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Ruthenium in PDB 2bt6: Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin

Protein crystallography data

The structure of Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin, PDB code: 2bt6 was solved by A.Halavaty, J.J.Mueller, J.Contzen, C.Jung, F.Hannemann, R.Bernhardt, M.Galander, F.Lendzian, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.510, 56.970, 79.080, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.6

Other elements in 2bt6:

The structure of Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 4 atoms

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin (pdb code 2bt6). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 4 binding sites of Ruthenium where determined in the Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin, PDB code: 2bt6:
Jump to Ruthenium binding site number: 1; 2; 3; 4;

Ruthenium binding site 1 out of 4 in 2bt6

Go back to Ruthenium Binding Sites List in 2bt6
Ruthenium binding site 1 out of 4 in the Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1110

b:17.9
occ:0.40
RU A:RUA1110 0.0 17.9 0.4
N14 A:RUA1110 1.3 6.8 0.4
N37 A:RUA1110 1.4 4.8 0.4
C36 A:RUA1110 1.5 25.7 0.4
RU A:RUA1110 1.7 27.2 0.4
N14 A:RUA1110 1.9 24.5 0.4
N2 A:RUA1110 1.9 20.0 0.4
N37 A:RUA1110 1.9 21.7 0.4
N26 A:RUA1110 1.9 21.7 0.4
N13 A:RUA1110 1.9 20.2 0.4
N25 A:RUA1110 1.9 19.8 0.4
C19 A:RUA1110 2.0 26.4 0.4
N25 A:RUA1110 2.2 21.4 0.4
C15 A:RUA1110 2.2 25.9 0.4
C20 A:RUA1110 2.4 23.4 0.4
N13 A:RUA1110 2.7 19.1 0.4
C7 A:RUA1110 2.8 17.4 0.4
C32 A:RUA1110 2.8 24.2 0.4
C8 A:RUA1110 2.8 20.4 0.4
C19 A:RUA1110 2.8 19.3 0.4
C32 A:RUA1110 2.8 20.4 0.4
C31 A:RUA1110 2.8 18.2 0.4
C35 A:RUA1110 2.8 22.5 0.4
C15 A:RUA1110 2.8 19.7 0.4
C27 A:RUA1110 2.8 16.6 0.4
C20 A:RUA1110 2.8 18.5 0.4
C3 A:RUA1110 2.9 20.8 0.4
C36 A:RUA1110 2.9 19.6 0.4
C24 A:RUA1110 2.9 20.8 0.4
C12 A:RUA1110 2.9 16.7 0.4
C12 A:RUA1110 3.1 20.3 0.4
C18 A:RUA1110 3.1 26.1 0.4
C16 A:RUA1110 3.2 25.2 0.4
N26 A:RUA1110 3.3 16.2 0.4
N2 A:RUA1110 3.3 23.8 0.4
C24 A:RUA1110 3.3 25.5 0.4
C17 A:RUA1110 3.6 25.8 0.4
C31 A:RUA1110 3.6 19.4 0.4
C21 A:RUA1110 3.6 29.0 0.4
C33 A:RUA1110 3.7 24.1 0.4
C34 A:RUA1110 3.7 24.5 0.4
C8 A:RUA1110 3.8 24.6 0.4
C6 A:RUA1110 4.1 20.7 0.4
C7 A:RUA1110 4.1 24.0 0.4
C18 A:RUA1110 4.1 23.2 0.4
C21 A:RUA1110 4.1 18.3 0.4
C16 A:RUA1110 4.1 20.7 0.4
C4 A:RUA1110 4.1 23.5 0.4
C28 A:RUA1110 4.1 19.6 0.4
C9 A:RUA1110 4.1 22.6 0.4
C33 A:RUA1110 4.2 20.8 0.4
C30 A:RUA1110 4.2 21.2 0.4
C35 A:RUA1110 4.2 21.2 0.4
C3 A:RUA1110 4.2 24.7 0.4
C11 A:RUA1110 4.2 19.3 0.4
C23 A:RUA1110 4.2 17.2 0.4
C23 A:RUA1110 4.3 23.4 0.4
C11 A:RUA1110 4.4 23.1 0.4
C27 A:RUA1110 4.5 23.1 0.4
C22 A:RUA1110 4.5 25.5 0.4
C5 A:RUA1110 4.7 21.4 0.4
C17 A:RUA1110 4.7 21.5 0.4
C29 A:RUA1110 4.7 20.6 0.4
C34 A:RUA1110 4.7 21.0 0.4
C10 A:RUA1110 4.7 17.4 0.4
C22 A:RUA1110 4.7 20.2 0.4
C9 A:RUA1110 5.0 26.2 0.4
C30 A:RUA1110 5.0 22.3 0.4
O A:HOH2109 5.0 24.0 1.0

