Ruthenium in PDB 5ob7: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2)

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2)

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2):
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-Im), Im=Imidazole (Crystal 2), PDB code: 5ob7 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)*	55.84 / 2.10
*Space group*	P 4₃ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	78.968, 78.968, 36.604, 90.00, 90.00, 90.00
*R / R_free (%)*	15.3 / 23.4

Other elements in 5ob7:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2) 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-Im), Im=Imidazole (Crystal 2) (pdb code 5ob7). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 3 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-Im), Im=Imidazole (Crystal 2), PDB code: 5ob7:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in 5ob7

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Ruthenium Binding Sites List in 5ob7

Ruthenium binding site 1 out of 3 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2)

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-Im), Im=Imidazole (Crystal 2) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ru204 b:44.2 occ:0.80	RU1	A:9QB204	0.0	44.2	0.8
	C1	A:9QB204	1.8	39.9	0.8
	C2	A:9QB204	1.9	47.3	0.8
	C3	A:9QB204	1.9	45.6	0.8
	CL1	A:9QB204	2.0	41.4	0.8
	NE2	A:HIS15	2.2	44.2	1.0
	O4	A:9QB204	2.3	40.4	0.8
	O1	A:9QB204	2.9	41.9	0.8
	O2	A:9QB204	2.9	44.8	0.8
	O3	A:9QB204	3.0	42.5	0.8
	CE1	A:HIS15	3.2	49.1	1.0
	CD2	A:HIS15	3.2	45.6	1.0
	OD1	A:ASP87	4.0	46.0	1.0
	ND1	A:HIS15	4.3	43.4	1.0
	CG	A:HIS15	4.3	43.4	1.0
	OG1	A:THR89	5.0	35.5	1.0

Ruthenium binding site 2 out of 3 in 5ob7

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Ruthenium Binding Sites List in 5ob7

Ruthenium binding site 2 out of 3 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2)

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-Im), Im=Imidazole (Crystal 2) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ru205 b:51.0 occ:0.50	RU	A:9Q8205	0.0	51.0	0.5
	C1	A:9Q8205	1.9	46.3	0.5
	C2	A:9Q8205	2.0	43.3	0.5
	OD2	A:ASP18	2.2	46.5	1.0
	O6	A:9Q8205	2.4	43.1	0.5
	O4	A:9Q8205	2.4	43.7	0.5
	O5	A:9Q8205	2.4	44.5	0.5
	O1	A:9Q8205	2.9	52.4	0.5
	CG	A:ASP18	3.0	44.7	1.0
	OD1	A:ASP18	3.0	45.5	1.0
	O2	A:9Q8205	3.0	37.3	0.5
	NZ	A:LYS13	3.9	40.2	0.5
	NZ	A:LYS13	4.0	39.3	0.5
	CB	A:ASP18	4.4	39.5	1.0
	CE	A:LYS13	4.9	41.2	0.5

Ruthenium binding site 3 out of 3 in 5ob7

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Ruthenium Binding Sites List in 5ob7

Ruthenium binding site 3 out of 3 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2)

Mono view

Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ru206 b:46.4 occ:0.30	O	A:HOH384	2.6	58.3	1.0
	NH2	A:ARG125	2.7	61.3	1.0
	OD2	A:ASP119	2.7	62.2	1.0
	OD1	A:ASP119	2.8	48.6	1.0
	CG	A:ASP119	3.0	50.3	1.0
	OE1	A:GLN121	3.6	58.1	1.0
	CZ	A:ARG125	3.9	64.2	1.0
	CB	A:ASP119	4.5	44.6	1.0
	NH1	A:ARG125	4.6	67.3	1.0
	NE	A:ARG125	4.7	56.5	1.0
	CD	A:GLN121	4.7	56.2	1.0
	CB	A:GLN121	4.8	43.1	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 13:01:29 2024

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