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Cadmium in PDB 1yit: Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yit 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) 29.99 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.583, 299.758, 573.560, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.1

Other elements in 1yit:

The structure of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium (Mg) 118 atoms
Potassium (K) 1 atom
Chlorine (Cl) 22 atoms
Sodium (Na) 85 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1yit). 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 Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yit:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1yit

Go back to Cadmium Binding Sites List in 1yit
Cadmium binding site 1 out of 5 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


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 Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:58.0
occ:1.00
SG 1:CYS34 2.4 33.3 1.0
SG 1:CYS37 2.4 34.8 1.0
SG 1:CYS22 2.4 33.6 1.0
SG 1:CYS19 2.6 30.0 1.0
CB 1:CYS22 3.1 31.0 1.0
CB 1:CYS19 3.2 30.5 1.0
CB 1:CYS34 3.2 28.9 1.0
CB 1:CYS37 3.3 28.6 1.0
N 1:CYS22 3.6 32.5 1.0
N 1:CYS37 3.7 28.7 1.0
CA 1:CYS22 3.9 31.7 1.0
CA 1:CYS37 4.1 28.7 1.0
CB 1:PHE39 4.3 34.5 1.0
CB 1:ARG21 4.6 31.3 1.0
CA 1:CYS34 4.6 28.8 1.0
CA 1:CYS19 4.6 31.3 1.0
CB 1:SER36 4.7 25.2 1.0
C 1:ARG21 4.7 32.5 1.0
C 1:CYS22 4.7 31.0 1.0
C 1:CYS37 4.7 28.5 1.0
N 1:PHE39 4.8 32.0 1.0
CD 1:ARG21 4.8 32.6 1.0
N 1:GLY23 4.9 30.3 1.0
C 1:SER36 4.9 27.8 1.0
N 1:GLY38 4.9 28.8 1.0
CA 1:ARG21 5.0 31.6 1.0

Cadmium binding site 2 out of 5 in 1yit

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Cadmium binding site 2 out of 5 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


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 Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:69.7
occ:1.00
SG 3:CYS11 2.4 67.1 1.0
SG 3:CYS71 2.4 55.0 1.0
SG 3:CYS14 2.5 73.2 1.0
SG 3:CYS74 2.5 69.5 1.0
CB 3:CYS71 3.2 57.9 1.0
CB 3:CYS11 3.5 63.3 1.0
CB 3:CYS14 3.6 69.6 1.0
CB 3:CYS74 3.7 67.5 1.0
N 3:CYS14 3.9 68.8 1.0
N 3:CYS74 4.0 66.5 1.0
CA 3:CYS14 4.4 69.5 1.0
CB 3:HIS13 4.4 65.4 1.0
CA 3:CYS74 4.4 66.9 1.0
CA 3:CYS71 4.7 59.8 1.0
CB 3:GLU73 4.8 68.7 1.0
CA 3:CYS11 4.9 62.2 1.0
C 3:HIS13 4.9 67.9 1.0
CB 3:GLN18 5.0 66.0 1.0

Cadmium binding site 3 out of 5 in 1yit

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Cadmium binding site 3 out of 5 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


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 Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:88.2
occ:1.00
ND1 O:HIS40 2.6 34.8 1.0
CE1 O:HIS40 3.6 36.4 1.0
CG O:HIS40 3.6 35.0 1.0
CB O:HIS40 3.8 36.9 1.0
CG O:ARG37 4.4 43.3 1.0
CZ O:ARG37 4.6 39.4 1.0
CB O:ARG37 4.6 41.3 1.0
NE O:ARG37 4.7 40.2 1.0
NE2 O:HIS40 4.7 36.8 1.0
CD2 O:HIS40 4.7 36.0 1.0
NH1 O:ARG37 4.8 39.1 1.0
CA O:ARG37 4.8 40.8 1.0
NH2 O:ARG37 4.9 35.8 1.0
O O:ARG37 5.0 42.2 1.0

Cadmium binding site 4 out of 5 in 1yit

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Cadmium binding site 4 out of 5 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


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 Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:58.2
occ:1.00
SG U:CYS36 2.3 57.8 1.0
SG U:CYS6 2.4 48.0 1.0
SG U:CYS32 2.4 36.9 1.0
SG U:CYS9 2.5 54.5 1.0
CB U:CYS6 3.2 51.3 1.0
CB U:CYS9 3.4 53.1 1.0
CB U:CYS32 3.6 41.4 1.0
CB U:CYS36 3.6 56.2 1.0
N U:CYS9 3.8 52.2 1.0
N U:CYS32 4.0 42.5 1.0
CA U:CYS9 4.2 54.1 1.0
CA U:CYS32 4.3 43.7 1.0
CB U:TYR8 4.4 48.4 1.0
OG U:SER33 4.5 46.8 1.0
OG1 U:THR11 4.6 62.3 1.0
N U:SER33 4.6 46.2 1.0
CA U:CYS6 4.7 53.1 1.0
N U:GLY10 4.9 56.0 1.0
C U:CYS32 4.9 45.3 1.0
C U:TYR8 4.9 51.2 1.0
CA U:CYS36 5.0 55.3 1.0
C U:CYS9 5.0 54.8 1.0

Cadmium binding site 5 out of 5 in 1yit

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Cadmium binding site 5 out of 5 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


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 Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:84.4
occ:1.00
SG Z:CYS60 2.4 76.5 1.0
SG Z:CYS39 2.5 88.2 1.0
SG Z:CYS57 2.5 85.0 1.0
SG Z:CYS42 3.0 88.5 1.0
CB Z:CYS39 3.3 85.3 1.0
CB Z:CYS60 3.4 76.9 1.0
CB Z:CYS57 3.4 83.0 1.0
N Z:CYS60 3.6 78.7 1.0
N Z:CYS42 3.8 90.5 1.0
CB Z:ASN41 3.9 89.3 1.0
CB Z:CYS42 4.0 89.5 1.0
CA Z:CYS60 4.1 77.4 1.0
CD2 Z:TYR59 4.2 86.1 1.0
CB Z:TYR59 4.2 82.9 1.0
CA Z:CYS42 4.5 90.3 1.0
CB Z:TYR62 4.7 71.7 1.0
CA Z:ASN41 4.7 89.8 1.0
CG Z:TYR59 4.7 85.1 1.0
C Z:TYR59 4.8 80.8 1.0
C Z:ASN41 4.8 90.4 1.0
CA Z:CYS39 4.8 85.4 1.0
N Z:ASN41 4.8 89.2 1.0
C Z:CYS60 4.9 77.8 1.0
CA Z:CYS57 4.9 82.0 1.0
CG Z:ASN41 4.9 89.4 1.0
N Z:ASP61 4.9 78.1 1.0
CA Z:TYR59 5.0 82.1 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: Wed Oct 28 09:58:26 2020
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