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

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

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-Mbi), Mbi=Methyl-Benzimidazole:
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-Mbi), Mbi=Methyl-Benzimidazole, PDB code: 5obe 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) 73.05 / 1.82
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.651, 32.983, 73.046, 90.00, 90.21, 90.00
R / Rfree (%) 16.5 / 23.6

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-Mbi), Mbi=Methyl-Benzimidazole (pdb code 5obe). 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-Mbi), Mbi=Methyl-Benzimidazole, PDB code: 5obe:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 5obe

Go back to Ruthenium Binding Sites List in 5obe
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-Mbi), Mbi=Methyl-Benzimidazole


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-Mbi), Mbi=Methyl-Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru201

b:58.8
occ:0.50
 RU A:RU2201 0.0 58.8 0.5
C2 A:RU2201 2.0 52.0 0.5
O1 A:RU2201 2.3 48.7 0.5
NE2 A:HIS105 2.3 27.2 1.0
O3 A:RU2201 2.3 49.2 0.5
O2 A:RU2201 3.2 48.3 0.5
CE1 A:HIS105 3.2 27.2 1.0
CD2 A:HIS105 3.3 28.5 1.0
O A:HOH451 3.7 47.2 1.0
O A:HOH309 4.1 58.3 1.0
O A:HOH340 4.2 26.5 0.5
ND1 A:HIS105 4.4 28.0 1.0
CG2 A:THR78 4.4 30.8 1.0
O A:HOH429 4.4 39.9 1.0
CG A:HIS105 4.4 25.4 1.0

Ruthenium binding site 2 out of 2 in 5obe

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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-Mbi), Mbi=Methyl-Benzimidazole


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-Mbi), Mbi=Methyl-Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru201

b:44.0
occ:0.60
 RU B:9Q8201 0.0 44.0 0.6
C1 B:9Q8201 1.9 42.3 0.6
C2 B:9Q8201 2.0 40.7 0.6
C3 B:9Q8201 2.0 42.2 0.6
ND1 B:HIS119 2.3 27.2 1.0
O5 B:9Q8201 2.4 41.9 0.6
O B:HOH360 3.0 7.7 0.4
O1 B:9Q8201 3.0 40.5 0.6
O2 B:9Q8201 3.1 38.5 0.6
O3 B:9Q8201 3.1 44.5 0.6
CE1 B:HIS119 3.1 30.5 1.0
CG B:HIS119 3.4 28.6 1.0
CB B:HIS119 3.7 25.0 1.0
CA B:HIS119 4.0 23.7 1.0
O B:HOH405 4.2 27.0 1.0
NE2 B:HIS119 4.3 32.5 1.0
O B:VAL118 4.4 20.8 1.0
CD2 B:HIS119 4.5 31.9 1.0
N B:PHE120 4.6 21.6 1.0
O B:HOH334 4.7 25.0 1.0
O B:HOH455 4.8 38.8 1.0
C B:HIS119 4.8 21.4 1.0
O B:HOH463 4.9 29.4 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 13:02:30 2024

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