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Ruthenium in PDB 5lvk: Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]

Enzymatic activity of Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]

All present enzymatic activity of Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]:
3.2.1.17;

Protein crystallography data

The structure of Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)], PDB code: 5lvk was solved by K.Kurpiewska, A.Szura, K.Lewinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.37 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.039, 64.100, 111.311, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 28.1

Other elements in 5lvk:

The structure of Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Sodium (Na) 3 atoms

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] (pdb code 5lvk). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)], PDB code: 5lvk:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 5lvk

Go back to Ruthenium Binding Sites List in 5lvk
Ruthenium binding site 1 out of 2 in the Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru201

b:58.0
occ:0.76
NE B:ARG113 3.1 15.1 0.4
CG B:ARG113 3.3 18.6 0.4
NE2 B:GLN117 3.4 9.9 1.0
CD B:ARG113 3.5 18.4 0.4
O B:HOH413 3.5 16.1 1.0
NH2 B:ARG107 3.6 18.5 1.0
NE B:ARG113 3.6 16.0 0.6
NH2 B:ARG113 3.7 23.9 0.6
CZ B:ARG113 3.9 22.6 0.4
NH1 B:ARG107 3.9 25.7 1.0
CZ B:ARG113 4.1 20.2 0.6
CZ B:ARG107 4.1 19.6 1.0
NH2 B:ARG113 4.3 27.6 0.4
CD B:GLN117 4.5 19.8 1.0
CB B:ARG113 4.6 14.0 0.4
CB B:ARG113 4.6 13.9 0.6
CD B:ARG113 4.7 16.4 0.6
NH1 B:ARG113 4.8 17.5 0.4
OE1 B:GLN117 4.8 23.4 1.0

Ruthenium binding site 2 out of 2 in 5lvk

Go back to Ruthenium Binding Sites List in 5lvk
Ruthenium binding site 2 out of 2 in the Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Human Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru202

b:52.0
occ:0.69
O B:HOH407 2.4 34.5 1.0
O B:HOH425 3.0 36.2 1.0
N B:GLY127 3.2 13.7 1.0
O B:HOH397 3.4 30.7 1.0
CA B:GLY127 3.5 27.6 1.0
O B:HOH404 3.8 48.6 1.0
O B:HOH406 4.0 33.4 1.0
N B:GLY129 4.0 18.1 1.0
C B:GLY127 4.1 13.5 1.0
N B:CYS128 4.2 21.6 1.0
C B:GLN126 4.3 19.4 1.0
O B:HOH387 4.4 28.2 1.0
CA B:GLY129 4.5 12.9 1.0
O B:VAL125 4.6 11.3 1.0
CA B:GLN126 4.6 18.6 1.0
O B:GLY127 4.9 13.6 1.0

Reference:

M.Oszajca, K.Kurpiewska, P.Halajko, A.Szura, K.Lewinski, M.Brindell. Ligand-Dependent Interaction of Anticancer Ruthenium Complexes with Hen Egg White Lysozyme and Human Lysozyme To Be Published.
Page generated: Wed Dec 16 02:08:37 2020

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