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Cadmium in PDB 1qvg: Structure of Cca Oligonucleotide Bound to the Trna Binding Sites of the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of Structure of Cca Oligonucleotide Bound to the Trna Binding Sites of the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1qvg 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 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 213.517, 300.612, 573.929, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 25.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Cca Oligonucleotide Bound to the Trna Binding Sites of the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1qvg). 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 Cca Oligonucleotide Bound to the Trna Binding Sites of the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1qvg:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1qvg

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Cadmium binding site 1 out of 5 in the Structure of Cca Oligonucleotide Bound to the Trna Binding Sites 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 Cca Oligonucleotide Bound to the Trna Binding Sites of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cd8405

b:90.8
occ:1.00
ND1 N:HIS40 2.4 44.3 1.0
O N:HOH5650 2.4 25.6 1.0
CE1 N:HIS40 3.3 43.5 1.0
CG N:HIS40 3.3 44.7 1.0
CB N:HIS40 3.6 47.3 1.0
CG N:ARG37 4.4 59.0 1.0
NE2 N:HIS40 4.4 43.7 1.0
CD2 N:HIS40 4.5 43.2 1.0
NH1 N:ARG37 4.7 58.5 1.0
O N:ARG37 4.7 53.5 1.0
CB N:ARG37 4.7 57.3 1.0
CA N:ARG37 4.8 56.2 1.0
CZ N:ARG37 4.8 60.3 1.0

Cadmium binding site 2 out of 5 in 1qvg

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Cadmium binding site 2 out of 5 in the Structure of Cca Oligonucleotide Bound to the Trna Binding Sites 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 Cca Oligonucleotide Bound to the Trna Binding Sites of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cd8401

b:78.5
occ:1.00
SG T:CYS36 2.3 61.1 1.0
SG T:CYS32 2.4 39.1 1.0
SG T:CYS6 2.4 63.5 1.0
SG T:CYS9 2.6 59.9 1.0
CB T:CYS6 3.2 65.0 1.0
CB T:CYS9 3.4 58.8 1.0
CB T:CYS36 3.6 59.5 1.0
CB T:CYS32 3.7 46.5 1.0
N T:CYS9 3.8 60.1 1.0
N T:CYS32 4.1 49.6 1.0
CA T:CYS9 4.2 59.2 1.0
OG1 T:THR11 4.4 66.7 1.0
CB T:TYR8 4.5 58.3 1.0
CA T:CYS32 4.5 49.0 1.0
OG T:SER33 4.6 55.1 1.0
CA T:CYS6 4.7 65.1 1.0
N T:SER33 4.8 51.9 1.0
N T:GLY10 4.8 59.5 1.0
C T:TYR8 4.9 60.6 1.0
CD2 T:TYR8 4.9 55.4 1.0
C T:CYS9 4.9 59.0 1.0
CA T:CYS36 4.9 58.8 1.0

Cadmium binding site 3 out of 5 in 1qvg

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Cadmium binding site 3 out of 5 in the Structure of Cca Oligonucleotide Bound to the Trna Binding Sites 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 Cca Oligonucleotide Bound to the Trna Binding Sites of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Cd8403

b:82.2
occ:1.00
SG Y:CYS57 2.3 84.0 1.0
SG Y:CYS60 2.3 69.1 1.0
SG Y:CYS39 2.4 69.0 1.0
SG Y:CYS42 2.9 77.0 1.0
CB Y:CYS57 3.2 85.2 1.0
CB Y:CYS39 3.2 69.5 1.0
CB Y:CYS60 3.3 70.5 1.0
CB Y:CYS42 3.4 80.6 1.0
N Y:CYS60 3.8 75.0 1.0
N Y:CYS42 3.8 81.8 1.0
CA Y:CYS60 4.1 71.8 1.0
CA Y:CYS42 4.2 82.1 1.0
CB Y:HIS59 4.5 83.3 1.0
CA Y:CYS57 4.7 84.0 1.0
CD2 Y:HIS59 4.7 87.2 1.0
CA Y:CYS39 4.7 71.3 1.0
CB Y:VAL41 4.7 79.5 1.0
CB Y:TYR62 4.7 67.9 1.0
C Y:CYS60 4.9 70.8 1.0
C Y:CYS42 4.9 83.8 1.0
C Y:HIS59 4.9 78.4 1.0
C Y:VAL41 5.0 81.4 1.0
CG Y:HIS59 5.0 86.3 1.0

Cadmium binding site 4 out of 5 in 1qvg

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Cadmium binding site 4 out of 5 in the Structure of Cca Oligonucleotide Bound to the Trna Binding Sites 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 Cca Oligonucleotide Bound to the Trna Binding Sites of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8402

b:75.0
occ:1.00
SG Z:CYS37 2.3 42.2 1.0
SG Z:CYS19 2.4 47.5 1.0
SG Z:CYS22 2.4 46.4 1.0
SG Z:CYS34 2.5 40.8 1.0
CB Z:CYS19 3.0 44.5 1.0
CB Z:CYS22 3.2 44.5 1.0
CB Z:CYS37 3.4 40.8 1.0
CB Z:CYS34 3.4 39.3 1.0
N Z:CYS22 3.6 45.6 1.0
N Z:CYS37 3.8 40.4 1.0
CA Z:CYS22 4.0 45.5 1.0
CA Z:CYS37 4.2 40.3 1.0
O Z:HOH8420 4.4 35.7 1.0
CA Z:CYS19 4.4 45.1 1.0
CB Z:PHE39 4.5 51.2 1.0
CB Z:ARG21 4.5 45.0 1.0
C Z:ARG21 4.6 45.8 1.0
C Z:CYS22 4.6 46.1 1.0
N Z:GLY23 4.7 46.3 1.0
CB Z:SER36 4.8 39.3 1.0
CD Z:ARG21 4.8 46.2 1.0
CA Z:CYS34 4.8 40.1 1.0
C Z:CYS37 4.9 40.3 1.0
C Z:SER36 4.9 40.3 1.0
CA Z:ARG21 4.9 46.0 1.0
C Z:CYS19 4.9 46.2 1.0
N Z:GLU24 4.9 49.6 1.0
N Z:ARG21 5.0 46.8 1.0

Cadmium binding site 5 out of 5 in 1qvg

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Cadmium binding site 5 out of 5 in the Structure of Cca Oligonucleotide Bound to the Trna Binding Sites 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 Cca Oligonucleotide Bound to the Trna Binding Sites of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Cd8404

b:76.2
occ:1.00
SG 2:CYS71 2.3 51.0 1.0
SG 2:CYS74 2.3 73.3 1.0
SG 2:CYS11 2.5 80.5 1.0
SG 2:CYS14 2.6 77.4 1.0
CB 2:CYS14 3.2 74.3 1.0
CB 2:CYS71 3.3 59.0 1.0
CB 2:CYS74 3.4 73.1 1.0
CB 2:CYS11 3.6 75.5 1.0
N 2:CYS14 3.8 73.7 1.0
CA 2:CYS14 4.0 74.6 1.0
N 2:CYS74 4.1 74.3 1.0
CA 2:CYS74 4.3 74.1 1.0
OE1 2:GLN18 4.6 84.0 1.0
CB 2:HIS13 4.7 72.9 1.0
CA 2:CYS71 4.7 63.3 1.0
C 2:HIS13 4.9 73.6 1.0
O 2:HOH8530 4.9 39.5 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: Fri Aug 28 12:23:32 2020
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