Ruthenium in PDB 5jlg: The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Compound I, A Piano-Stool Organometallic Ru(II) Arene Compound Containing An O,S-Chelating Ligand

Enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Compound I, A Piano-Stool Organometallic Ru(II) Arene Compound Containing An O,S-Chelating Ligand

All present enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Compound I, A Piano-Stool Organometallic Ru(II) Arene Compound Containing An O,S-Chelating Ligand:
3.1.27.5;

Protein crystallography data

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Compound I, A Piano-Stool Organometallic Ru(II) Arene Compound Containing An O,S-Chelating Ligand, PDB code: 5jlg was solved by G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	72.47 / 1.79
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	100.510, 32.700, 72.470, 90.00, 90.03, 90.00
*R / R_free (%)*	17.2 / 23.6

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Compound I, A Piano-Stool Organometallic Ru(II) Arene Compound Containing An O,S-Chelating Ligand (pdb code 5jlg). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Compound I, A Piano-Stool Organometallic Ru(II) Arene Compound Containing An O,S-Chelating Ligand, PDB code: 5jlg:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 5jlg

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Ruthenium Binding Sites List in 5jlg

Ruthenium binding site 1 out of 2 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Compound I, A Piano-Stool Organometallic Ru(II) Arene Compound Containing An O,S-Chelating Ligand

Mono view

Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Compound I, A Piano-Stool Organometallic Ru(II) Arene Compound Containing An O,S-Chelating Ligand within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ru201 b:27.7 occ:0.40	O1	A:6L6202	1.9	24.3	0.4
	O	A:HOH413	2.2	28.5	0.4
	O	A:HOH338	2.2	21.4	0.4
	O	A:HOH396	2.2	22.7	0.4
	S1	A:6L6202	2.3	28.3	0.4
	NE2	A:HIS105	2.3	25.1	1.0
	C3	A:6L6202	2.9	25.2	0.4
	CE1	A:HIS105	3.1	24.5	1.0
	C1	A:6L6202	3.2	27.4	0.4
	CD2	A:HIS105	3.4	22.9	1.0
	C2	A:6L6202	3.4	27.3	0.4
	C4	A:6L6202	4.2	24.9	0.4
	ND1	A:HIS105	4.3	21.7	1.0
	CG	A:HIS105	4.5	19.6	1.0
	C9	A:6L6202	4.6	23.9	0.4
	CG2	A:THR78	4.7	23.1	1.0
	S2	A:6L6202	4.8	32.0	0.4

Ruthenium binding site 2 out of 2 in 5jlg

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Ruthenium Binding Sites List in 5jlg

Ruthenium binding site 2 out of 2 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Compound I, A Piano-Stool Organometallic Ru(II) Arene Compound Containing An O,S-Chelating Ligand

Mono view

Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Compound I, A Piano-Stool Organometallic Ru(II) Arene Compound Containing An O,S-Chelating Ligand within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Ru201 b:15.6 occ:0.50	O1	B:6L6202	2.1	16.7	0.5
	O	B:HOH335	2.1	12.8	0.5
	NE2	B:HIS105	2.1	16.3	1.0
	S	B:DMS204	2.2	15.7	0.5
	S1	B:6L6202	2.3	18.9	0.5
	S	B:DMS203	2.3	17.5	0.5
	O	B:DMS204	3.0	17.5	0.5
	C3	B:6L6202	3.0	17.3	0.5
	O	B:DMS203	3.0	18.5	0.5
	CE1	B:HIS105	3.0	16.0	1.0
	C2	B:DMS203	3.1	17.3	0.5
	CD2	B:HIS105	3.1	15.6	1.0
	C1	B:6L6202	3.1	18.5	0.5
	C2	B:DMS204	3.3	15.8	0.5
	C2	B:6L6202	3.4	18.2	0.5
	C1	B:DMS204	3.5	15.8	0.5
	C1	B:DMS203	3.7	17.0	0.5
	ND1	B:HIS105	4.2	16.0	1.0
	CG	B:HIS105	4.2	15.3	1.0
	C4	B:6L6202	4.4	18.1	0.5
	O	B:HOH375	4.5	29.9	1.0
	O	B:HOH387	4.5	34.2	1.0
	S2	B:6L6202	4.9	24.7	0.5
	C9	B:6L6202	4.9	18.7	0.5
	CG2	B:THR78	4.9	15.7	1.0

Reference:

J.Hildebrandt, H.Gorls, N.Hafner, G.Ferraro, M.Durst, I.B.Runnebaum, W.Weigand, A.Merlino. Unusual Mode of Protein Binding By A Cytotoxic Pi-Arene Ruthenium(II) Piano-Stool Compound Containing An O,S-Chelating Ligand. Dalton Trans V. 45 12283 2016.
ISSN: ESSN 1477-9234
PubMed: 27427335
DOI: 10.1039/C6DT02380K

Page generated: Wed Dec 16 02:08:34 2020

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