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Cadmium in PDB 1qvf: Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1qvf was solved by 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) 50.00 / 3.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 213.522, 300.817, 574.861, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.9

Other elements in 1qvf:

The structure of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium (Mg) 119 atoms
Potassium (K) 2 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 86 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1qvf). 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 A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1qvf:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1qvf

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Cadmium binding site 1 out of 5 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large 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 Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cd8405

b:0.0
occ:1.00
ND1 N:HIS40 2.5 55.9 1.0
O 0:HOH5737 2.7 46.4 1.0
CG N:HIS40 3.4 55.1 1.0
CE1 N:HIS40 3.5 55.4 1.0
CB N:HIS40 3.6 54.5 1.0
CG N:ARG37 4.4 56.4 1.0
NE2 N:HIS40 4.5 56.3 1.0
CD2 N:HIS40 4.5 55.3 1.0
O 0:HOH3844 4.6 43.2 1.0
CA N:ARG37 4.8 55.0 1.0
O N:ARG37 4.8 53.4 1.0
CZ N:ARG37 4.8 57.8 1.0
NH1 N:ARG37 4.9 56.4 1.0
CB N:ARG37 4.9 55.2 1.0
NE N:ARG37 5.0 57.7 1.0

Cadmium binding site 2 out of 5 in 1qvf

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Cadmium binding site 2 out of 5 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large 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 Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cd8401

b:82.4
occ:1.00
SG T:CYS36 2.4 65.9 1.0
SG T:CYS6 2.4 69.8 1.0
SG T:CYS32 2.5 45.4 1.0
SG T:CYS9 2.7 63.8 1.0
CB T:CYS6 3.2 70.9 1.0
CB T:CYS9 3.4 66.3 1.0
CB T:CYS36 3.5 65.7 1.0
CB T:CYS32 3.6 54.1 1.0
N T:CYS9 3.7 67.2 1.0
N T:CYS32 4.0 54.9 1.0
CA T:CYS9 4.1 66.4 1.0
CA T:CYS32 4.4 56.2 1.0
CB T:TYR8 4.4 66.5 1.0
OG T:SER33 4.5 62.6 1.0
OG1 T:THR11 4.6 70.3 1.0
CA T:CYS6 4.6 70.1 1.0
N T:SER33 4.7 60.5 1.0
N T:GLY10 4.7 66.9 1.0
C T:TYR8 4.8 67.0 1.0
C T:CYS9 4.9 66.7 1.0
CA T:CYS36 4.9 64.7 1.0
CD2 T:TYR8 5.0 65.3 1.0
C T:CYS32 5.0 58.5 1.0

Cadmium binding site 3 out of 5 in 1qvf

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Cadmium binding site 3 out of 5 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large 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 Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Cd8403

b:79.6
occ:1.00
SG Y:CYS60 2.3 63.5 1.0
SG Y:CYS57 2.5 83.6 1.0
SG Y:CYS39 2.5 67.0 1.0
SG Y:CYS42 2.8 81.1 1.0
CB Y:CYS57 3.2 83.0 1.0
CB Y:CYS39 3.3 68.2 1.0
CB Y:CYS42 3.4 81.4 1.0
CB Y:CYS60 3.5 67.7 1.0
N Y:CYS42 3.8 82.2 1.0
N Y:CYS60 3.9 71.9 1.0
CA Y:CYS42 4.2 82.6 1.0
CA Y:CYS60 4.3 69.5 1.0
CB Y:HIS59 4.6 80.9 1.0
CD2 Y:HIS59 4.7 83.1 1.0
CB Y:TYR62 4.7 72.8 1.0
CA Y:CYS39 4.8 70.4 1.0
CB Y:VAL41 4.8 80.1 1.0
CA Y:CYS57 4.8 82.2 1.0
C Y:CYS42 4.8 83.9 1.0
CG1 Y:VAL41 4.9 78.8 1.0
C Y:VAL41 5.0 81.3 1.0

Cadmium binding site 4 out of 5 in 1qvf

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Cadmium binding site 4 out of 5 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large 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 Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8402

b:68.6
occ:1.00
SG Z:CYS34 2.4 44.5 1.0
SG Z:CYS19 2.5 49.4 1.0
SG Z:CYS37 2.5 51.7 1.0
SG Z:CYS22 2.6 43.0 1.0
CB Z:CYS19 3.0 44.9 1.0
CB Z:CYS34 3.2 41.5 1.0
CB Z:CYS37 3.3 46.8 1.0
CB Z:CYS22 3.3 42.8 1.0
N Z:CYS22 3.7 45.3 1.0
N Z:CYS37 3.8 46.3 1.0
CA Z:CYS22 4.1 44.2 1.0
CA Z:CYS37 4.1 46.2 1.0
CB Z:PHE39 4.3 52.6 1.0
CA Z:CYS19 4.5 44.2 1.0
CB Z:ARG21 4.6 44.5 1.0
CA Z:CYS34 4.6 42.1 1.0
C Z:ARG21 4.7 45.3 1.0
O Z:HOH8422 4.7 37.4 1.0
C Z:CYS37 4.8 45.9 1.0
C Z:CYS22 4.8 44.4 1.0
N Z:GLY23 4.8 44.8 1.0
CB Z:SER36 4.8 44.7 1.0
C Z:SER36 4.9 46.4 1.0
N Z:PHE39 4.9 50.3 1.0
N Z:GLY38 4.9 45.4 1.0
CD Z:ARG21 4.9 45.6 1.0
CA Z:ARG21 5.0 45.0 1.0

Cadmium binding site 5 out of 5 in 1qvf

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Cadmium binding site 5 out of 5 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large 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 Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Cd8404

b:74.1
occ:1.00
SG 2:CYS71 2.2 50.2 1.0
SG 2:CYS74 2.5 73.9 1.0
SG 2:CYS11 2.5 76.1 1.0
SG 2:CYS14 2.8 80.1 1.0
CB 2:CYS71 3.0 56.6 1.0
CB 2:CYS14 3.1 77.3 1.0
O 2:HOH8549 3.1 0.4 1.0
CB 2:CYS74 3.4 72.7 1.0
CB 2:CYS11 3.6 73.4 1.0
N 2:CYS14 3.7 76.2 1.0
CA 2:CYS14 4.0 76.9 1.0
N 2:CYS74 4.0 72.0 1.0
CA 2:CYS74 4.3 72.2 1.0
CA 2:CYS71 4.5 59.5 1.0
OE1 2:GLN18 4.7 85.7 1.0
CB 2:HIS13 4.7 75.0 1.0
C 2:HIS13 4.9 76.0 1.0
C 2:CYS74 5.0 72.3 1.0
CA 2:CYS11 5.0 72.3 1.0

Reference:

T.M.Schmeing, P.B.Moore, T.A.Steitz. Structures of Deacylated Trna Mimics Bound to the E Site of the Large Ribosomal Subunit Rna V. 9 1345 2003.
ISSN: ISSN 1355-8382
PubMed: 14561884
DOI: 10.1261/RNA.5120503
Page generated: Wed Oct 28 09:56:00 2020
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