Atomistry » Iridium » PDB 7onq-9did » 7uor
Atomistry »
  Iridium »
    PDB 7onq-9did »
      7uor »

Iridium in PDB 7uor: Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.

Protein crystallography data

The structure of Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin., PDB code: 7uor was solved by J.H.Pereira, B.J.Bloomer, J.F.Hartwig, P.D.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.15 / 3.16
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 190.213, 190.213, 266.773, 90, 90, 90
R / Rfree (%) 18.1 / 22.9

Other elements in 7uor:

The structure of Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Iridium Binding Sites:

The binding sites of Iridium atom in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. (pdb code 7uor). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 6 binding sites of Iridium where determined in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin., PDB code: 7uor:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6;

Iridium binding site 1 out of 6 in 7uor

Go back to Iridium Binding Sites List in 7uor
Iridium binding site 1 out of 6 in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir401

b:59.6
occ:1.00
IR A:HIR401 0.0 59.6 1.0
NB A:HIR401 2.0 55.8 1.0
NC A:HIR401 2.1 66.8 1.0
ND A:HIR401 2.1 58.1 1.0
NA A:HIR401 2.1 65.6 1.0
CH3 A:HIR401 2.2 40.0 1.0
C4B A:HIR401 3.0 56.9 1.0
C1B A:HIR401 3.0 60.1 1.0
C1C A:HIR401 3.1 62.3 1.0
C1D A:HIR401 3.1 57.2 1.0
C4C A:HIR401 3.1 57.0 1.0
C4D A:HIR401 3.1 59.5 1.0
C4A A:HIR401 3.1 55.9 1.0
C1A A:HIR401 3.1 63.8 1.0
OH A:HIR401 3.2 33.1 1.0
CHC A:HIR401 3.4 56.0 1.0
CHB A:HIR401 3.4 57.5 1.0
CHD A:HIR401 3.4 57.2 1.0
CHA A:HIR401 3.5 59.4 1.0
C3B A:HIR401 4.2 56.4 1.0
C2B A:HIR401 4.2 57.1 1.0
C3C A:HIR401 4.3 60.8 1.0
C2C A:HIR401 4.3 59.8 1.0
C2D A:HIR401 4.3 66.6 1.0
C3D A:HIR401 4.3 59.5 1.0
CA A:GLY317 4.3 65.5 1.0
C3A A:HIR401 4.3 55.1 1.0
C2A A:HIR401 4.4 54.9 1.0
N A:GLY319 4.8 70.5 1.0
CD1 A:PHE310 5.0 46.9 1.0
C A:GLY317 5.0 65.9 1.0

Iridium binding site 2 out of 6 in 7uor

Go back to Iridium Binding Sites List in 7uor
Iridium binding site 2 out of 6 in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ir401

b:62.8
occ:1.00
IR B:HIR401 0.0 62.8 1.0
NB B:HIR401 2.0 50.7 1.0
ND B:HIR401 2.0 52.4 1.0
NC B:HIR401 2.0 61.0 1.0
NA B:HIR401 2.1 55.8 1.0
CH3 B:HIR401 2.1 45.8 1.0
C4B B:HIR401 3.0 51.1 1.0
C4D B:HIR401 3.0 52.1 1.0
C1C B:HIR401 3.0 52.7 1.0
C1D B:HIR401 3.0 54.0 1.0
C4C B:HIR401 3.1 64.2 1.0
C1B B:HIR401 3.1 50.4 1.0
OH B:HIR401 3.1 42.8 1.0
C1A B:HIR401 3.1 50.7 1.0
C4A B:HIR401 3.2 51.4 1.0
CHC B:HIR401 3.3 53.6 1.0
CHA B:HIR401 3.4 50.0 1.0
CHD B:HIR401 3.5 52.5 1.0
CHB B:HIR401 3.5 52.4 1.0
C3B B:HIR401 4.2 50.1 1.0
CA B:GLY317 4.2 61.1 1.0
C3D B:HIR401 4.3 63.1 1.0
C2D B:HIR401 4.3 68.9 1.0
C2C B:HIR401 4.3 51.2 1.0
C3C B:HIR401 4.3 53.1 1.0
C2B B:HIR401 4.3 52.1 1.0
C3A B:HIR401 4.4 49.2 1.0
C2A B:HIR401 4.4 51.7 1.0
N B:GLY319 4.8 62.4 1.0
C B:GLY317 4.9 66.2 1.0
CD1 B:PHE310 4.9 63.7 1.0
N B:LEU318 4.9 64.9 1.0