Ruthenium binding site 2 out of 4 in 2bt6

Go back to Ruthenium Binding Sites List in 2bt6
Ruthenium binding site 2 out of 4 in the Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru1110

b:27.2
occ:0.40
RU A:RUA1110 0.0 27.2 0.4
N14 A:RUA1110 1.1 24.5 0.4
RU A:RUA1110 1.7 17.9 0.4
C15 A:RUA1110 1.8 19.7 0.4
N37 A:RUA1110 1.8 4.8 0.4
N26 A:RUA1110 1.9 16.2 0.4
N2 A:RUA1110 1.9 23.8 0.4
N14 A:RUA1110 1.9 6.8 0.4
N13 A:RUA1110 1.9 19.1 0.4
N25 A:RUA1110 1.9 21.4 0.4
N2 A:RUA1110 1.9 20.0 0.4
C3 A:RUA1110 2.0 20.8 0.4
C19 A:RUA1110 2.1 19.3 0.4
N26 A:RUA1110 2.5 21.7 0.4
N25 A:RUA1110 2.6 19.8 0.4
C32 A:RUA1110 2.7 24.2 0.4
C15 A:RUA1110 2.8 25.9 0.4
C31 A:RUA1110 2.8 19.4 0.4
C20 A:RUA1110 2.8 18.5 0.4
C7 A:RUA1110 2.8 24.0 0.4
C8 A:RUA1110 2.8 24.6 0.4
C36 A:RUA1110 2.8 25.7 0.4
C3 A:RUA1110 2.8 24.7 0.4
C24 A:RUA1110 2.8 25.5 0.4
C27 A:RUA1110 2.9 23.1 0.4
C20 A:RUA1110 2.9 23.4 0.4
C19 A:RUA1110 2.9 26.4 0.4
C16 A:RUA1110 2.9 20.7 0.4
C12 A:RUA1110 2.9 20.3 0.4
C27 A:RUA1110 2.9 16.6 0.4
C18 A:RUA1110 3.1 23.2 0.4
N37 A:RUA1110 3.1 21.7 0.4
C7 A:RUA1110 3.3 17.4 0.4
C4 A:RUA1110 3.4 23.5 0.4
C17 A:RUA1110 3.4 21.5 0.4
N13 A:RUA1110 3.4 20.2 0.4
C31 A:RUA1110 3.6 18.2 0.4
C24 A:RUA1110 3.8 20.8 0.4
C32 A:RUA1110 3.9 20.4 0.4
C8 A:RUA1110 4.0 20.4 0.4
C36 A:RUA1110 4.0 19.6 0.4
C21 A:RUA1110 4.1 18.3 0.4
C33 A:RUA1110 4.1 24.1 0.4
C16 A:RUA1110 4.1 25.2 0.4
C30 A:RUA1110 4.1 22.3 0.4
C35 A:RUA1110 4.1 22.5 0.4
C6 A:RUA1110 4.1 24.2 0.4
C4 A:RUA1110 4.1 25.3 0.4
C9 A:RUA1110 4.1 26.2 0.4
C23 A:RUA1110 4.1 23.4 0.4
C28 A:RUA1110 4.1 24.1 0.4
C21 A:RUA1110 4.2 29.0 0.4
C18 A:RUA1110 4.2 26.1 0.4
C11 A:RUA1110 4.2 23.1 0.4
C28 A:RUA1110 4.2 19.6 0.4
C6 A:RUA1110 4.3 20.7 0.4
C5 A:RUA1110 4.3 21.4 0.4
C12 A:RUA1110 4.6 16.7 0.4
C34 A:RUA1110 4.6 24.5 0.4
C29 A:RUA1110 4.6 23.8 0.4
C5 A:RUA1110 4.7 27.2 0.4
C17 A:RUA1110 4.7 25.8 0.4
C22 A:RUA1110 4.7 25.5 0.4
C10 A:RUA1110 4.7 25.3 0.4
C30 A:RUA1110 4.7 21.2 0.4
C23 A:RUA1110 4.9 17.2 0.4
C38 A:RUA1110 4.9 22.6 0.4
C29 A:RUA1110 5.0 20.6 0.4
C22 A:RUA1110 5.0 20.2 0.4

