Chlorine 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:

Ruthenium	(Ru)	3 atoms
Sodium	(Na)	1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5ob7

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Chlorine Binding Sites List in 5ob7

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl201 b:33.4 occ:1.00	OH	A:TYR23	3.0	25.0	1.0
	O	A:HOH348	3.4	29.2	1.0
	CE2	A:TYR23	3.6	23.6	1.0
	CZ	A:TYR23	3.6	23.8	1.0
	CA	A:GLY104	4.1	31.5	1.0
	O	A:ARG21	4.5	29.1	0.5
	O	A:ARG21	4.5	29.4	0.5
	N	A:GLY104	4.7	29.1	1.0
	CE1	A:TYR23	4.8	23.1	1.0
	CD2	A:TYR23	4.8	24.6	1.0
	NH2	A:ARG21	5.0	38.2	0.5

Chlorine binding site 2 out of 3 in 5ob7

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Chlorine Binding Sites List in 5ob7

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl203 b:42.4 occ:1.00	N	A:THR69	3.0	29.6	1.0
	O	A:HOH400	3.0	39.0	1.0
	O	A:HOH369	3.2	23.5	1.0
	O	A:HOH402	3.2	57.7	1.0
	O	A:THR69	3.2	33.7	1.0
	N	A:ARG68	3.4	30.7	0.5
	N	A:ARG68	3.4	32.4	0.5
	C	A:GLY67	3.5	32.2	1.0
	C	A:THR69	3.6	30.7	1.0
	CA	A:GLY67	3.6	30.2	1.0
	N	A:GLY67	3.7	29.2	1.0
	CA	A:THR69	3.7	30.0	1.0
	OD1	A:ASN65	3.7	37.6	1.0
	O	A:HOH320	3.7	38.5	1.0
	OG	A:SER72	3.8	39.8	1.0
	C	A:ARG68	4.0	30.3	0.5
	C	A:ARG68	4.0	31.9	0.5
	CB	A:THR69	4.0	28.0	1.0
	CA	A:ARG68	4.1	28.7	0.5
	CA	A:ARG68	4.1	31.2	0.5
	O	A:GLY67	4.2	33.1	1.0
	O	A:HOH365	4.2	28.8	1.0
	OD1	A:ASP66	4.3	28.5	1.0
	N	A:PRO70	4.5	37.0	1.0
	OG1	A:THR69	4.6	24.9	1.0
	NA	A:NA202	4.7	42.0	1.0
	C	A:ASP66	4.8	30.4	1.0
	CB	A:SER72	4.9	46.2	1.0
	CG	A:ASN65	4.9	36.4	1.0
	N	A:ASP66	5.0	27.7	1.0

Chlorine binding site 3 out of 3 in 5ob7

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Chlorine Binding Sites List in 5ob7

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl204 b:41.4 occ:0.80	CL1	A:9QB204	0.0	41.4	0.8
	RU1	A:9QB204	2.0	44.2	0.8
	C2	A:9QB204	2.3	47.3	0.8
	C1	A:9QB204	2.7	39.9	0.8
	NE2	A:HIS15	3.0	44.2	1.0
	O2	A:9QB204	3.1	44.8	0.8
	O4	A:9QB204	3.1	40.4	0.8
	OD1	A:ASP87	3.3	46.0	1.0
	O1	A:9QB204	3.5	41.9	0.8
	CD2	A:HIS15	3.8	45.6	1.0
	CE1	A:HIS15	3.8	49.1	1.0
	N	A:ILE88	3.8	38.2	1.0
	CG1	A:ILE88	3.9	36.4	1.0
	C3	A:9QB204	3.9	45.6	0.8
	O	A:HOH353	3.9	51.3	1.0
	CA	A:ASP87	4.1	36.4	1.0
	CG	A:ASP87	4.3	45.5	1.0
	C	A:ASP87	4.5	35.7	1.0
	CB	A:ASP87	4.6	43.1	1.0
	O	A:SER86	4.7	35.5	1.0
	CB	A:ILE88	4.8	34.3	1.0
	CA	A:ILE88	4.8	35.6	1.0
	ND1	A:HIS15	4.8	43.4	1.0
	CG	A:HIS15	4.8	43.4	1.0
	CD1	A:ILE88	4.8	36.9	1.0
	O3	A:9QB204	5.0	42.5	0.8
	CB	A:ALA11	5.0	35.6	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: Fri Jul 26 14:22:13 2024

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