Atomistry » Cadmium » PDB 1qvg-1vqo » 1vqn
Atomistry »
  Cadmium »
    PDB 1qvg-1vqo »
      1vqn »

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

Go back to Cadmium Binding Sites List in 1vqn
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: Fri Jul 19 14:22:19 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy