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Cadmium in PDB 1s72: Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution

Protein crystallography data

The structure of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1s72 was solved by D.J.Klein, T.M.Schmeing, 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) 15.00 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.660, 299.670, 573.770, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.2

Other elements in 1s72:

The structure of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 116 atoms
Potassium (K) 2 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 86 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution (pdb code 1s72). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1s72:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1s72

Go back to Cadmium Binding Sites List in 1s72
Cadmium binding site 1 out of 5 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8405

b:73.6
occ:1.00
 ND1 O:HIS40 2.6 27.1 1.0
O O:HOH5650 2.6 35.8 1.0
O 0:HOH5541 3.0 30.6 1.0
CE1 O:HIS40 3.5 30.9 1.0
CG O:HIS40 3.5 28.2 1.0
CB O:HIS40 3.8 29.4 1.0
CG O:ARG37 4.3 39.8 1.0
NE2 O:HIS40 4.6 33.4 1.0
CD2 O:HIS40 4.6 31.0 1.0
O 0:HOH3866 4.7 44.5 1.0
CZ O:ARG37 4.8 41.7 1.0
NH1 O:ARG37 4.8 41.2 1.0
NE O:ARG37 4.9 41.0 1.0
CB O:ARG37 4.9 36.5 1.0
CA O:ARG37 4.9 35.2 1.0
O O:ARG37 5.0 36.2 1.0

Cadmium binding site 2 out of 5 in 1s72

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Cadmium binding site 2 out of 5 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8401

b:52.1
occ:1.00
 SG U:CYS32 2.5 30.0 1.0
SG U:CYS36 2.5 47.0 1.0
SG U:CYS6 2.6 48.3 1.0
SG U:CYS9 2.7 44.1 1.0
CB U:CYS6 3.3 48.0 1.0
CB U:CYS9 3.3 45.1 1.0
CB U:CYS36 3.5 45.8 1.0
CB U:CYS32 3.7 34.7 1.0
N U:CYS9 3.8 47.2 1.0
N U:CYS32 4.1 36.2 1.0
CA U:CYS9 4.1 46.5 1.0
OG U:SER33 4.4 37.7 1.0
CA U:CYS32 4.5 37.0 1.0
OG1 U:THR11 4.5 52.2 1.0
CB U:TYR8 4.6 45.1 1.0
N U:SER33 4.8 40.0 1.0
CA U:CYS6 4.8 49.4 1.0
N U:GLY10 4.8 48.0 1.0
C U:TYR8 4.9 47.4 1.0
C U:CYS9 4.9 47.5 1.0
CA U:CYS36 4.9 45.0 1.0
C U:CYS32 5.0 39.1 1.0

Cadmium binding site 3 out of 5 in 1s72

Go back to Cadmium Binding Sites List in 1s72
Cadmium binding site 3 out of 5 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8403

b:48.6
occ:1.00
 SG Z:CYS60 2.3 47.7 1.0
SG Z:CYS57 2.5 44.0 1.0
SG Z:CYS39 2.5 52.4 1.0
SG Z:CYS42 2.8 60.7 1.0
CB Z:CYS39 3.2 53.9 1.0
CB Z:CYS57 3.2 46.6 1.0
CB Z:CYS60 3.5 49.0 1.0
CB Z:CYS42 3.7 58.1 1.0
N Z:CYS42 3.8 58.7 1.0
N Z:CYS60 3.9 50.8 1.0
CA Z:CYS60 4.3 49.5 1.0
CB Z:ASN41 4.3 60.7 1.0
CA Z:CYS42 4.3 58.0 1.0
CB Z:TYR62 4.6 45.5 1.0
CD2 Z:TYR59 4.6 56.0 1.0
CB Z:TYR59 4.7 53.1 1.0
CA Z:CYS39 4.7 54.2 1.0
CA Z:CYS57 4.7 45.2 1.0
C Z:CYS42 4.9 57.5 1.0
C Z:ASN41 4.9 59.4 1.0
C Z:CYS60 5.0 49.4 1.0

Cadmium binding site 4 out of 5 in 1s72

Go back to Cadmium Binding Sites List in 1s72
Cadmium binding site 4 out of 5 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8402

b:44.2
occ:1.00
 SG 1:CYS37 2.4 26.8 1.0
SG 1:CYS22 2.5 25.0 1.0
SG 1:CYS34 2.5 24.8 1.0
SG 1:CYS19 2.5 22.9 1.0
CB 1:CYS19 3.1 21.3 1.0
CB 1:CYS34 3.2 19.8 1.0
CB 1:CYS37 3.2 23.7 1.0
CB 1:CYS22 3.3 23.2 1.0
N 1:CYS22 3.7 27.0 1.0
N 1:CYS37 3.8 24.8 1.0
CA 1:CYS37 4.0 23.8 1.0
CA 1:CYS22 4.0 25.2 1.0
CB 1:PHE39 4.3 25.2 1.0
CA 1:CYS19 4.6 25.0 1.0
CA 1:CYS34 4.6 21.9 1.0
CB 1:ARG21 4.7 29.0 1.0
C 1:ARG21 4.7 28.0 1.0
C 1:CYS37 4.7 24.4 1.0
CB 1:SER36 4.8 24.6 1.0
O 1:HOH8418 4.8 24.5 1.0
C 1:CYS22 4.8 24.7 1.0
N 1:PHE39 4.9 23.8 1.0
C 1:SER36 4.9 26.5 1.0
N 1:GLY38 4.9 23.9 1.0
N 1:GLY23 4.9 25.2 1.0

Cadmium binding site 5 out of 5 in 1s72

Go back to Cadmium Binding Sites List in 1s72
Cadmium binding site 5 out of 5 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8404

b:49.5
occ:1.00
 SG 3:CYS71 2.4 50.2 1.0
SG 3:CYS11 2.5 43.2 1.0
SG 3:CYS74 2.6 54.2 1.0
SG 3:CYS14 2.9 56.1 1.0
CB 3:CYS14 3.1 53.9 1.0
CB 3:CYS71 3.1 50.9 1.0
O 3:HOH8559 3.2 97.1 1.0
CB 3:CYS74 3.3 52.2 1.0
CB 3:CYS11 3.6 44.3 1.0
N 3:CYS14 3.7 53.7 1.0
CA 3:CYS14 3.9 54.6 1.0
N 3:CYS74 4.1 53.4 1.0
CA 3:CYS74 4.3 52.2 1.0
CB 3:HIS13 4.6 51.2 1.0
CA 3:CYS71 4.6 50.4 1.0
OE1 3:GLN18 4.6 62.0 1.0
C 3:HIS13 4.8 52.3 1.0
CD 3:GLN18 5.0 58.0 1.0
C 3:CYS74 5.0 51.3 1.0

Reference:

D.J.Klein, P.B.Moore, T.A.Steitz. The Roles of Ribosomal Proteins in the Structure, Assembly and Evolution of the Large Ribosomal Subunit J.Mol.Biol. V. 340 141 2004.
ISSN: ISSN 0022-2836
PubMed: 15184028
DOI: 10.1016/J.JMB.2004.03.076
Page generated: Sat Dec 12 08:12:46 2020

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