Iridium binding site 3 out of 6 in 7uor

Go back to Iridium Binding Sites List in 7uor
Iridium binding site 3 out of 6 in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ir401

b:67.5
occ:1.00
IR C:HIR401 0.0 67.5 1.0
NB C:HIR401 2.0 66.0 1.0
ND C:HIR401 2.1 69.1 1.0
NC C:HIR401 2.1 71.4 1.0
NA C:HIR401 2.1 65.8 1.0
CH3 C:HIR401 2.1 23.4 1.0
C4B C:HIR401 3.0 67.3 1.0
C1D C:HIR401 3.1 72.7 1.0
C1C C:HIR401 3.1 68.2 1.0
C4C C:HIR401 3.1 72.5 1.0
C1A C:HIR401 3.1 64.9 1.0
C4D C:HIR401 3.1 62.2 1.0
C1B C:HIR401 3.1 56.2 1.0
OH C:HIR401 3.1 25.8 1.0
C4A C:HIR401 3.1 61.0 1.0
CHC C:HIR401 3.4 64.9 1.0
CHD C:HIR401 3.4 68.6 1.0
CHA C:HIR401 3.4 65.0 1.0
CHB C:HIR401 3.5 55.1 1.0
C3B C:HIR401 4.2 62.1 1.0
CA C:GLY317 4.2 70.9 1.0
C2D C:HIR401 4.3 75.2 1.0
C3C C:HIR401 4.3 65.8 1.0
C2B C:HIR401 4.3 56.0 1.0
C3D C:HIR401 4.3 67.8 1.0
C2A C:HIR401 4.3 53.6 1.0
C2C C:HIR401 4.3 65.2 1.0
C3A C:HIR401 4.3 57.4 1.0
N C:GLY319 4.8 73.2 1.0
CD1 C:PHE310 4.9 63.5 1.0
C C:GLY317 4.9 70.0 1.0
N C:LEU318 5.0 78.3 1.0

Iridium binding site 4 out of 6 in 7uor

Go back to Iridium Binding Sites List in 7uor
Iridium binding site 4 out of 6 in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ir401

b:68.9
occ:1.00
IR D:HIR401 0.0 68.9 1.0
ND D:HIR401 2.0 64.1 1.0
NB D:HIR401 2.0 59.0 1.0
NA D:HIR401 2.1 62.0 1.0
NC D:HIR401 2.1 75.0 1.0
CH3 D:HIR401 2.1 25.5 1.0
C4B D:HIR401 3.0 54.5 1.0
C4D D:HIR401 3.0 64.1 1.0
C1D D:HIR401 3.0 63.4 1.0
C1B D:HIR401 3.1 64.7 1.0
C1A D:HIR401 3.1 62.9 1.0
OH D:HIR401 3.1 25.8 1.0
C1C D:HIR401 3.1 65.6 1.0
C4A D:HIR401 3.1 53.6 1.0
C4C D:HIR401 3.1 64.2 1.0
CHA D:HIR401 3.4 58.4 1.0
CHC D:HIR401 3.4 56.2 1.0
CHD D:HIR401 3.5 56.0 1.0
CHB D:HIR401 3.5 54.1 1.0
C3B D:HIR401 4.2 54.9 1.0
C3D D:HIR401 4.2 63.8 1.0
C2D D:HIR401 4.2 66.6 1.0
C2B D:HIR401 4.3 55.9 1.0
C2A D:HIR401 4.3 60.7 1.0
C3A D:HIR401 4.3 54.5 1.0
CA D:GLY317 4.3 81.3 1.0
C3C D:HIR401 4.3 55.7 1.0
C2C D:HIR401 4.3 58.0 1.0
N D:GLY319 4.8 86.8 1.0
CD1 D:PHE310 4.9 51.4 1.0
C D:GLY317 5.0 89.9 1.0

