CYS6 2.5 55.5 1.0
CB U:CYS6 3.2 59.0 1.0
CB U:CYS9 3.6 63.1 1.0
CB U:CYS32 3.6 52.9 1.0
CB U:CYS36 3.7 65.2 1.0
N U:CYS32 4.0 54.1 1.0
N U:CYS9 4.0 61.9 1.0
CA U:CYS32 4.3 55.3 1.0
OG1 U:THR11 4.3 70.7 1.0
OG U:SER33 4.3 60.4 1.0
CA U:CYS9 4.4 62.8 1.0
N U:SER33 4.5 59.8 1.0
CA U:CYS6 4.7 60.0 1.0
CB U:TYR8 4.7 58.2 1.0
C U:CYS32 4.8 58.0 1.0
N U:GLY10 4.8 63.9 1.0
CA U:CYS36 5.0 63.2 1.0

Cadmium binding site 3 out of 5 in 1yj9

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Cadmium binding site 3 out of 5 in the Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:71.1
occ:1.00
SG Z:CYS39 2.3 61.4 1.0
SG Z:CYS60 2.3 66.1 1.0
SG Z:CYS57 2.4 72.4 1.0
SG Z:CYS42 2.6 77.6 1.0
CB Z:CYS60 3.1 68.2 1.0
CB Z:CYS42 3.2 78.8 1.0
CB Z:CYS57 3.2 73.8 1.0
CB Z:CYS39 3.2 67.0 1.0
N Z:CYS42 3.3 80.3 1.0
N Z:CYS60 3.7 71.8 1.0
CB Z:ASN41 3.8 80.2 1.0
CA Z:CYS42 3.8 79.5 1.0
CA Z:CYS60 3.9 69.4 1.0
C Z:ASN41 4.3 80.2 1.0
CD2 Z:TYR59 4.5 84.3 1.0
CA Z:ASN41 4.5 79.5 1.0
CB Z:TYR62 4.6 63.7 1.0
CB Z:TYR59 4.6 80.0 1.0
N Z:ASN41 4.6 78.7 1.0
N Z:GLY43 4.7 78.7 1.0
CA Z:CYS39 4.7 69.2 1.0
C Z:CYS60 4.7 70.2 1.0
CA Z:CYS57 4.7 73.6 1.0
C Z:CYS42 4.8 79.2 1.0
C Z:TYR59 4.9 75.1 1.0
N Z:ASP61 4.9 70.0 1.0
N Z:TYR62 4.9 66.8 1.0
CG Z:ASN41 5.0 80.4 1.0

Cadmium binding site 4 out of 5 in 1yj9

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Cadmium binding site 4 out of 5 in the Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:68.8
occ:1.00
SG 1:CYS37 2.3 45.2 1.0
SG 1:CYS22 2.4 44.6 1.0
SG 1:CYS34 2.5 45.5 1.0
SG 1:CYS19 2.5 47.0 1.0
CB 1:CYS19 3.1 42.8 1.0
CB 1:CYS22 3.2 41.0 1.0
CB 1:CYS37 3.2 39.5 1.0
CB 1:CYS34 3.2 39.7 1.0
N 1:CYS22 3.6 42.2 1.0
N 1:CYS37 3.8 38.9 1.0
CA 1:CYS22 3.9 41.9 1.0
CA 1:CYS37 4.1 38.6 1.0
CB 1:PHE39 4.3 45.9 1.0
CB 1:ARG21 4.5 43.3 1.0
C 1:ARG21 4.6 43.3 1.0
CA 1:CYS19 4.6 44.1 1.0
C 1:CYS22 4.6 41.7 1.0
CA 1:CYS34 4.7 39.2 1.0
O 1:HOH1020 4.7 41.3 1.0
C 1:CYS37 4.8 38.1 1.0
CB 1:SER36 4.8 38.0 1.0
N 1:GLY23 4.8 41.9 1.0
CD 1:ARG21 4.8 44.2 1.0
N 1:PHE39 4.9 43.4 1.0
CA 1:ARG21 4.9 43.1 1.0
N 1:GLY38 4.9 39.3 1.0
C 1:SER36 4.9 39.2 1.0
N 1:ARG21 4.9 44.0 1.0

Cadmium binding site 5 out of 5 in 1yj9

Go back to Cadmium Binding Sites List in 1yj9
Cadmium binding site 5 out of 5 in the Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of the Mutant 50S Ribosomal Subunit of Haloarcula Marismortui Containing A Three Residue Deletion in L22 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:72.6
occ:1.00
SG 3:CYS14 2.2 77.0 1.0
SG 3:CYS71 2.3 54.0 1.0
SG 3:CYS11 2.3 70.8 1.0
SG 3:CYS74 2.3 70.5 1.0
CB 3:CYS71 2.9 59.1 1.0
CB 3:CYS11 3.5 66.5 1.0
O 3:HOH8858 3.5 0.6 1.0
CB 3:CYS74 3.5 70.2 1.0
CB 3:CYS14 3.6 73.2 1.0
N 3:CYS74 4.0 71.0 1.0
N 3:CYS14 4.1 72.0 1.0
CA 3:CYS74 4.3 70.9 1.0
CA 3:CYS71 4.4 60.5 1.0
CA 3:CYS14 4.5 72.9 1.0
CB 3:HIS13 4.6 70.9 1.0
O 3:HOH8836 4.7 54.6 1.0
N 3:GLY75 4.8 70.3 1.0
C 3:CYS71 4.8 62.0 1.0
C 3:CYS74 4.9 70.6 1.0
CA 3:CYS11 4.9 65.8 1.0
O 3:CYS71 4.9 62.4 1.0
O 3:LYS76 5.0 71.4 1.0

Reference:

D.Tu, G.Blaha, P.B.Moore, T.A.Steitz. Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide A Structural Explanation For Resistance. Cell(Cambridge,Mass.) V. 121 257 2005.
ISSN: ISSN 0092-8674
PubMed: 15851032
DOI: 10.1016/J.CELL.2005.02.005
Page generated: Fri Aug 28 12:42:57 2020
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