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Ruthenium in PDB 5ob9: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Ethylene Glycol

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Ethylene Glycol

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Ethylene Glycol:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Ethylene Glycol, PDB code: 5ob9 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) 54.97 / 2.38
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.744, 77.744, 37.168, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 30.8

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Ethylene Glycol (pdb code 5ob9). 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 Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Ethylene Glycol, PDB code: 5ob9:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 5ob9

Go back to Ruthenium Binding Sites List in 5ob9
Ruthenium binding site 1 out of 2 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Ethylene Glycol


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 Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Ethylene Glycol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru207

b:49.0
occ:0.60
RU A:9Q8207 0.0 49.0 0.6
C3 A:9Q8207 1.8 44.5 0.6
C2 A:9Q8207 1.9 46.9 0.6
C1 A:9Q8207 2.0 46.1 0.6
OE1 A:GLN121 2.1 62.9 1.0
O5 A:9Q8207 2.4 44.4 0.6
OD2 A:ASP119 2.7 50.2 1.0
O3 A:9Q8207 2.9 48.2 0.6
O2 A:9Q8207 3.0 47.9 0.6
OD1 A:ASP119 3.0 45.6 1.0
O1 A:9Q8207 3.2 40.8 0.6
CG A:ASP119 3.2 46.3 1.0
CD A:GLN121 3.2 62.1 1.0
CG A:GLN121 4.0 58.7 1.0
O A:HOH321 4.1 56.3 1.0
NE2 A:GLN121 4.2 65.5 1.0
CB A:GLN121 4.5 55.6 1.0
CB A:ASP119 4.6 46.0 1.0

Ruthenium binding site 2 out of 2 in 5ob9

Go back to Ruthenium Binding Sites List in 5ob9
Ruthenium binding site 2 out of 2 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Ethylene Glycol


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 Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Ethylene Glycol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru208

b:55.1
occ:0.40
RU A:9Q8208 0.0 55.1 0.4
C2 A:9Q8208 1.9 45.0 0.4
C3 A:9Q8208 1.9 49.0 0.4
NE2 A:HIS15 2.3 56.2 1.0
O5 A:9Q8208 2.3 47.3 0.4
O4 A:9Q8208 2.4 46.3 0.4
O2 A:9Q8208 3.0 41.2 0.4
O3 A:9Q8208 3.0 48.4 0.4
CD2 A:HIS15 3.1 53.0 1.0
CE1 A:HIS15 3.4 58.8 1.0
OD1 A:ASP87 3.7 53.3 1.0
CG A:HIS15 4.3 51.6 1.0
OG1 A:THR89 4.4 40.7 1.0
ND1 A:HIS15 4.4 52.4 1.0
CG A:ASP87 4.9 50.5 1.0
CD A:ARG14 4.9 83.4 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: Wed Dec 16 02:08:38 2020

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