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 Structure of A C-Di-Gmp Riboswitch From V. Cholerae (pdb 3irw)






The binding sites of Iridium atom in the structure of Structure of A C-Di-Gmp Riboswitch From V. Cholerae (pdb code 3irw). This binding sites where shown with 5.0 Angstroms radius around Iridium atom.
The 3irw structure was solved by K.D.SMITH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)43.7-2.7
Space groupP1211
a (A)49.461
b (A)45.123
c (A)76.573
alpha (°)90.00
beta (°)96.79
gamma (°)90.00
Rfactor (%)19.6
Rfree (%)25.1


Iridium Binding Sites:

Iridium binding site 1 out of 9 in 3irw


Iridium binding site 1 out of 9 in 3irw
Click to enlarge
stereopicture of Iridium binding site 1 out of 9 in 3irw
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iridium in the PDB 3irw. 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: R: C46, R: A47, R: A49, R: Iri670, R: Hoh182,

conact list:


AtomAtomDistance (A)
IrO3' R:C464.29
IrOP1 R:A473.46
IrP R:A474.36
IrO5' R:A474.50
IrOP1 R:A493.90
IrP R:A494.67
IrOP2 R:A494.38
IrN1 R:Iri6702.01
IrN6 R:Iri6702.02
IrN3 R:Iri6702.02
IrN2 R:Iri6702.02
IrIR R:Iri6700.00
IrN5 R:Iri6702.02
IrN4 R:Iri6702.02
IrO R:Hoh1823.62

interactive model:


Iridium binding site 2 out of 9 in 3irw


Iridium binding site 2 out of 9 in 3irw
Click to enlarge
stereopicture of Iridium binding site 2 out of 9 in 3irw
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iridium in the PDB 3irw. 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: R: U53, R: G56, R: G57, R: C58, R: G80, R: U81, R: Iri2, R: Iri672, R: Hoh102, R: Hoh104,

conact list:


AtomAtomDistance (A)
IrO2 R:U534.65
IrO2' R:U534.92
IrC6 R:G564.87
IrC5 R:G564.87
IrN7 R:G564.23
IrO6 R:G564.25
IrC6 R:G574.66
IrC5 R:G574.85
IrN7 R:G574.25
IrO6 R:G573.79
IrN4 R:C584.79
IrO6 R:G804.65
IrO4 R:U814.28
IrN1 R:Iri22.02
IrN6 R:Iri22.03
IrN3 R:Iri22.02
IrN2 R:Iri22.02
IrIR R:Iri20.00
IrN5 R:Iri22.02
IrN4 R:Iri22.02
IrN6 R:Iri6723.90
IrO R:Hoh1024.15
IrO R:Hoh1043.74

interactive model:


Iridium binding site 3 out of 9 in 3irw


Iridium binding site 3 out of 9 in 3irw
Click to enlarge
stereopicture of Iridium binding site 3 out of 9 in 3irw
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iridium in the PDB 3irw. 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: R: G19, R: G20, R: C2e1, R: Iri3,

conact list:


AtomAtomDistance (A)
IrN7 R:G194.71
IrO6 R:G194.90
IrN7 R:G204.44
IrO6 R:G204.44
IrO1P R:C2e13.06
IrO2P R:C2e14.30
IrP1 R:C2e14.37
IrN1 R:Iri32.02
IrN6 R:Iri32.02
IrN3 R:Iri32.02
IrN2 R:Iri32.03
IrIR R:Iri30.00
IrN5 R:Iri32.03
IrN4 R:Iri32.02

interactive model:


Iridium binding site 4 out of 9 in 3irw


Iridium binding site 4 out of 9 in 3irw
Click to enlarge
stereopicture of Iridium binding site 4 out of 9 in 3irw
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iridium in the PDB 3irw. 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: R: C52, R: G85, R: G86, R: G87, R: Iri4, R: Iri7, R: Hoh172,

conact list:


AtomAtomDistance (A)
IrN4 R:C524.84
IrOP2 R:G854.79
IrC8 R:G864.22
IrC5 R:G864.76
IrN7 R:G863.62
IrOP2 R:G863.91
IrC6 R:G874.73
IrN7 R:G874.58
IrO6 R:G873.80
IrN1 R:Iri42.02
IrN6 R:Iri42.02
IrN3 R:Iri42.02
IrN2 R:Iri42.02
IrIR R:Iri40.00
IrN5 R:Iri42.03
IrN4 R:Iri42.03
IrN6 R:Iri74.09
IrN3 R:Iri73.43
IrN2 R:Iri73.34
IrIR R:Iri74.35
IrO R:Hoh1723.65

interactive model:


