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Cadmium in PDB 1vq6: The Structure of C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq6 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 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.050, 300.187, 573.987, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.3

Other elements in 1vq6:

The structure of The Structure of C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium (Mg) 117 atoms
Potassium (K) 2 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 86 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The Structure of C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vq6). 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 C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1vq6

Go back to Cadmium Binding Sites List in 1vq6
Cadmium binding site 1 out of 5 in the The Structure of C-Hpmn and Cca-Phe-Cap-Bio 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 C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd9205

b:0.8
occ:1.00
 ND1 O:HIS40 2.6 44.2 1.0
O O:HOH5650 2.6 76.0 1.0
O 0:HOH6263 3.2 39.9 1.0
CE1 O:HIS40 3.4 44.3 1.0
CG O:HIS40 3.6 43.4 1.0
CB O:HIS40 3.9 46.5 1.0
CG O:ARG37 4.3 56.0 1.0
O O:HOH3002 4.4 53.6 1.0
NE2 O:HIS40 4.6 45.3 1.0
CB O:ARG37 4.6 54.1 1.0
CZ O:ARG37 4.7 54.2 1.0
NE O:ARG37 4.7 56.7 1.0
CD2 O:HIS40 4.7 44.3 1.0
CA O:ARG37 4.8 53.1 1.0
NH1 O:ARG37 4.9 52.7 1.0
CD O:ARG37 5.0 56.5 1.0

Cadmium binding site 2 out of 5 in 1vq6

Go back to Cadmium Binding Sites List in 1vq6
Cadmium binding site 2 out of 5 in the The Structure of C-Hpmn and Cca-Phe-Cap-Bio 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 C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd9201

b:78.4
occ:1.00
 SG U:CYS32 2.2 47.2 1.0
SG U:CYS36 2.4 65.1 1.0
SG U:CYS9 2.5 66.0 1.0
SG U:CYS6 2.6 70.2 1.0
CB U:CYS6 3.2 71.1 1.0
CB U:CYS9 3.5 65.6 1.0
CB U:CYS32 3.6 57.3 1.0
CB U:CYS36 3.6 65.4 1.0
N U:CYS9 3.9 67.1 1.0
N U:CYS32 3.9 58.2 1.0
OG U:SER33 4.3 62.7 1.0
CA U:CYS9 4.3 67.1 1.0
CA U:CYS32 4.3 58.7 1.0
OG1 U:THR11 4.4 74.5 1.0
N U:SER33 4.5 61.6 1.0
CB U:TYR8 4.5 63.7 1.0
CA U:CYS6 4.7 71.0 1.0
C U:CYS32 4.8 60.9 1.0
O U:HOH6621 4.8 85.7 1.0
N U:GLY10 4.9 68.0 1.0
C U:TYR8 5.0 67.3 1.0
CA U:CYS36 5.0 63.7 1.0

Cadmium binding site 3 out of 5 in 1vq6

Go back to Cadmium Binding Sites List in 1vq6
Cadmium binding site 3 out of 5 in the The Structure of C-Hpmn and Cca-Phe-Cap-Bio 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 C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd9203

b:76.1
occ:1.00
 SG Z:CYS39 2.2 72.1 1.0
SG Z:CYS60 2.2 66.2 1.0
SG Z:CYS57 2.3 73.1 1.0
SG Z:CYS42 2.9 84.6 1.0
CB Z:CYS57 3.2 74.7 1.0
CB Z:CYS39 3.2 75.1 1.0
CB Z:CYS60 3.4 69.4 1.0
N Z:CYS42 3.5 81.5 1.0
CB Z:CYS42 3.6 80.8 1.0
N Z:CYS60 3.8 73.0 1.0
CB Z:ASN41 3.9 84.1 1.0
CA Z:CYS42 4.2 80.5 1.0
CA Z:CYS60 4.2 70.7 1.0
CB Z:TYR59 4.4 78.4 1.0
CD2 Z:TYR59 4.5 83.5 1.0
C Z:ASN41 4.6 82.1 1.0
CB Z:TYR62 4.6 63.7 1.0
CA Z:CYS39 4.6 76.7 1.0
CA Z:CYS57 4.7 73.2 1.0
CA Z:ASN41 4.7 82.2 1.0
ND2 Z:ASN41 4.8 86.0 1.0
N Z:ASN41 4.8 81.3 1.0
C Z:CYS60 4.9 70.7 1.0
C Z:TYR59 4.9 74.8 1.0
CG Z:ASN41 4.9 85.5 1.0
C Z:CYS39 4.9 78.1 1.0
C Z:CYS42 4.9 79.3 1.0
O Z:CYS39 5.0 79.7 1.0
N Z:GLY43 5.0 78.2 1.0
CG Z:TYR59 5.0 81.5 1.0