Iridium binding site 5 out of 6 in 7uor

Go back to Iridium Binding Sites List in 7uor
Iridium binding site 5 out of 6 in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ir401

b:81.2
occ:1.00
IR E:HIR401 0.0 81.2 1.0
ND E:HIR401 1.9 71.4 1.0
NA E:HIR401 2.0 58.8 1.0
NB E:HIR401 2.0 61.2 1.0
NC E:HIR401 2.1 82.5 1.0
CH3 E:HIR401 2.1 42.1 1.0
C4D E:HIR401 2.9 77.3 1.0
C1A E:HIR401 3.0 77.4 1.0
C4B E:HIR401 3.0 69.5 1.0
C1D E:HIR401 3.0 88.0 1.0
C4A E:HIR401 3.0 81.1 1.0
C1B E:HIR401 3.1 76.2 1.0
C1C E:HIR401 3.1 89.5 1.0
OH E:HIR401 3.1 42.0 1.0
C4C E:HIR401 3.1 83.3 1.0
CHA E:HIR401 3.3 78.7 1.0
CHC E:HIR401 3.4 76.3 1.0
CHB E:HIR401 3.5 76.0 1.0
CHD E:HIR401 3.5 73.7 1.0
C3D E:HIR401 4.2 63.7 1.0
C2A E:HIR401 4.2 58.2 1.0
C2D E:HIR401 4.2 68.2 1.0
C3A E:HIR401 4.2 56.7 1.0
C3B E:HIR401 4.2 60.9 1.0
C2B E:HIR401 4.3 56.6 1.0
CA E:GLY317 4.3 68.3 1.0
C2C E:HIR401 4.3 64.4 1.0
C3C E:HIR401 4.3 64.8 1.0
N E:GLY319 4.9 75.0 1.0
CD1 E:PHE310 4.9 57.0 1.0

Iridium binding site 6 out of 6 in 7uor

Go back to Iridium Binding Sites List in 7uor
Iridium binding site 6 out of 6 in the Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin.


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Crystal Structure of Cytochrome P450 Enzyme CYP119 in Complex with Methyliridium(III) Mesoporphyrin. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ir401

b:79.8
occ:1.00
IR F:HIR401 0.0 79.8 1.0
ND F:HIR401 2.0 62.2 1.0
NB F:HIR401 2.0 60.2 1.0
NC F:HIR401 2.1 79.7 1.0
NA F:HIR401 2.1 59.0 1.0
CH3 F:HIR401 2.1 79.5 1.0
C4B F:HIR401 3.0 60.6 1.0
C4D F:HIR401 3.0 60.2 1.0
C1D F:HIR401 3.0 72.2 1.0
C1C F:HIR401 3.0 78.7 1.0
C1B F:HIR401 3.1 68.2 1.0
OH F:HIR401 3.1 73.5 1.0
C1A F:HIR401 3.1 55.9 1.0
C4A F:HIR401 3.1 69.4 1.0
C4C F:HIR401 3.1 72.8 1.0
CHC F:HIR401 3.4 62.7 1.0
CHA F:HIR401 3.4 66.3 1.0
CHD F:HIR401 3.4 63.0 1.0
CHB F:HIR401 3.5 66.5 1.0
CA F:GLY317 4.2 72.4 1.0
C3B F:HIR401 4.2 71.1 1.0
C2D F:HIR401 4.2 81.4 1.0
C3D F:HIR401 4.2 66.5 1.0
C2B F:HIR401 4.3 62.9 1.0
C2C F:HIR401 4.3 76.0 1.0
C3C F:HIR401 4.3 73.9 1.0
C3A F:HIR401 4.3 60.7 1.0
C2A F:HIR401 4.3 54.5 1.0
C F:GLY317 4.8 91.8 1.0
N F:GLY319 4.8 88.3 1.0
N F:LEU318 4.9 98.1 1.0
CD1 F:PHE310 5.0 65.9 1.0

Reference:

B.J.Bloomer, S.N.Natoli, M.Garcia-Borras, J.H.Pereira, D.B.Hu, P.D.Adams, K.N.Houk, D.S.Clark, J.F.Hartwig. Mechanistic and Structural Characterization of An Iridium-Containing Cytochrome Reveals Kinetically Relevant Cofactor Dynamics Nat Catal V. 6 39 2023.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-022-00899-9
Page generated: Sat Aug 9 01:22:35 2025

Last articles

Mg in 1B70
Mg in 1B25
Mg in 1B4S
Mg in 1B63
Mg in 1B62
Mg in 1B4K
Mg in 1B23
Mg in 1B39
Mg in 1B38
Mg in 1B0P
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy