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Ruthenium in PDB 1k2o: Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II)

Enzymatic activity of Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II)

All present enzymatic activity of Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II):
1.14.15.1;

Protein crystallography data

The structure of Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II), PDB code: 1k2o was solved by A.R.Dunn, I.J.Dmochowski, A.M.Bilwes, H.B.Gray, B.R.Crane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 1.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.870, 67.050, 72.520, 71.16, 65.20, 62.31
R / Rfree (%) 21 / 22.6

Other elements in 1k2o:

The structure of Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II) also contains other interesting chemical elements:

Fluorine (F) 32 atoms
Arsenic (As) 5 atoms
Iron (Fe) 2 atoms

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II) (pdb code 1k2o). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 4 binding sites of Ruthenium where determined in the Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II), PDB code: 1k2o:
Jump to Ruthenium binding site number: 1; 2; 3; 4;

Ruthenium binding site 1 out of 4 in 1k2o

Go back to Ruthenium Binding Sites List in 1k2o
Ruthenium binding site 1 out of 4 in the Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru900

b:29.6
occ:0.41
 RU A:RFA900 0.0 29.6 0.4
RU A:RFB901 0.1 28.5 0.5
N26 A:RFB901 1.9 28.8 0.5
N2 A:RFB901 2.0 28.7 0.5
N14 A:RFA900 2.0 29.6 0.4
N37 A:RFA900 2.0 29.9 0.4
N13 A:RFA900 2.0 29.9 0.4
N2 A:RFA900 2.0 29.9 0.4
N25 A:RFA900 2.0 29.3 0.4
N26 A:RFA900 2.1 29.8 0.4
N13 A:RFB901 2.1 28.6 0.5
N37 A:RFB901 2.1 28.9 0.5
N14 A:RFB901 2.1 28.5 0.5
N25 A:RFB901 2.2 28.2 0.5
C31 A:RFB901 2.8 28.9 0.5
C32 A:RFB901 2.8 28.9 0.5
C7 A:RFB901 2.8 28.7 0.5
C19 A:RFA900 2.8 29.3 0.4
C20 A:RFA900 2.9 28.9 0.4
C8 A:RFB901 2.9 28.7 0.5
C32 A:RFA900 2.9 29.9 0.4
C8 A:RFA900 2.9 30.1 0.4
C27 A:RFB901 2.9 29.0 0.5
C7 A:RFA900 2.9 30.1 0.4
C31 A:RFA900 2.9 29.9 0.4
C19 A:RFB901 2.9 28.3 0.5
C15 A:RFA900 3.0 29.6 0.4
C3 A:RFB901 3.0 28.9 0.5
C20 A:RFB901 3.0 27.9 0.5
C36 A:RFA900 3.0 29.9 0.4
C12 A:RFA900 3.0 30.1 0.4
C3 A:RFA900 3.0 30.2 0.4
C24 A:RFA900 3.1 28.6 0.4
C15 A:RFB901 3.1 28.5 0.5
C27 A:RFA900 3.1 29.9 0.4
C12 A:RFB901 3.1 28.7 0.5
C36 A:RFB901 3.1 29.0 0.5
C24 A:RFB901 3.1 27.7 0.5
C30 A:RFB901 4.1 29.0 0.5
C6 A:RFB901 4.2 28.8 0.5
C28 A:RFB901 4.2 29.2 0.5
C18 A:RFA900 4.2 29.5 0.4
C33 A:RFB901 4.2 29.0 0.5
C21 A:RFA900 4.2 28.1 0.4
C6 A:RFA900 4.2 30.1 0.4
C9 A:RFA900 4.2 30.2 0.4
C33 A:RFA900 4.2 30.0 0.4
C9 A:RFB901 4.2 28.7 0.5
C30 A:RFA900 4.2 29.9 0.4
C18 A:RFB901 4.3 28.5 0.5
C16 A:RFA900 4.3 29.6 0.4
C4 A:RFB901 4.3 29.0 0.5
C11 A:RFA900 4.3 30.1 0.4
C35 A:RFA900 4.3 30.1 0.4
C4 A:RFA900 4.3 30.2 0.4
C21 A:RFB901 4.3 27.2 0.5
C23 A:RFA900 4.3 27.8 0.4
C28 A:RFA900 4.4 29.9 0.4
C11 A:RFB901 4.4 28.8 0.5
C35 A:RFB901 4.4 29.1 0.5
C16 A:RFB901 4.4 28.6 0.5
C23 A:RFB901 4.4 27.0 0.5
C29 A:RFB901 4.6 29.1 0.5
C5 A:RFB901 4.7 28.9 0.5
C17 A:RFA900 4.7 29.6 0.4
C5 A:RFA900 4.8 30.1 0.4
C10 A:RFA900 4.8 30.2 0.4
C34 A:RFA900 4.8 30.0 0.4
C34 A:RFB901 4.8 29.0 0.5
C29 A:RFA900 4.8 30.0 0.4
C22 A:RFA900 4.8 27.2 0.4
C10 A:RFB901 4.8 28.8 0.5
C17 A:RFB901 4.9 28.5 0.5
C22 A:RFB901 4.9 26.5 0.5

Ruthenium binding site 2 out of 4 in 1k2o

Go back to Ruthenium Binding Sites List in 1k2o
Ruthenium binding site 2 out of 4 in the Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru901

b:28.5
occ:0.53
 RU A:RFB901 0.0 28.5 0.5
RU A:RFA900 0.1 29.6 0.4
N25 A:RFA900 1.9 29.3 0.4
N37 A:RFA900 2.0 29.9 0.4
N14 A:RFA900 2.0 29.6 0.4
N26 A:RFB901 2.0 28.8 0.5
N37 A:RFB901 2.0 28.9 0.5
N25 A:RFB901 2.0 28.2 0.5
N2 A:RFB901 2.0 28.7 0.5
N14 A:RFB901 2.0 28.5 0.5
N13 A:RFB901 2.1 28.6 0.5
N26 A:RFA900 2.1 29.8 0.4
N2 A:RFA900 2.1 29.9 0.4
N13 A:RFA900 2.2 29.9 0.4
C20 A:RFA900 2.8 28.9 0.4
C19 A:RFA900 2.8 29.3 0.4
C32 A:RFA900 2.8 29.9 0.4
C32 A:RFB901 2.8 28.9 0.5
C31 A:RFB901 2.8 28.9 0.5
C19 A:RFB901 2.9 28.3 0.5
C31 A:RFA900 2.9 29.9 0.4
C20 A:RFB901 2.9 27.9 0.5
C7 A:RFB901 2.9 28.7 0.5
C8 A:RFB901 2.9 28.7 0.5
C24 A:RFA900 3.0 28.6 0.4
C36 A:RFA900 3.0 29.9 0.4
C7 A:RFA900 3.0 30.1 0.4
C8 A:RFA900 3.0 30.1 0.4
C27 A:RFB901 3.0 29.0 0.5
C15 A:RFA900 3.0 29.6 0.4
C24 A:RFB901 3.0 27.7 0.5
C3 A:RFB901 3.0 28.9 0.5
C36 A:RFB901 3.0 29.0 0.5
C3 A:RFA900 3.1 30.2 0.4
C15 A:RFB901 3.1 28.5 0.5
C12 A:RFB901 3.1 28.7 0.5
C27 A:RFA900 3.1 29.9 0.4
C12 A:RFA900 3.1 30.1 0.4
C21 A:RFA900 4.1 28.1 0.4
C18 A:RFA900 4.1 29.5 0.4
C33 A:RFA900 4.2 30.0 0.4
C30 A:RFB901 4.2 29.0 0.5
C33 A:RFB901 4.2 29.0 0.5
C18 A:RFB901 4.2 28.5 0.5
C6 A:RFB901 4.2 28.8 0.5
C21 A:RFB901 4.2 27.2 0.5
C23 A:RFA900 4.2 27.8 0.4
C30 A:RFA900 4.2 29.9 0.4
C35 A:RFA900 4.3 30.1 0.4
C9 A:RFB901 4.3 28.7 0.5
C16 A:RFA900 4.3 29.6 0.4
C28 A:RFB901 4.3 29.2 0.5
C23 A:RFB901 4.3 27.0 0.5
C6 A:RFA900 4.3 30.1 0.4
C35 A:RFB901 4.3 29.1 0.5
C4 A:RFB901 4.3 29.0 0.5
C9 A:RFA900 4.3 30.2 0.4
C4 A:RFA900 4.4 30.2 0.4
C11 A:RFB901 4.4 28.8 0.5
C28 A:RFA900 4.4 29.9 0.4
C16 A:RFB901 4.4 28.6 0.5
C11 A:RFA900 4.4 30.1 0.4
C22 A:RFA900 4.7 27.2 0.4
C17 A:RFA900 4.7 29.6 0.4
C34 A:RFA900 4.7 30.0 0.4
C29 A:RFB901 4.8 29.1 0.5
C34 A:RFB901 4.8 29.0 0.5
C5 A:RFB901 4.8 28.9 0.5
C22 A:RFB901 4.8 26.5 0.5
C29 A:RFA900 4.8 30.0 0.4
C10 A:RFB901 4.8 28.8 0.5
C5 A:RFA900 4.9 30.1 0.4
C17 A:RFB901 4.9 28.5 0.5
C10 A:RFA900 4.9 30.2 0.4

Ruthenium binding site 3 out of 4 in 1k2o

Go back to Ruthenium Binding Sites List in 1k2o
Ruthenium binding site 3 out of 4 in the Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru902

b:27.9
occ:0.54
 RU B:RFA902 0.0 27.9 0.5
RU B:RFB903 0.2 27.9 0.4
N13 B:RFB903 1.9 28.2 0.4
N37 B:RFB903 1.9 28.3 0.4
N25 B:RFB903 2.0 28.0 0.4
N14 B:RFA902 2.0 28.3 0.5
N37 B:RFA902 2.0 28.6 0.5
N13 B:RFA902 2.0 28.8 0.5
N26 B:RFA902 2.0 28.5 0.5
N2 B:RFA902 2.0 28.8 0.5
N25 B:RFA902 2.1 28.0 0.5
N26 B:RFB903 2.1 28.3 0.4
N2 B:RFB903 2.2 28.3 0.4
N14 B:RFB903 2.2 28.1 0.4
C32 B:RFB903 2.8 28.3 0.4
C8 B:RFB903 2.8 28.2 0.4
C32 B:RFA902 2.9 28.7 0.5
C19 B:RFA902 2.9 28.1 0.5
C31 B:RFA902 2.9 28.6 0.5
C8 B:RFA902 2.9 29.0 0.5
C12 B:RFB903 2.9 28.1 0.4
C7 B:RFA902 2.9 29.0 0.5
C20 B:RFA902 2.9 27.7 0.5
C24 B:RFB903 2.9 27.7 0.4
C31 B:RFB903 2.9 28.4 0.4
C20 B:RFB903 2.9 27.9 0.4
C36 B:RFB903 2.9 28.3 0.4
C7 B:RFB903 2.9 28.2 0.4
C19 B:RFB903 3.0 28.1 0.4
C15 B:RFA902 3.0 28.3 0.5
C12 B:RFA902 3.0 28.9 0.5
C27 B:RFA902 3.0 28.6 0.5
C3 B:RFA902 3.0 29.0 0.5
C36 B:RFA902 3.0 28.7 0.5
C24 B:RFA902 3.1 27.5 0.5
C27 B:RFB903 3.1 28.5 0.4
C3 B:RFB903 3.2 28.3 0.4
C15 B:RFB903 3.3 28.2 0.4
C33 B:RFB903 4.1 28.4 0.4
C9 B:RFB903 4.2 28.2 0.4
C11 B:RFB903 4.2 28.1 0.4
C23 B:RFB903 4.2 27.5 0.4
C21 B:RFB903 4.2 27.6 0.4
C18 B:RFA902 4.2 28.2 0.5
C35 B:RFB903 4.2 28.5 0.4
C30 B:RFA902 4.2 28.7 0.5
C6 B:RFA902 4.2 29.2 0.5
C33 B:RFA902 4.2 28.8 0.5
C9 B:RFA902 4.2 29.1 0.5
C21 B:RFA902 4.2 27.1 0.5
C30 B:RFB903 4.2 28.6 0.4
C6 B:RFB903 4.3 28.3 0.4
C16 B:RFA902 4.3 28.4 0.5
C11 B:RFA902 4.3 29.2 0.5
C35 B:RFA902 4.3 28.8 0.5
C4 B:RFA902 4.3 29.3 0.5
C28 B:RFA902 4.3 28.7 0.5
C18 B:RFB903 4.3 28.2 0.4
C23 B:RFA902 4.4 26.9 0.5
C28 B:RFB903 4.4 28.6 0.4
C4 B:RFB903 4.5 28.5 0.4
C16 B:RFB903 4.6 28.3 0.4
C10 B:RFB903 4.7 28.1 0.4
C34 B:RFB903 4.7 28.4 0.4
C22 B:RFB903 4.7 27.3 0.4
C29 B:RFA902 4.8 28.6 0.5
C17 B:RFA902 4.8 28.4 0.5
C5 B:RFA902 4.8 29.3 0.5
C10 B:RFA902 4.8 29.2 0.5
C34 B:RFA902 4.8 28.9 0.5
C22 B:RFA902 4.8 26.5 0.5
C29 B:RFB903 4.8 28.6 0.4
C5 B:RFB903 4.9 28.4 0.4
O B:HOH1650 5.0 36.9 1.0

