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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 / Rfree (%) 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

Go back to 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

Go back to 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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