Chemical elements
  Iridium
    Isotopes
    Energy
    Production
    Application
    Physical Properties
    Chemical Properties
    PDB 1c1k-4enb
      1c1k
      1icg
      1k26
      2b0u
      2gis
      3b31
      3d0u
      3dio
      3f2t
      3irw
      3owz
      486d
      4akm
      4enb

Iridium in the structure of Crystal Structure of Lysine Riboswitch Bound to Lysine (pdb 3d0u)






The binding sites of Iridium atom in the structure of Crystal Structure of Lysine Riboswitch Bound to Lysine (pdb code 3d0u). This binding sites where shown with 5.0 Angstroms radius around Iridium atom.
The 3d0u structure was solved by A.D.GARST, A.HEROUX, R.P.RAMBO, R.T.BATEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)32.6-2.8
Space groupP32
a (A)119.823
b (A)119.823
c (A)58.744
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)18.2
Rfree (%)20.9


Iridium Binding Sites:

Iridium binding site 1 out of 3 in 3d0u


Iridium binding site 1 out of 3 in 3d0u
Click to enlarge
stereopicture of Iridium binding site 1 out of 3 in 3d0u
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iridium in the PDB 3d0u. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: U137, A: G138, A: U139, A: G149, A: G150, A: Iri202, A: Hoh212,

conact list:


AtomAtomDistance (A)
IrO4 A:U1374.82
IrO6 A:G1384.59
IrO4 A:U1394.37
IrC6 A:G1494.42
IrC5 A:G1494.68
IrN7 A:G1494.26
IrO6 A:G1493.61
IrO6 A:G1504.72
IrN1 A:Iri2022.26
IrN6 A:Iri2022.23
IrN3 A:Iri2022.26
IrN2 A:Iri2022.23
IrIR A:Iri2020.00
IrN5 A:Iri2022.25
IrN4 A:Iri2022.27
IrO A:Hoh2124.57

interactive model:


Iridium binding site 2 out of 3 in 3d0u


Iridium binding site 2 out of 3 in 3d0u
Click to enlarge
stereopicture of Iridium binding site 2 out of 3 in 3d0u
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iridium in the PDB 3d0u. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: G120, A: G122, A: Iri203,

conact list:


AtomAtomDistance (A)
IrN7 A:G1204.44
IrO6 A:G1204.86
IrO6 A:G1224.14
IrN1 A:Iri2032.27
IrN6 A:Iri2032.24
IrN3 A:Iri2032.27
IrN2 A:Iri2032.23
IrIR A:Iri2030.00
IrN5 A:Iri2032.25
IrN4 A:Iri2032.27

interactive model:


Iridium binding site 3 out of 3 in 3d0u


Iridium binding site 3 out of 3 in 3d0u
Click to enlarge
stereopicture of Iridium binding site 3 out of 3 in 3d0u
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iridium in the PDB 3d0u. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iridium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: G80, A: C81, A: U106, A: Iri204,

conact list:


AtomAtomDistance (A)
IrN7 A:G804.97
IrC6 A:C814.97
IrC5 A:C814.05
IrC4 A:C814.78
IrN4 A:C814.52
IrO4 A:U1064.63
IrN1 A:Iri2042.27
IrN6 A:Iri2042.24
IrN3 A:Iri2042.27
IrN2 A:Iri2042.23
IrIR A:Iri2040.00
IrN5 A:Iri2042.25
IrN4 A:Iri2042.28

interactive model:




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