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

Protein crystallography data

The structure of The Structure of Cc-Hpmn and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqn 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 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.721, 298.782, 575.272, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 24.8

Other elements in 1vqn:

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

Strontium (Sr) 114 atoms
Magnesium (Mg) 94 atoms
Potassium (K) 2 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 75 atoms

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 5 in 1vqn

Go back to Cadmium Binding Sites List in 1vqn
Cadmium binding site 1 out of 5 in the The Structure of Cc-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 Cc-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:0.4
occ:1.00
O O:HOH5650 2.6 68.3 1.0
ND1 O:HIS40 2.8 34.8 1.0
CE1 O:HIS40 3.6 34.4 1.0
CG O:HIS40 3.7 35.9 1.0
CB O:HIS40 3.9 39.4 1.0
CG O:ARG37 4.4 53.7 1.0
O O:HOH3002 4.7 51.8 1.0
NH1 O:ARG37 4.7 50.3 1.0
NE2 O:HIS40 4.7 37.2 1.0
CZ O:ARG37 4.7 50.1 1.0
CD2 O:HIS40 4.8 36.5 1.0
CB O:ARG37 4.9 51.5 1.0
NE O:ARG37 4.9 50.3 1.0
CA O:ARG37 5.0 50.2 1.0

Cadmium binding site 2 out of 5 in 1vqn

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Cadmium binding site 2 out of 5 in the The Structure of Cc-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 Cc-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:53.8
occ:1.00
SG U:CYS36 2.4 51.6 1.0
SG U:CYS9 2.5 57.1 1.0
SG U:CYS6 2.5 51.0 1.0
SG U:CYS32 2.5 40.1 1.0
CB U:CYS6 3.2 52.8 1.0
CB U:CYS9 3.4 53.6 1.0
CB U:CYS36 3.5 52.5 1.0
CB U:CYS32 3.7 44.2 1.0
N U:CYS9 3.8 53.5 1.0
N U:CYS32 4.1 44.4 1.0
CA U:CYS9 4.2 55.7 1.0
OG1 U:THR11 4.3 62.6 1.0
CA U:CYS32 4.5 46.0 1.0
OG U:SER33 4.5 47.0 1.0
CB U:TYR8 4.7 50.0 1.0
CA U:CYS6 4.7 52.9 1.0
N U:SER33 4.8 48.8 1.0
N U:GLY10 4.9 58.5 1.0
C U:TYR8 4.9 53.0 1.0
CA U:CYS36 5.0 51.9 1.0
C U:CYS32 5.0 48.3 1.0
C U:CYS9 5.0 57.2 1.0

Cadmium binding site 3 out of 5 in 1vqn

Go back to Cadmium Binding Sites List in 1vqn
Cadmium binding site 3 out of 5 in the The Structure of Cc-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 Cc-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:85.0
occ:1.00
SG Z:CYS60 2.4 68.6 1.0
SG Z:CYS39 2.4 70.7 1.0
SG Z:CYS57 2.5 76.0 1.0
SG Z:CYS42 2.7 89.9 1.0
CB Z:CYS39 3.0 78.8 1.0
CB Z:CYS57 3.4 72.2 1.0
CB Z:CYS60 3.6 72.1 1.0
N Z:CYS60 3.8 75.0 1.0
CD2 Z:TYR59 3.8 85.5 1.0
CB Z:CYS42 3.8 84.3 1.0
CB Z:TYR59 4.0 80.5 1.0
N Z:CYS42 4.2 83.9 1.0
ND2 Z:ASN41 4.2 82.5 1.0
CB Z:ASN41 4.3 82.6 1.0
CA Z:CYS60 4.3 72.5 1.0
CG Z:TYR59 4.4 84.0 1.0
CA Z:CYS39 4.5 81.3 1.0
CA Z:CYS42 4.6 83.8 1.0
C Z:ASN41 4.7 82.7 1.0
C Z:TYR59 4.8 77.1 1.0
CG Z:ASN41 4.8 83.1 1.0
CE2 Z:TYR59 4.8 87.7 1.0
CB Z:GLU44 4.8 88.7 1.0
CA Z:CYS57 4.9 71.1 1.0
CA Z:TYR59 4.9 78.0 1.0
CA Z:ASN41 4.9 81.8 1.0
C Z:CYS39 4.9 82.0 1.0

Cadmium binding site 4 out of 5 in 1vqn

Go back to Cadmium Binding Sites List in 1vqn
Cadmium binding site 4 out of 5 in the The Structure of Cc-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 Cc-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:54.4
occ:1.00
SG 1:CYS22 2.4 34.3 1.0
SG 1:CYS34 2.4 37.5 1.0
SG 1:CYS37 2.5 37.0 1.0
SG 1:CYS19 2.5 37.1 1.0
CB 1:CYS19 3.1 36.6 1.0
CB 1:CYS34 3.2 33.2 1.0
CB 1:CYS22 3.3 35.6 1.0
CB 1:CYS37 3.3 29.5 1.0
N 1:CYS22 3.7 38.9 1.0
N 1:CYS37 3.8 34.5 1.0
CA 1:CYS22 4.1 36.5 1.0
CA 1:CYS37 4.1 33.2 1.0
CB 1:PHE39 4.4 33.5 1.0
CB 1:ARG21 4.5 37.5 1.0
CA 1:CYS19 4.6 38.2 1.0
CA 1:CYS34 4.6 34.5 1.0
C 1:ARG21 4.7 39.1 1.0
CB 1:SER36 4.7 32.9 1.0
O 1:HOH9480 4.7 47.3 1.0
C 1:CYS37 4.8 31.6 1.0
C 1:SER36 4.8 36.2 1.0
C 1:CYS22 4.9 36.2 1.0
N 1:PHE39 4.9 33.3 1.0
N 1:GLY38 4.9 32.1 1.0
N 1:GLY23 4.9 36.8 1.0
CD 1:ARG21 5.0 37.3 1.0
CA 1:ARG21 5.0 38.9 1.0

Cadmium binding site 5 out of 5 in 1vqn

Go back to Cadmium Binding Sites List in 1vqn
Cadmium binding site 5 out of 5 in the The Structure of Cc-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 Cc-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:64.4
occ:1.00
SG 3:CYS71 2.2 67.0 1.0
SG 3:CYS11 2.4 56.9 1.0
SG 3:CYS14 2.4 72.3 1.0
SG 3:CYS74 2.4 66.5 1.0
CB 3:CYS71 3.0 67.9 1.0
CB 3:CYS14 3.4 66.8 1.0
CB 3:CYS74 3.4 67.8 1.0
CB 3:CYS11 3.5 58.0 1.0
N 3:CYS14 3.6 67.2 1.0
N 3:CYS74 4.0 69.3 1.0
CA 3:CYS14 4.1 66.9 1.0
OE1 3:GLN18 4.1 68.7 1.0
CA 3:CYS74 4.3 67.8 1.0
CB 3:HIS13 4.4 66.4 1.0
CA 3:CYS71 4.4 67.5 1.0
C 3:HIS13 4.7 67.0 1.0
O 3:HOH9497 4.7 0.6 1.0
CD 3:GLN18 4.8 65.7 1.0
CA 3:CYS11 4.9 59.2 1.0
CA 3:HIS13 4.9 66.4 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: Wed Oct 28 09:57:27 2020
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