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Ruthenium in PDB 5ob8: 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 Nacl)

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 Nacl)

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 Nacl):
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 Nacl), PDB code: 5ob8 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) 55.56 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.573, 78.573, 36.664, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 23

Other elements in 5ob8:

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 Nacl) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

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 Nacl) (pdb code 5ob8). 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 Nacl), PDB code: 5ob8:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 5ob8

Go back to Ruthenium Binding Sites List in 5ob8
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 Nacl)


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 Nacl) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru206

b:43.4
occ:0.80
RU1 A:9QB206 0.0 43.4 0.8
C2 A:9QB206 1.6 38.2 0.8
C1 A:9QB206 1.8 45.9 0.8
O5 A:9QB206 2.1 41.3 0.8
NE2 A:HIS15 2.2 37.9 1.0
CL1 A:9QB206 2.3 48.8 0.8
O4 A:9QB206 2.3 35.5 0.8
O2 A:9QB206 2.5 32.5 0.8
O1 A:9QB206 2.7 38.6 0.8
CE1 A:HIS15 3.1 49.2 1.0
CD2 A:HIS15 3.2 37.0 1.0
OD1 A:ASP87 3.6 54.9 1.0
ND1 A:HIS15 4.2 41.5 1.0
O A:HOH303 4.3 51.7 1.0
CG A:HIS15 4.3 38.8 1.0
CG A:ARG14 4.7 48.1 1.0
CG A:ASP87 4.9 47.7 1.0

Ruthenium binding site 2 out of 2 in 5ob8

Go back to Ruthenium Binding Sites List in 5ob8
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 Nacl)


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 Nacl) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru207

b:56.7
occ:0.40
RU A:RU2207 0.0 56.7 0.4
C2 A:RU2207 1.9 47.9 0.4
OD2 A:ASP18 2.3 52.2 1.0
O3 A:RU2207 2.3 49.2 0.4
O5 A:RU2207 2.4 50.4 0.4
O1 A:RU2207 2.4 44.8 0.4
O4 A:RU2207 2.4 48.5 0.4
O2 A:RU2207 3.0 41.5 0.4
CG A:ASP18 3.0 44.8 1.0
OD1 A:ASP18 3.1 43.3 1.0
NZ A:LYS13 4.0 41.2 0.5
CE A:LYS13 4.3 41.8 0.5
CB A:ASP18 4.5 42.9 1.0
ND2 A:ASN19 4.7 62.3 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: Wed Dec 16 02:08:38 2020

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