Ruthenium binding site 4 out of 4 in 1k2o

Go back to Ruthenium Binding Sites List in 1k2o
Ruthenium binding site 4 out of 4 in the Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of Cytochrome P450CAM with Bound Bis(2,2'-Bipyridine)-(5-Methyl-2-2'- Bipyridine)-C2-Adamantane Ruthenium (II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru903

b:27.9
occ:0.40
 RU B:RFB903 0.0 27.9 0.4
RU B:RFA902 0.2 27.9 0.5
N2 B:RFA902 1.9 28.8 0.5
N14 B:RFA902 1.9 28.3 0.5
N13 B:RFA902 2.0 28.8 0.5
N26 B:RFB903 2.0 28.3 0.4
N2 B:RFB903 2.0 28.3 0.4
N37 B:RFB903 2.0 28.3 0.4
N25 B:RFB903 2.0 28.0 0.4
N13 B:RFB903 2.0 28.2 0.4
N14 B:RFB903 2.1 28.1 0.4
N25 B:RFA902 2.1 28.0 0.5
N26 B:RFA902 2.2 28.5 0.5
N37 B:RFA902 2.2 28.6 0.5
C7 B:RFA902 2.7 29.0 0.5
C8 B:RFA902 2.7 29.0 0.5
C19 B:RFA902 2.8 28.1 0.5
C31 B:RFB903 2.9 28.4 0.4
C32 B:RFB903 2.9 28.3 0.4
C15 B:RFA902 2.9 28.3 0.5
C7 B:RFB903 2.9 28.2 0.4
C8 B:RFB903 2.9 28.2 0.4
C3 B:RFA902 2.9 29.0 0.5
C20 B:RFA902 2.9 27.7 0.5
C19 B:RFB903 2.9 28.1 0.4
C20 B:RFB903 2.9 27.9 0.4
C27 B:RFB903 3.0 28.5 0.4
C12 B:RFA902 3.0 28.9 0.5
C3 B:RFB903 3.0 28.3 0.4
C24 B:RFB903 3.0 27.7 0.4
C12 B:RFB903 3.1 28.1 0.4
C36 B:RFB903 3.1 28.3 0.4
C31 B:RFA902 3.1 28.6 0.5
C32 B:RFA902 3.1 28.7 0.5
C15 B:RFB903 3.1 28.2 0.4
C27 B:RFA902 3.1 28.6 0.5
C36 B:RFA902 3.2 28.7 0.5
C24 B:RFA902 3.2 27.5 0.5
C6 B:RFA902 4.0 29.2 0.5
C9 B:RFA902 4.1 29.1 0.5
C18 B:RFA902 4.1 28.2 0.5
C16 B:RFA902 4.2 28.4 0.5
C4 B:RFA902 4.2 29.3 0.5
C30 B:RFB903 4.2 28.6 0.4
C6 B:RFB903 4.2 28.3 0.4
C33 B:RFB903 4.2 28.4 0.4
C9 B:RFB903 4.2 28.2 0.4
C18 B:RFB903 4.2 28.2 0.4
C21 B:RFB903 4.2 27.6 0.4
C21 B:RFA902 4.3 27.1 0.5
C11 B:RFA902 4.3 29.2 0.5
C28 B:RFB903 4.3 28.6 0.4
C23 B:RFB903 4.3 27.5 0.4
C4 B:RFB903 4.3 28.5 0.4
C11 B:RFB903 4.3 28.1 0.4
C35 B:RFB903 4.3 28.5 0.4
C30 B:RFA902 4.4 28.7 0.5
C33 B:RFA902 4.4 28.8 0.5
C28 B:RFA902 4.4 28.7 0.5
C16 B:RFB903 4.4 28.3 0.4
C35 B:RFA902 4.5 28.8 0.5
C23 B:RFA902 4.5 26.9 0.5
C5 B:RFA902 4.6 29.3 0.5
C17 B:RFA902 4.7 28.4 0.5
C10 B:RFA902 4.7 29.2 0.5
C29 B:RFB903 4.7 28.6 0.4
C5 B:RFB903 4.8 28.4 0.4
C34 B:RFB903 4.8 28.4 0.4
C10 B:RFB903 4.8 28.1 0.4
C22 B:RFB903 4.8 27.3 0.4
C22 B:RFA902 4.9 26.5 0.5
C17 B:RFB903 4.9 28.3 0.4
C29 B:RFA902 4.9 28.6 0.5
C34 B:RFA902 5.0 28.9 0.5

Reference:

A.R.Dunn, I.J.Dmochowski, A.M.Bilwes, H.B.Gray, B.R.Crane. Probing the Open State of Cytochrome P450CAM with Ruthenium-Linker Substrates. Proc.Natl.Acad.Sci.Usa V. 98 12420 2001.
ISSN: ISSN 0027-8424
PubMed: 11606730
DOI: 10.1073/PNAS.221297998
Page generated: Thu Oct 10 12:43:03 2024

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