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Ruthenium in PDB 5obd: X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole:
3.1.27.5;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole, PDB code: 5obd was solved by N.Pontillo, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.25 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.628, 32.773, 72.246, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 27.9

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (pdb code 5obd). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole, PDB code: 5obd:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 5obd

Go back to Ruthenium Binding Sites List in 5obd
Ruthenium binding site 1 out of 2 in the X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru201

b:61.8
occ:0.70
 RU A:9Q8201 0.0 61.8 0.7
C2 A:9Q8201 2.0 58.5 0.7
C1 A:9Q8201 2.0 57.2 0.7
O5 A:9Q8201 2.3 53.1 0.7
NE2 A:HIS105 2.5 22.1 1.0
O2 A:9Q8201 3.1 55.3 0.7
O1 A:9Q8201 3.1 54.7 0.7
O A:HOH375 3.3 56.0 1.0
CD2 A:HIS105 3.4 21.0 1.0
CE1 A:HIS105 3.4 21.4 1.0
O A:HOH368 4.2 46.4 1.0
O A:HOH379 4.2 53.1 1.0
O A:HOH465 4.4 38.0 1.0
ND1 A:HIS105 4.5 23.0 1.0
CG A:HIS105 4.5 21.2 1.0
O A:HOH312 4.8 51.8 1.0
CG2 A:THR78 4.9 30.5 1.0
O A:HOH460 5.0 39.0 1.0

Ruthenium binding site 2 out of 2 in 5obd

Go back to Ruthenium Binding Sites List in 5obd
Ruthenium binding site 2 out of 2 in the X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru201

b:51.5
occ:0.70
 RU B:9Q8201 0.0 51.5 0.7
C3 B:9Q8201 1.8 50.8 0.7
C1 B:9Q8201 2.1 51.6 0.7
C2 B:9Q8201 2.1 46.3 0.7
ND1 B:HIS119 2.3 22.5 1.0
O B:HOH439 2.9 29.8 0.3
O3 B:9Q8201 2.9 45.9 0.7
O B:HOH344 3.1 5.4 0.3
CG B:HIS119 3.2 22.5 1.0
O2 B:9Q8201 3.3 44.7 0.7
O1 B:9Q8201 3.3 53.4 0.7
CE1 B:HIS119 3.3 22.4 1.0
CB B:HIS119 3.3 20.7 1.0
CA B:HIS119 3.8 19.9 1.0
O B:HOH374 4.2 22.5 1.0
CD2 B:HIS119 4.3 26.2 1.0
NE2 B:HIS119 4.4 25.2 1.0
O B:VAL118 4.4 20.0 1.0
N B:PHE120 4.5 20.3 1.0
O B:HOH413 4.6 47.9 1.0
O B:HOH471 4.7 25.4 1.0
C B:HIS119 4.7 18.7 1.0
O B:HOH304 4.7 23.2 1.0
O B:HOH345 4.8 51.6 1.0
N B:HIS119 5.0 17.4 1.0
O B:HOH357 5.0 50.3 1.0

Reference:

N.Pontillo, G.Ferraro, L.Messori, G.Tamasi, A.Merlino. Ru-Based Co Releasing Molecules with Azole Ligands: Interaction with Proteins and the Co Release Mechanism Disclosed By X-Ray Crystallography. Dalton Trans V. 46 9621 2017.
ISSN: ESSN 1477-9234
PubMed: 28702564
DOI: 10.1039/C7DT01991B
Page generated: Thu Oct 10 13:02:13 2024

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