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 Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak (pdb 3dio)






The binding sites of Iridium atom in the structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak (pdb code 3dio). This binding sites where shown with 5.0 Angstroms radius around Iridium atom.
The 3dio structure was solved by A.A.SERGANOV, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)20.0-2.4
Space groupP212121
a (A)53.918
b (A)78.004
c (A)140.835
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)20.4
Rfree (%)24.3


Iridium Binding Sites:

Iridium binding site 1 out of 18 in 3dio


Iridium binding site 1 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 1 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iridium in the PDB 3dio. 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: X: G1, X: G2, X: G172, X: U173, X: Iri250, X: Hoh320, X: Hoh321, X: Hoh555, X: Hoh558,

conact list:


AtomAtomDistance (A)
IrO6 X:G14.13
IrO6 X:G24.95
IrO6 X:G1724.06
IrC4 X:U1734.91
IrO4 X:U1733.85
IrN1 X:Iri2502.03
IrN6 X:Iri2502.03
IrN3 X:Iri2502.03
IrN2 X:Iri2502.03
IrIR X:Iri2500.00
IrN5 X:Iri2502.03
IrN4 X:Iri2502.03
IrO X:Hoh3203.92
IrO X:Hoh3213.91
IrO X:Hoh5554.15
IrO X:Hoh5584.04

interactive model:


Iridium binding site 2 out of 18 in 3dio


Iridium binding site 2 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 2 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iridium in the PDB 3dio. 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: X: U109, X: G110, X: Iri251, X: Hoh366,

conact list:


AtomAtomDistance (A)
IrOP1 X:U1093.92
IrP X:U1094.78
IrOP2 X:U1094.81
IrOP2 X:G1103.90
IrN1 X:Iri2512.02
IrN6 X:Iri2512.02
IrN3 X:Iri2512.02
IrN2 X:Iri2512.02
IrIR X:Iri2510.00
IrN5 X:Iri2512.03
IrN4 X:Iri2512.02
IrO X:Hoh3664.68

interactive model:


Iridium binding site 3 out of 18 in 3dio


Iridium binding site 3 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 3 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iridium in the PDB 3dio. 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: X: G123, X: G124, X: G125, X: Iri252, X: Hoh489,

conact list:


AtomAtomDistance (A)
IrC6 X:G1234.92
IrC5 X:G1234.88
IrN7 X:G1234.16
IrO6 X:G1234.28
IrO6 X:G1244.81
IrC6 X:G1254.58
IrN1 X:G1254.87
IrO6 X:G1253.76
IrN1 X:Iri2522.03
IrN6 X:Iri2522.02
IrN3 X:Iri2522.03
IrN2 X:Iri2522.02
IrIR X:Iri2520.00
IrN5 X:Iri2522.02
IrN4 X:Iri2522.03
IrO X:Hoh4894.38

interactive model:


Iridium binding site 4 out of 18 in 3dio


Iridium binding site 4 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 4 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iridium in the PDB 3dio. 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: X: G56, X: G57, X: Iri253,

conact list:


AtomAtomDistance (A)
IrC6 X:G564.70
IrC5 X:G564.90
IrN7 X:G564.35
IrO6 X:G563.85
IrC6 X:G574.53
IrO6 X:G573.54
IrN1 X:Iri2532.02
IrN6 X:Iri2532.03
IrN6 X:Iri2534.08
IrN3 X:Iri2532.02
IrN3 X:Iri2532.13
IrN2 X:Iri2532.03
IrN2 X:Iri2533.90
IrIR X:Iri2530.00
IrIR X:Iri2533.93
IrN5 X:Iri2532.02
IrN5 X:Iri2534.74
IrN4 X:Iri2532.02
IrN4 X:Iri2534.89

interactive model:


Iridium binding site 5 out of 18 in 3dio


Iridium binding site 5 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 5 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iridium in the PDB 3dio. 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: X: G54, X: G55, X: Iri253,

conact list:


AtomAtomDistance (A)
IrOP2 X:G544.60
IrN7 X:G554.30
IrO6 X:G554.38
IrN1 X:Iri2533.03
IrN1 X:Iri2532.03
IrN6 X:Iri2534.78
IrN6 X:Iri2532.02
IrN3 X:Iri2532.02
IrN2 X:Iri2532.02
IrIR X:Iri2533.93
IrIR X:Iri2530.00
IrN5 X:Iri2534.04
IrN5 X:Iri2532.03
IrN4 X:Iri2532.82
IrN4 X:Iri2532.03

interactive model:


Iridium binding site 6 out of 18 in 3dio


Iridium binding site 6 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 6 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iridium in the PDB 3dio. 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: X: G83, X: G84, X: U109, X: Iri254, X: Hoh368, X: Hoh515, X: Hoh549, X: Hoh554, X: Hoh556,

conact list:


AtomAtomDistance (A)
IrN7 X:G834.27
IrO6 X:G834.65
IrN7 X:G844.63
IrO6 X:G844.62
IrC4 X:U1094.94
IrO4 X:U1093.79
IrN1 X:Iri2542.03
IrN6 X:Iri2542.03
IrN3 X:Iri2542.02
IrN2 X:Iri2542.03
IrIR X:Iri2540.00
IrN5 X:Iri2542.03
IrN4 X:Iri2542.02
IrO X:Hoh3684.45
IrO X:Hoh5153.80
IrO X:Hoh5494.43
IrO X:Hoh5544.43
IrO X:Hoh5563.53

interactive model:


Iridium binding site 7 out of 18 in 3dio


Iridium binding site 7 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 7 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iridium in the PDB 3dio. 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: X: C13, X: C15, X: G116, X: G117, X: C131, X: Iri255, X: Hoh312, X: Hoh383,

conact list:


AtomAtomDistance (A)
IrC2 X:C134.96
IrO2 X:C134.17
IrOP1 X:C154.19
IrO3' X:G1164.83
IrOP1 X:G1173.92
IrOP1 X:C1314.32
IrN1 X:Iri2552.03
IrN6 X:Iri2552.03
IrN3 X:Iri2552.03
IrN2 X:Iri2552.03
IrIR X:Iri2550.00
IrN5 X:Iri2552.03
IrN4 X:Iri2552.03
IrO X:Hoh3123.99
IrO X:Hoh3834.19

interactive model:


Iridium binding site 8 out of 18 in 3dio


Iridium binding site 8 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 8 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iridium in the PDB 3dio. 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: X: G146, X: G147, X: Iri256, X: Hoh470, X: Hoh471, X: Hoh472,

conact list:


AtomAtomDistance (A)
IrOP2 X:G1464.26
IrOP2 X:G1474.53
IrN1 X:Iri2562.03
IrN6 X:Iri2562.03
IrN3 X:Iri2562.02
IrN2 X:Iri2562.02
IrIR X:Iri2560.00
IrN5 X:Iri2562.02
IrN4 X:Iri2562.02
IrO X:Hoh4704.32
IrO X:Hoh4713.79
IrO X:Hoh4724.47

interactive model:


Iridium binding site 9 out of 18 in 3dio


Iridium binding site 9 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 9 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Iridium in the PDB 3dio. 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: X: G149, X: G150, X: Iri257, X: Hoh517,

conact list:


AtomAtomDistance (A)
IrC6 X:G1494.91
IrC5 X:G1494.93
IrN7 X:G1494.21
IrO6 X:G1494.18
IrO6 X:G1504.17
IrN1 X:Iri2572.03
IrN6 X:Iri2572.03
IrN3 X:Iri2572.03
IrN2 X:Iri2572.03
IrIR X:Iri2570.00
IrN5 X:Iri2572.03
IrN4 X:Iri2572.02
IrO X:Hoh5174.67

interactive model:


Iridium binding site 10 out of 18 in 3dio


Iridium binding site 10 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 10 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Iridium in the PDB 3dio. 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: X: U113, X: G114, X: G115, X: Iri258, X: Hoh387,

conact list:


AtomAtomDistance (A)
IrO3' X:U1134.31
IrO2' X:U1134.60
IrOP1 X:G1143.99
IrP X:G1144.81
IrC8 X:G1154.97
IrN7 X:G1154.10
IrOP2 X:G1154.45
IrO6 X:G1154.67
IrN1 X:Iri2582.03
IrN6 X:Iri2582.03
IrN3 X:Iri2582.03
IrN2 X:Iri2582.03
IrIR X:Iri2580.00
IrN5 X:Iri2582.03
IrN4 X:Iri2582.03
IrO X:Hoh3873.99

interactive model:


Iridium binding site 11 out of 18 in 3dio


Iridium binding site 11 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 11 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Iridium in the PDB 3dio. 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: X: G124, X: G125, X: A127, X: Iri259, X: Hoh322, X: Hoh323,

conact list:


AtomAtomDistance (A)
IrP X:G1244.95
IrOP2 X:G1244.01
IrC8 X:G1254.90
IrN7 X:G1254.22
IrOP2 X:G1254.71
IrOP1 X:A1274.21
IrOP2 X:A1274.80
IrN1 X:Iri2592.03
IrN6 X:Iri2592.03
IrN3 X:Iri2592.02
IrN2 X:Iri2592.02
IrIR X:Iri2590.00
IrN5 X:Iri2592.02
IrN4 X:Iri2592.02
IrO X:Hoh3223.41
IrO X:Hoh3233.85

interactive model:


Iridium binding site 12 out of 18 in 3dio


Iridium binding site 12 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 12 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Iridium in the PDB 3dio. 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: X: C139, X: U140, X: C157, X: G158, X: Iri260, X: Iri265, X: Hoh324, X: Hoh390, X: Hoh408, X: Hoh409, X: Hoh505,

conact list:


AtomAtomDistance (A)
IrOP1 X:C1394.66
IrOP2 X:U1404.19
IrOP1 X:C1574.50
IrP X:C1574.90
IrOP2 X:C1574.46
IrP X:G1584.73
IrOP2 X:G1583.47
IrN1 X:Iri2602.03
IrN6 X:Iri2602.03
IrN6 X:Iri2604.01
IrN3 X:Iri2602.03
IrN3 X:Iri2603.64
IrN2 X:Iri2602.03
IrIR X:Iri2600.00
IrIR X:Iri2603.89
IrN5 X:Iri2602.03
IrN5 X:Iri2604.74
IrN4 X:Iri2602.03
IrN4 X:Iri2602.25
IrN6 X:Iri2654.83
IrO X:Hoh3244.46
IrO X:Hoh3903.92
IrO X:Hoh4083.97
IrO X:Hoh4094.72
IrO X:Hoh5053.50

interactive model:


Iridium binding site 13 out of 18 in 3dio


Iridium binding site 13 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 13 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Iridium in the PDB 3dio. 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: X: C139, X: U140, X: C157, X: Iri260, X: Hoh390,

conact list:


AtomAtomDistance (A)
IrOP1 X:C1393.96
IrOP1 X:U1404.81
IrOP2 X:U1404.98
IrOP1 X:C1574.35
IrN1 X:Iri2604.67
IrN1 X:Iri2602.03
IrN6 X:Iri2602.87
IrN6 X:Iri2602.03
IrN3 X:Iri2604.09
IrN3 X:Iri2602.02
IrN2 X:Iri2602.85
IrN2 X:Iri2602.02
IrIR X:Iri2603.89
IrIR X:Iri2600.00
IrN5 X:Iri2602.03
IrN4 X:Iri2602.02
IrO X:Hoh3903.32

interactive model:


Iridium binding site 14 out of 18 in 3dio


Iridium binding site 14 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 14 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Iridium in the PDB 3dio. 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: X: A26, X: G27, X: Iri261, X: Hoh344,

conact list:


AtomAtomDistance (A)
IrO3' X:A264.68
IrO2' X:A264.83
IrP X:G274.74
IrO4' X:G275.00
IrOP2 X:G274.30
IrO5' X:G274.16
IrN1 X:Iri2612.02
IrN6 X:Iri2612.02
IrN3 X:Iri2612.03
IrN2 X:Iri2612.02
IrIR X:Iri2610.00
IrN5 X:Iri2612.03
IrN4 X:Iri2612.02
IrO X:Hoh3443.41

interactive model:


Iridium binding site 15 out of 18 in 3dio


Iridium binding site 15 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 15 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Iridium in the PDB 3dio. 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: X: U40, X: U52, X: C53, X: Iri262,

conact list:


AtomAtomDistance (A)
IrC4 X:U404.82
IrO4 X:U403.79
IrO2' X:U523.61
IrOP2 X:C534.20
IrN1 X:Iri2622.02
IrN6 X:Iri2622.03
IrN3 X:Iri2622.02
IrN2 X:Iri2622.02
IrIR X:Iri2620.00
IrN5 X:Iri2622.02
IrN4 X:Iri2622.03

interactive model:


Iridium binding site 16 out of 18 in 3dio


Iridium binding site 16 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 16 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Iridium in the PDB 3dio. 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: X: A91, X: G92, X: C98, X: Iri263, X: Hoh438,

conact list:


AtomAtomDistance (A)
IrOP1 X:A914.71
IrP X:A914.97
IrOP2 X:A914.45
IrOP2 X:G923.99
IrOP1 X:C984.86
IrOP2 X:C984.54
IrN1 X:Iri2632.03
IrN6 X:Iri2632.02
IrN3 X:Iri2632.02
IrN2 X:Iri2632.03
IrIR X:Iri2630.00
IrN5 X:Iri2632.03
IrN4 X:Iri2632.02
IrO X:Hoh4384.81

interactive model:


Iridium binding site 17 out of 18 in 3dio


Iridium binding site 17 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 17 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Iridium in the PDB 3dio. 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: X: G8, X: G9, X: G80, X: Na204, X: Iri264, X: Hoh301, X: Hoh397, X: Hoh398,

conact list:


AtomAtomDistance (A)
IrN7 X:G84.97
IrO6 X:G84.54
IrC6 X:G94.86
IrN7 X:G94.42
IrO6 X:G93.97
IrOP1 X:G804.65
IrNA X:Na2045.00
IrN1 X:Iri2642.02
IrN6 X:Iri2642.03
IrN3 X:Iri2642.02
IrN2 X:Iri2642.02
IrIR X:Iri2640.00
IrN5 X:Iri2642.02
IrN4 X:Iri2642.03
IrO X:Hoh3013.76
IrO X:Hoh3974.06
IrO X:Hoh3983.71

interactive model:


Iridium binding site 18 out of 18 in 3dio


Iridium binding site 18 out of 18 in 3dio
Click to enlarge
stereopicture of Iridium binding site 18 out of 18 in 3dio
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 18 of Iridium in the PDB 3dio. 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: X: U140, X: G141, X: U142, X: U159, X: G160, X: Iri265, X: Hoh325, X: Hoh547, X: Hoh548,

conact list:


AtomAtomDistance (A)
IrO4 X:U1404.50
IrO6 X:G1414.66
IrO4 X:U1423.85
IrO4 X:U1594.56
IrC6 X:G1604.47
IrC5 X:G1604.75
IrN7 X:G1604.27
IrO6 X:G1603.57
IrN1 X:Iri2652.03
IrN6 X:Iri2652.02
IrN3 X:Iri2652.02
IrN2 X:Iri2652.02
IrIR X:Iri2650.00
IrN5 X:Iri2652.02
IrN4 X:Iri2652.02
IrO X:Hoh3254.81
IrO X:Hoh5474.11
IrO X:Hoh5484.55

interactive model:




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