Ruthenium binding site 3 out of 4 in 2bt6

Go back to Ruthenium Binding Sites List in 2bt6
Ruthenium binding site 3 out of 4 in the Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru1110

b:24.2
occ:0.60
RU B:RUA1110 0.0 24.2 0.6
N14 B:RUA1110 0.9 21.2 0.4
C15 B:RUA1110 1.6 21.2 0.4
C19 B:RUA1110 1.7 21.6 0.4
N14 B:RUA1110 1.9 24.8 0.6
N37 B:RUA1110 1.9 30.2 0.6
N26 B:RUA1110 1.9 29.6 0.6
N2 B:RUA1110 1.9 22.9 0.6
N25 B:RUA1110 1.9 25.4 0.6
N13 B:RUA1110 1.9 24.9 0.6
C3 B:RUA1110 1.9 20.2 0.4
RU B:RUA1110 2.0 20.6 0.4
N2 B:RUA1110 2.0 13.2 0.4
C20 B:RUA1110 2.6 24.2 0.4
C16 B:RUA1110 2.6 22.2 0.4
N25 B:RUA1110 2.7 19.7 0.4
C18 B:RUA1110 2.7 24.5 0.4
N26 B:RUA1110 2.7 12.1 0.4
C7 B:RUA1110 2.8 21.3 0.6
C19 B:RUA1110 2.8 24.5 0.6
C32 B:RUA1110 2.8 32.4 0.6
C31 B:RUA1110 2.8 28.3 0.6
C8 B:RUA1110 2.8 26.1 0.6
C20 B:RUA1110 2.8 27.3 0.6
C27 B:RUA1110 2.8 29.4 0.6
C3 B:RUA1110 2.9 27.1 0.6
C15 B:RUA1110 2.9 25.2 0.6
C36 B:RUA1110 2.9 31.0 0.6
C24 B:RUA1110 2.9 24.5 0.6
C12 B:RUA1110 2.9 24.9 0.6
C17 B:RUA1110 3.0 23.5 0.4
C27 B:RUA1110 3.1 19.9 0.4
C4 B:RUA1110 3.3 19.5 0.4
N37 B:RUA1110 3.4 16.4 0.4
C7 B:RUA1110 3.4 20.4 0.4
N13 B:RUA1110 3.7 7.3 0.4
C31 B:RUA1110 3.8 18.1 0.4
C21 B:RUA1110 3.8 23.1 0.4
C24 B:RUA1110 3.9 23.0 0.4
C32 B:RUA1110 4.1 19.9 0.4
C21 B:RUA1110 4.1 26.6 0.6
C30 B:RUA1110 4.1 30.1 0.6
C33 B:RUA1110 4.1 29.1 0.6
C18 B:RUA1110 4.1 26.6 0.6
C6 B:RUA1110 4.1 26.7 0.6
C28 B:RUA1110 4.1 29.4 0.6
C9 B:RUA1110 4.1 27.2 0.6
C4 B:RUA1110 4.2 23.9 0.6
C16 B:RUA1110 4.2 25.9 0.6
C35 B:RUA1110 4.2 30.7 0.6
C8 B:RUA1110 4.2 19.5 0.4
C11 B:RUA1110 4.2 23.2 0.6
C23 B:RUA1110 4.2 21.6 0.6
C36 B:RUA1110 4.3 18.9 0.4
C28 B:RUA1110 4.3 18.4 0.4
C5 B:RUA1110 4.3 19.3 0.4
C6 B:RUA1110 4.4 21.4 0.4
C38 B:RUA1110 4.5 23.1 0.4
C29 B:RUA1110 4.7 29.3 0.6
C34 B:RUA1110 4.7 29.6 0.6
C5 B:RUA1110 4.7 25.1 0.6
C17 B:RUA1110 4.7 24.3 0.6
C10 B:RUA1110 4.7 23.6 0.6
C22 B:RUA1110 4.7 25.8 0.6
C22 B:RUA1110 4.8 22.3 0.4
C23 B:RUA1110 4.9 23.6 0.4
C30 B:RUA1110 4.9 18.8 0.4
C12 B:RUA1110 4.9 10.3 0.4