Iridium binding site 5 out of 9 in 3irw


Iridium binding site 5 out of 9 in 3irw
Click to enlarge
stereopicture of Iridium binding site 5 out of 9 in 3irw
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iridium in the PDB 3irw. 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: R: Gtp8, R: G9, R: U10, R: U96, R: G97, R: Iri5,

conact list:


AtomAtomDistance (A)
IrO3B R:Gtp84.70
IrO2B R:Gtp83.39
IrO1B R:Gtp83.68
IrPB R:Gtp84.06
IrO6 R:G94.54
IrO4 R:U103.93
IrO4 R:U964.83
IrC6 R:G974.51
IrN7 R:G974.85
IrO6 R:G973.47
IrN1 R:Iri52.02
IrN6 R:Iri52.02
IrN3 R:Iri52.03
IrN2 R:Iri52.02
IrIR R:Iri50.00
IrN5 R:Iri52.03
IrN4 R:Iri52.03

interactive model:


Iridium binding site 6 out of 9 in 3irw


Iridium binding site 6 out of 9 in 3irw
Click to enlarge
stereopicture of Iridium binding site 6 out of 9 in 3irw
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iridium in the PDB 3irw. 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: R: G32, R: Iri6, R: Hoh180,

conact list:


AtomAtomDistance (A)
IrC6 R:G324.92
IrN7 R:G324.55
IrO6 R:G324.19
IrN1 R:Iri62.03
IrN6 R:Iri62.02
IrN3 R:Iri62.03
IrN2 R:Iri62.02
IrIR R:Iri60.00
IrN5 R:Iri62.02
IrN4 R:Iri62.02
IrO R:Hoh1803.78

interactive model:


Iridium binding site 7 out of 9 in 3irw


Iridium binding site 7 out of 9 in 3irw
Click to enlarge
stereopicture of Iridium binding site 7 out of 9 in 3irw
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iridium in the PDB 3irw. 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: R: G87, R: G88, R: U89, R: Iri4, R: Iri7,

conact list:


AtomAtomDistance (A)
IrC8 R:G874.83
IrC6 R:G874.97
IrC5 R:G874.77
IrN7 R:G874.04
IrOP2 R:G874.76
IrO6 R:G874.56
IrC6 R:G884.96
IrN7 R:G884.52
IrO6 R:G884.07
IrO4 R:U894.42
IrN6 R:Iri43.15
IrN3 R:Iri43.65
IrIR R:Iri44.35
IrN4 R:Iri44.11
IrN1 R:Iri72.03
IrN6 R:Iri72.03
IrN3 R:Iri72.02
IrN2 R:Iri72.03
IrIR R:Iri70.00
IrN5 R:Iri72.03
IrN4 R:Iri72.03

interactive model:


Iridium binding site 8 out of 9 in 3irw


Iridium binding site 8 out of 9 in 3irw
Click to enlarge
stereopicture of Iridium binding site 8 out of 9 in 3irw
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iridium in the PDB 3irw. 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: R: A24, R: A25, R: G83, R: C84, R: Iri671,

conact list:


AtomAtomDistance (A)
IrO3' R:A244.87
IrOP1 R:A254.55
IrO2' R:G834.34
IrOP2 R:C844.31
IrN1 R:Iri6712.03
IrN6 R:Iri6712.03
IrN3 R:Iri6712.03
IrN2 R:Iri6712.02
IrIR R:Iri6710.00
IrN5 R:Iri6712.03
IrN4 R:Iri6712.03

interactive model:


Iridium binding site 9 out of 9 in 3irw


Iridium binding site 9 out of 9 in 3irw
Click to enlarge
stereopicture of Iridium binding site 9 out of 9 in 3irw
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Iridium in the PDB 3irw. 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: R: G79, R: Iri2, R: Iri672, R: Hoh104,

conact list:


AtomAtomDistance (A)
IrC8 R:G794.58
IrC6 R:G794.77
IrC5 R:G794.54
IrN7 R:G793.66
IrO6 R:G794.25
IrN2 R:Iri24.92
IrN1 R:Iri6722.02
IrN6 R:Iri6722.02
IrN3 R:Iri6722.02
IrN2 R:Iri6722.02
IrIR R:Iri6720.00
IrN5 R:Iri6722.03
IrN4 R:Iri6722.03
IrO R:Hoh1044.39

interactive model:




© Copyright 2008-2012 by atomistry.com