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Cadmium in PDB 1vq7: The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq7 was solved by T.M.Schmeing, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.150, 300.130, 573.290, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vq7). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq7:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1vq7

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Cadmium binding site 1 out of 5 in the The Structure of the Transition State Analogue "Dca" Bound to 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 The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd9205

b:0.5
occ:1.00
O O:HOH5650 2.6 69.4 1.0
ND1 O:HIS40 2.7 34.9 1.0
O 0:HOH6292 3.4 56.7 1.0
CE1 O:HIS40 3.6 37.3 1.0
CG O:HIS40 3.6 34.7 1.0
CB O:HIS40 3.9 39.2 1.0
O 0:HOH4663 4.4 63.0 1.0
CG O:ARG37 4.5 51.1 1.0
NH1 O:ARG37 4.7 53.4 1.0
NE2 O:HIS40 4.7 37.1 1.0
CZ O:ARG37 4.7 53.4 1.0
CD2 O:HIS40 4.8 36.1 1.0
CB O:ARG37 4.9 48.1 1.0
CA O:ARG37 4.9 45.7 1.0
NE O:ARG37 5.0 54.2 1.0

Cadmium binding site 2 out of 5 in 1vq7

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Cadmium binding site 2 out of 5 in the The Structure of the Transition State Analogue "Dca" Bound to 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 The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd9201

b:73.5
occ:1.00
SG U:CYS32 2.3 41.2 1.0
SG U:CYS9 2.5 61.2 1.0
SG U:CYS36 2.6 56.8 1.0
SG U:CYS6 2.6 61.9 1.0
CB U:CYS6 3.3 63.8 1.0
CB U:CYS9 3.5 62.1 1.0
CB U:CYS36 3.6 57.1 1.0
CB U:CYS32 3.7 49.6 1.0
N U:CYS9 3.9 63.1 1.0
N U:CYS32 4.0 50.5 1.0
OG1 U:THR11 4.1 68.7 1.0
CA U:CYS9 4.3 63.4 1.0
OG U:SER33 4.3 56.1 1.0
CA U:CYS32 4.4 50.8 1.0
CB U:TYR8 4.6 61.0 1.0
N U:SER33 4.6 54.1 1.0
CA U:CYS6 4.8 64.1 1.0
N U:GLY10 4.9 64.2 1.0
C U:CYS32 4.9 52.9 1.0
C U:TYR8 5.0 62.7 1.0

Cadmium binding site 3 out of 5 in 1vq7

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Cadmium binding site 3 out of 5 in the The Structure of the Transition State Analogue "Dca" Bound to 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 The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd9203

b:61.2
occ:1.00
SG Z:CYS60 2.3 57.0 1.0
SG Z:CYS57 2.4 57.6 1.0
SG Z:CYS39 2.4 63.8 1.0
SG Z:CYS42 2.8 72.2 1.0
CB Z:CYS39 3.1 65.3 1.0
CB Z:CYS57 3.2 59.1 1.0
CB Z:CYS60 3.5 61.4 1.0
N Z:CYS42 3.8 72.0 1.0
CB Z:CYS42 3.8 70.9 1.0
N Z:CYS60 3.9 62.8 1.0
CB Z:ASN41 4.1 74.6 1.0
CA Z:CYS60 4.2 62.0 1.0
CA Z:CYS42 4.4 71.0 1.0
CD2 Z:TYR59 4.6 71.1 1.0
CA Z:CYS39 4.6 67.3 1.0
CB Z:TYR62 4.6 53.9 1.0
CB Z:TYR59 4.6 66.6 1.0
CA Z:CYS57 4.7 58.2 1.0
C Z:ASN41 4.8 73.0 1.0
CA Z:ASN41 4.9 73.2 1.0
C Z:CYS60 4.9 62.4 1.0
C Z:TYR59 5.0 64.0 1.0
N Z:ASN41 5.0 72.4 1.0

Cadmium binding site 4 out of 5 in 1vq7

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Cadmium binding site 4 out of 5 in the The Structure of the Transition State Analogue "Dca" Bound to 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 The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd9202

b:54.6
occ:1.00
SG 1:CYS37 2.4 35.8 1.0
SG 1:CYS34 2.5 32.8 1.0
SG 1:CYS22 2.5 31.2 1.0
SG 1:CYS19 2.6 33.2 1.0
CB 1:CYS19 3.1 34.6 1.0
CB 1:CYS34 3.2 31.6 1.0
CB 1:CYS22 3.2 32.7 1.0
CB 1:CYS37 3.4 33.5 1.0
N 1:CYS22 3.6 34.7 1.0
N 1:CYS37 3.7 34.7 1.0
CA 1:CYS22 4.0 34.3 1.0
CA 1:CYS37 4.1 34.4 1.0
CB 1:PHE39 4.3 34.8 1.0
CA 1:CYS19 4.6 36.4 1.0
CB 1:SER36 4.6 35.2 1.0
CB 1:ARG21 4.6 37.0 1.0
CA 1:CYS34 4.6 33.3 1.0
O 1:HOH1020 4.7 38.6 1.0
C 1:ARG21 4.7 36.2 1.0
C 1:CYS22 4.7 33.9 1.0
C 1:CYS37 4.8 33.9 1.0
C 1:SER36 4.8 36.7 1.0
N 1:GLY23 4.8 33.7 1.0
N 1:PHE39 4.9 33.6 1.0
N 1:GLY38 4.9 33.2 1.0
CA 1:ARG21 5.0 36.9 1.0
CD 1:ARG21 5.0 37.1 1.0
N 1:ARG21 5.0 36.9 1.0

Cadmium binding site 5 out of 5 in 1vq7

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Cadmium binding site 5 out of 5 in the The Structure of the Transition State Analogue "Dca" Bound to 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 The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd9204

b:62.2
occ:1.00
SG 3:CYS71 2.4 50.8 1.0
SG 3:CYS14 2.4 64.2 1.0
SG 3:CYS74 2.4 61.8 1.0
SG 3:CYS11 2.5 49.6 1.0
O 3:HOH9360 3.0 0.2 1.0
CB 3:CYS74 3.1 63.0 1.0
CB 3:CYS14 3.2 60.7 1.0
CB 3:CYS71 3.3 58.0 1.0
N 3:CYS14 3.5 61.1 1.0
CB 3:CYS11 3.5 52.6 1.0
CA 3:CYS14 3.9 60.9 1.0
N 3:CYS74 4.0 66.0 1.0
CA 3:CYS74 4.2 64.4 1.0
CB 3:HIS13 4.4 62.1 1.0
C 3:HIS13 4.5 61.4 1.0
CA 3:CYS71 4.7 57.6 1.0
OE1 3:GLN18 4.8 71.7 1.0
CA 3:HIS13 4.9 60.8 1.0
CA 3:CYS11 4.9 53.4 1.0
C 3:CYS74 5.0 64.0 1.0

Reference:

T.M.Schmeing, K.S.Huang, S.A.Strobel, T.A.Steitz. An Induced-Fit Mechanism to Promote Peptide Bond Formation and Exclude Hydrolysis of Peptidyl-Trna. Nature V. 438 520 2005.
ISSN: ISSN 0028-0836
PubMed: 16306996
DOI: 10.1038/NATURE04152
Page generated: Fri Aug 28 12:30:20 2020
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