Chlorine in PDB 5v4g: Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites

Enzymatic activity of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites

All present enzymatic activity of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites:
3.2.1.17;

Protein crystallography data

The structure of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites, PDB code: 5v4g was solved by M.P.Sullivan, C.G.Hartinger, D.C.Goldstone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	56.77 / 1.20
*Space group*	P 4₃ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	80.282, 80.282, 36.928, 90.00, 90.00, 90.00
*R / R_free (%)*	17.7 / 20.6

Other elements in 5v4g:

The structure of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites 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 Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites (pdb code 5v4g). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites, PDB code: 5v4g:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5v4g

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Chlorine Binding Sites List in 5v4g

Chlorine binding site 1 out of 4 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl202 b:27.1 occ:0.90	CL1	A:RU7202	0.0	27.1	0.9
	RU1	A:RU7202	2.4	23.7	0.9
	NE2	A:HIS15	3.2	19.0	1.0
	CL2	A:RU7202	3.2	26.7	0.9
	CD2	A:HIS15	3.2	19.4	1.0
	C6	A:RU7202	3.2	26.2	0.9
	C5	A:RU7202	3.3	24.2	0.9
	CB	A:ALA11	3.6	16.8	1.0
	CA	A:ALA11	3.7	17.3	1.0
	C1	A:RU7202	3.9	25.3	0.9
	O	A:ALA11	4.0	16.7	1.0
	C4	A:RU7202	4.0	25.4	0.9
	CB	A:ARG14	4.3	24.0	1.0
	C	A:ALA11	4.3	15.8	1.0
	CG	A:ARG14	4.3	29.1	1.0
	CE1	A:HIS15	4.5	20.6	1.0
	C2	A:RU7202	4.5	25.1	0.9
	C3	A:RU7202	4.5	24.8	0.9
	CG	A:HIS15	4.6	17.8	1.0
	C7	A:RU7202	4.6	29.5	0.9
	C10	A:RU7202	4.7	28.4	0.9
	C8	A:RU7202	4.9	27.6	0.9
	N	A:ALA11	4.9	16.6	1.0

Chlorine binding site 2 out of 4 in 5v4g

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Chlorine Binding Sites List in 5v4g

Chlorine binding site 2 out of 4 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl202 b:26.7 occ:0.90	CL2	A:RU7202	0.0	26.7	0.9
	RU1	A:RU7202	2.5	23.7	0.9
	NE2	A:HIS15	3.1	19.0	1.0
	CL1	A:RU7202	3.2	27.1	0.9
	N	A:ILE88	3.3	15.5	1.0
	C1	A:RU7202	3.3	25.3	0.9
	C2	A:RU7202	3.4	25.1	0.9
	C7	A:RU7202	3.5	29.5	0.9
	CG1	A:ILE88	3.7	15.5	1.0
	CE1	A:HIS15	3.8	20.6	1.0
	CA	A:ASP87	3.8	17.2	1.0
	O	A:HOH335	3.9	24.8	1.0
	C6	A:RU7202	3.9	26.2	0.9
	OD1	A:ASP87	4.0	22.6	1.0
	CD2	A:HIS15	4.0	19.4	1.0
	C3	A:RU7202	4.0	24.8	0.9
	C	A:ASP87	4.0	16.3	1.0
	CA	A:ILE88	4.3	14.8	1.0
	CB	A:ILE88	4.3	15.1	1.0
	O	A:SER86	4.3	19.7	1.0
	CG2	A:ILE88	4.4	16.6	1.0
	CG	A:ASP87	4.5	22.2	1.0
	C5	A:RU7202	4.5	24.2	0.9
	CD1	A:ILE88	4.6	16.2	1.0
	C4	A:RU7202	4.6	25.4	0.9
	CB	A:ASP87	4.7	19.7	1.0
	N	A:THR89	4.8	15.3	1.0
	CB	A:ALA11	4.9	16.8	1.0
	ND1	A:HIS15	4.9	19.9	1.0
	N	A:ASP87	4.9	15.8	1.0
	C	A:ILE88	5.0	13.7	1.0

Chlorine binding site 3 out of 4 in 5v4g

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Chlorine Binding Sites List in 5v4g

Chlorine binding site 3 out of 4 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl203 b:41.0 occ:0.50	CL1	A:RU7203	0.0	41.0	0.5
	RU1	A:RU7203	2.4	40.2	0.5
	RU1	A:RU7204	2.6	42.1	0.5
	C1	A:RU7203	3.2	32.3	0.5
	OD2	A:ASP101	3.2	33.3	1.0
	C2	A:RU7203	3.3	33.0	0.5
	OD1	A:ASP101	3.3	34.3	1.0
	C7	A:RU7203	3.3	31.6	0.5
	CG	A:ASP101	3.5	34.5	1.0
	CL1	A:RU7204	3.6	42.4	0.5
	C6	A:RU7203	3.8	30.1	0.5
	C3	A:RU7203	4.0	35.4	0.5
	C5	A:RU7203	4.5	29.6	0.5
	C4	A:RU7203	4.5	32.9	0.5
	CB	A:ASP101	4.7	30.0	1.0

Chlorine binding site 4 out of 4 in 5v4g

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Chlorine Binding Sites List in 5v4g

Chlorine binding site 4 out of 4 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl204 b:42.4 occ:0.50	CL1	A:RU7204	0.0	42.4	0.5
	RU1	A:RU7204	2.2	42.1	0.5
	RU1	A:RU7203	2.4	40.2	0.5
	C10	A:RU7203	3.0	25.6	0.5
	C4	A:RU7203	3.1	32.9	0.5
	C8	A:RU7203	3.1	29.0	0.5
	OD1	A:ASP101	3.2	34.3	1.0
	C3	A:RU7203	3.2	35.4	0.5
	OD2	A:ASP101	3.3	33.3	1.0
	CL1	A:RU7203	3.6	41.0	0.5
	CG	A:ASP101	3.6	34.5	1.0
	C5	A:RU7203	3.8	29.6	0.5
	C2	A:RU7203	3.9	33.0	0.5
	C6	A:RU7203	4.4	30.1	0.5
	C1	A:RU7203	4.5	32.3	0.5
	C9	A:RU7203	4.7	28.4	0.5

Reference:

M.P.Sullivan, M.Groessl, S.M.Meier, R.L.Kingston, D.C.Goldstone, C.G.Hartinger. The Metalation of Hen Egg White Lysozyme Impacts Protein Stability As Shown By Ion Mobility Mass Spectrometry, Differential Scanning Calorimetry, and X-Ray Crystallography. Chem. Commun. (Camb.) V. 53 4246 2017.
ISSN: ESSN 1364-548X
PubMed: 28361137
DOI: 10.1039/C6CC10150J

Page generated: Sat Jul 12 09:42:36 2025

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