Sodium 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
Chlorine	(Cl)	3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was 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:

Sodium binding site 1 out of 1 in 5ob7

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Sodium Binding Sites List in 5ob7

Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na202 b:42.0 occ:1.00	O	A:HOH369	2.3	23.5	1.0
	O	A:SER60	2.3	34.3	1.0
	O	A:CYS64	2.4	26.8	1.0
	O	A:HOH365	2.6	28.8	1.0
	OG	A:SER72	2.6	39.8	1.0
	O	A:ARG73	2.7	44.2	1.0
	C	A:SER60	3.4	31.6	1.0
	C	A:CYS64	3.5	27.0	1.0
	CB	A:SER72	3.6	46.2	1.0
	C	A:ARG73	3.7	43.4	1.0
	CA	A:ASN65	3.9	29.1	1.0
	CA	A:SER60	3.9	30.5	1.0
	CB	A:SER60	4.0	29.0	1.0
	N	A:ASN65	4.1	28.6	1.0
	N	A:ARG73	4.2	42.0	1.0
	C	A:SER72	4.4	47.0	1.0
	N	A:ASN74	4.5	38.0	1.0
	O	A:ARG61	4.5	43.1	1.0
	N	A:ARG61	4.5	35.4	1.0
	N	A:ASP66	4.5	27.7	1.0
	N	A:CYS64	4.5	25.7	1.0
	CA	A:ARG73	4.5	45.6	1.0
	CB	A:THR69	4.6	28.0	1.0
	CA	A:ASN74	4.6	36.6	1.0
	OD1	A:ASN65	4.6	37.6	1.0
	C	A:ARG61	4.6	37.6	1.0
	CA	A:SER72	4.6	47.5	1.0
	CA	A:CYS64	4.7	27.0	1.0
	C	A:ASN65	4.7	27.6	1.0
	CL	A:CL203	4.7	42.4	1.0
	CB	A:ASN65	4.8	31.1	1.0
	CB	A:ASN74	4.8	37.9	1.0
	CA	A:ARG61	4.8	38.1	1.0
	O	A:SER72	4.8	41.2	1.0
	OG	A:SER60	4.8	25.7	1.0
	OG1	A:THR69	5.0	24.9	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: Mon Oct 7 23:09:52 2024

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