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Ruthenium in PDB 3ase: Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster

Protein crystallography data

The structure of Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster, PDB code: 3ase was solved by T.Koshiyama, M.Shirai, T.Hikage, H.Tabe, K.Tanaka, S.Kitagawa, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.65 / 1.75
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 90.722, 90.722, 45.395, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 23.2

Other elements in 3ase:

The structure of Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster (pdb code 3ase). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 6 binding sites of Ruthenium where determined in the Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster, PDB code: 3ase:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6;

Ruthenium binding site 1 out of 6 in 3ase

Go back to Ruthenium Binding Sites List in 3ase
Ruthenium binding site 1 out of 6 in the Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru154

b:53.4
occ:0.80
RU1 A:RUO154 0.0 53.4 0.8
O1 A:RUO154 1.9 54.1 0.8
O A:HOH216 2.6 27.1 0.8
RU2 A:RUO154 3.3 52.3 0.8
RU3 A:RUO154 3.3 54.1 0.8
O A:HOH217 4.6 21.0 1.0
OD1 A:ASN122 4.6 25.0 1.0
CD2 A:LEU9 5.0 18.2 1.0

Ruthenium binding site 2 out of 6 in 3ase

Go back to Ruthenium Binding Sites List in 3ase
Ruthenium binding site 2 out of 6 in the Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru154

b:52.3
occ:0.80
RU2 A:RUO154 0.0 52.3 0.8
O1 A:RUO154 1.9 54.1 0.8
ND1 A:HIS12 2.3 30.0 1.0
CE1 A:HIS12 3.1 31.3 1.0
RU1 A:RUO154 3.3 53.4 0.8
RU3 A:RUO154 3.3 54.1 0.8
CG A:HIS12 3.4 23.0 1.0
CB A:HIS12 3.8 17.9 1.0
NE2 A:HIS12 4.2 31.8 1.0
CD2 A:HIS12 4.4 27.9 1.0
CD2 A:LEU9 4.5 18.2 1.0
O A:GLN8 4.6 14.3 1.0

Ruthenium binding site 3 out of 6 in 3ase

Go back to Ruthenium Binding Sites List in 3ase
Ruthenium binding site 3 out of 6 in the Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru154

b:54.1
occ:0.80
RU3 A:RUO154 0.0 54.1 0.8
O1 A:RUO154 1.9 54.1 0.8
RU1 A:RUO154 3.3 53.4 0.8
RU2 A:RUO154 3.3 52.3 0.8
CD2 A:LEU9 4.8 18.2 1.0

Ruthenium binding site 4 out of 6 in 3ase

Go back to Ruthenium Binding Sites List in 3ase
Ruthenium binding site 4 out of 6 in the Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru155

b:57.0
occ:0.30
RU1 A:RUO155 0.0 57.0 0.3
O1 A:RUO155 1.9 55.3 0.3
RU2 A:RUO155 3.2 55.5 0.3
RU3 A:RUO155 3.3 53.8 0.3
CB A:GLU83 4.3 26.6 1.0
CG A:GLU83 4.8 27.8 1.0

Ruthenium binding site 5 out of 6 in 3ase

Go back to Ruthenium Binding Sites List in 3ase
Ruthenium binding site 5 out of 6 in the Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 5 of Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru155

b:55.5
occ:0.30
RU2 A:RUO155 0.0 55.5 0.3
O1 A:RUO155 1.9 55.3 0.3
RU1 A:RUO155 3.2 57.0 0.3
RU3 A:RUO155 3.3 53.8 0.3

Ruthenium binding site 6 out of 6 in 3ase

Go back to Ruthenium Binding Sites List in 3ase
Ruthenium binding site 6 out of 6 in the Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 6 of Crystal Structure of Zinc Myoglobin Soaked with RU3O Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru155

b:53.8
occ:0.30
RU3 A:RUO155 0.0 53.8 0.3
O1 A:RUO155 1.9 55.3 0.3
ND1 A:HIS81 2.9 24.2 1.0
RU2 A:RUO155 3.3 55.5 0.3
RU1 A:RUO155 3.3 57.0 0.3
CG A:HIS81 3.8 21.6 1.0
CE1 A:HIS81 3.8 27.2 1.0
CB A:HIS81 3.9 20.9 1.0
CA A:HIS81 4.2 20.8 1.0
C A:HIS81 4.9 21.2 1.0
NE2 A:HIS81 5.0 27.3 1.0
CD2 A:HIS81 5.0 23.4 1.0

Reference:

T.Koshiyama, M.Shirai, T.Hikage, H.Tabe, K.Tanaka, S.Kitagawa, T.Ueno. Post-Crystal Engineering of Zinc-Substituted Myoglobin to Construct A Long-Lived Photoinduced Charge-Separation System Angew.Chem.Int.Ed.Engl. 2011.
ISSN: ESSN 1521-3773
PubMed: 21495132
DOI: 10.1002/ANIE.201008004
Page generated: Wed Dec 16 02:07:59 2020

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