Cadmium binding site 4 out of 5 in 1vq6

Go back to Cadmium Binding Sites List in 1vq6
Cadmium binding site 4 out of 5 in the The Structure of C-Hpmn and Cca-Phe-Cap-Bio 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 C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd9202

b:65.8
occ:1.00
 SG 1:CYS22 2.4 42.3 1.0
SG 1:CYS37 2.4 40.4 1.0
SG 1:CYS34 2.5 44.3 1.0
SG 1:CYS19 2.6 45.4 1.0
CB 1:CYS19 3.1 42.6 1.0
CB 1:CYS22 3.2 40.8 1.0
CB 1:CYS34 3.2 38.5 1.0
CB 1:CYS37 3.3 39.1 1.0
N 1:CYS22 3.6 42.7 1.0
N 1:CYS37 3.7 39.0 1.0
CA 1:CYS22 3.9 42.1 1.0
CA 1:CYS37 4.1 39.0 1.0
CB 1:PHE39 4.3 39.0 1.0
CB 1:ARG21 4.5 41.0 1.0
CB 1:SER36 4.6 40.1 1.0
C 1:ARG21 4.6 43.3 1.0
CA 1:CYS19 4.6 44.4 1.0
C 1:CYS22 4.7 41.4 1.0
CA 1:CYS34 4.7 39.9 1.0
C 1:CYS37 4.8 37.6 1.0
O 1:HOH1020 4.8 47.1 1.0
C 1:SER36 4.8 39.8 1.0
N 1:GLY23 4.8 40.5 1.0
N 1:GLY38 4.9 36.8 1.0
CA 1:ARG21 4.9 42.9 1.0
N 1:PHE39 4.9 39.2 1.0
CD 1:ARG21 4.9 43.4 1.0
N 1:ARG21 5.0 42.6 1.0

Cadmium binding site 5 out of 5 in 1vq6

Go back to Cadmium Binding Sites List in 1vq6
Cadmium binding site 5 out of 5 in the The Structure of C-Hpmn and Cca-Phe-Cap-Bio 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 C-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd9204

b:64.1
occ:1.00
 SG 3:CYS71 2.3 57.2 1.0
SG 3:CYS11 2.4 64.3 1.0
SG 3:CYS14 2.4 74.4 1.0
SG 3:CYS74 2.4 78.6 1.0
CB 3:CYS71 3.0 62.8 1.0
O 3:HOH9362 3.1 0.0 1.0
CB 3:CYS14 3.3 71.5 1.0
CB 3:CYS74 3.3 76.8 1.0
CB 3:CYS11 3.4 63.5 1.0
N 3:CYS14 3.7 70.9 1.0
N 3:CYS74 4.0 76.8 1.0
CA 3:CYS14 4.1 71.3 1.0
CA 3:CYS74 4.2 76.5 1.0
CA 3:CYS71 4.5 63.6 1.0
O 3:HOH9336 4.6 61.5 1.0
CB 3:HIS13 4.6 69.3 1.0
OE1 3:GLN18 4.7 83.8 1.0
CA 3:CYS11 4.8 62.8 1.0
C 3:HIS13 4.8 70.1 1.0
NE2 3:GLN18 4.9 81.8 1.0
CD 3:GLN18 4.9 79.8 1.0
C 3:CYS74 5.0 75.7 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: Sun Jan 24 09:43:00 2021

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