Ruthenium binding site 4 out of 4 in 2bt6

Go back to Ruthenium Binding Sites List in 2bt6
Ruthenium binding site 4 out of 4 in the Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of Ru(Bpy)2(Mbpy)-Modified Bovine Adrenodoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru1110

b:20.6
occ:0.40
RU B:RUA1110 0.0 20.6 0.4
C3 B:RUA1110 1.5 27.1 0.6
N14 B:RUA1110 1.6 24.8 0.6
N2 B:RUA1110 1.8 22.9 0.6
N13 B:RUA1110 1.8 7.3 0.4
N14 B:RUA1110 1.9 21.2 0.4
N37 B:RUA1110 1.9 16.4 0.4
N25 B:RUA1110 1.9 19.7 0.4
N26 B:RUA1110 1.9 12.1 0.4
N2 B:RUA1110 1.9 13.2 0.4
RU B:RUA1110 2.0 24.2 0.6
C15 B:RUA1110 2.3 25.2 0.6
C19 B:RUA1110 2.4 24.5 0.6
N25 B:RUA1110 2.7 25.4 0.6
N26 B:RUA1110 2.7 29.6 0.6
C19 B:RUA1110 2.8 21.6 0.4
C20 B:RUA1110 2.8 24.2 0.4
C8 B:RUA1110 2.8 19.5 0.4
C32 B:RUA1110 2.8 19.9 0.4
C31 B:RUA1110 2.8 18.1 0.4
C7 B:RUA1110 2.8 20.4 0.4
C24 B:RUA1110 2.8 23.0 0.4
C27 B:RUA1110 2.8 19.9 0.4
C36 B:RUA1110 2.9 18.9 0.4
C15 B:RUA1110 2.9 21.2 0.4
C12 B:RUA1110 2.9 10.3 0.4
C4 B:RUA1110 2.9 23.9 0.6
C20 B:RUA1110 2.9 27.3 0.6
C3 B:RUA1110 2.9 20.2 0.4
C27 B:RUA1110 3.0 29.4 0.6
C7 B:RUA1110 3.2 21.3 0.6
C16 B:RUA1110 3.3 25.9 0.6
C18 B:RUA1110 3.4 26.6 0.6
N37 B:RUA1110 3.6 30.2 0.6
N13 B:RUA1110 3.6 24.9 0.6
C17 B:RUA1110 3.7 24.3 0.6
C24 B:RUA1110 3.9 24.5 0.6
C31 B:RUA1110 3.9 28.3 0.6
C5 B:RUA1110 3.9 25.1 0.6
C8 B:RUA1110 4.0 26.1 0.6
C6 B:RUA1110 4.0 26.7 0.6
C21 B:RUA1110 4.1 23.1 0.4
C21 B:RUA1110 4.1 26.6 0.6
C18 B:RUA1110 4.1 24.5 0.4
C33 B:RUA1110 4.1 17.9 0.4
C23 B:RUA1110 4.1 23.6 0.4
C9 B:RUA1110 4.1 18.1 0.4
C30 B:RUA1110 4.1 18.8 0.4
C28 B:RUA1110 4.1 18.4 0.4
C35 B:RUA1110 4.1 19.4 0.4
C6 B:RUA1110 4.2 21.4 0.4
C16 B:RUA1110 4.2 22.2 0.4
C11 B:RUA1110 4.2 19.1 0.4
C4 B:RUA1110 4.2 19.5 0.4
C28 B:RUA1110 4.3 29.4 0.6
C32 B:RUA1110 4.3 32.4 0.6
C36 B:RUA1110 4.5 31.0 0.6
C22 B:RUA1110 4.6 22.3 0.4
C29 B:RUA1110 4.6 19.2 0.4
C34 B:RUA1110 4.7 18.5 0.4
C17 B:RUA1110 4.7 23.5 0.4
C10 B:RUA1110 4.7 19.1 0.4
C5 B:RUA1110 4.7 19.3 0.4
C12 B:RUA1110 4.8 24.9 0.6
C23 B:RUA1110 4.9 21.6 0.6
C30 B:RUA1110 5.0 30.1 0.6
C22 B:RUA1110 5.0 25.8 0.6

Reference:

A.Halavaty, J.J.Mueller, J.Contzen, C.Jung, F.Hannemann, R.Bernhardt, M.Galander, F.Lendzian, U.Heinemann. Light-Induced Reduction of Bovine Adrenodoxin Via the Covalently Bound Ruthenium(II) Bipyridyl Complex: Intramolecular Electron Transfer and Crystal Structure. Biochemistry V. 45 709 2006.
ISSN: ISSN 0006-2960
PubMed: 16411746
DOI: 10.1021/BI0510330
Page generated: Wed Dec 16 02:07:54 2020

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