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Ruthenium in PDB 4ny5: X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A

Enzymatic activity of X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A

All present enzymatic activity of X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A, PDB code: 4ny5 was solved by L.Messori, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.15 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.772, 77.772, 37.316, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 24

Other elements in 4ny5:

The structure of X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A (pdb code 4ny5). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A, PDB code: 4ny5:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 4ny5

Go back to Ruthenium Binding Sites List in 4ny5
Ruthenium binding site 1 out of 2 in the X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru201

b:61.1
occ:0.40
O A:HOH418 1.9 24.2 0.4
O A:HOH420 2.3 28.5 0.4
OD2 A:ASP119 2.4 50.5 1.0
O A:HOH421 2.4 40.2 0.4
OD1 A:ASP119 3.0 53.3 1.0
CG A:ASP119 3.0 45.8 1.0
OE1 A:GLN121 3.1 68.1 1.0
O A:HOH423 3.2 32.7 0.4
CD A:GLN121 4.3 54.8 1.0
CB A:ASP119 4.4 38.5 1.0

Ruthenium binding site 2 out of 2 in 4ny5

Go back to Ruthenium Binding Sites List in 4ny5
Ruthenium binding site 2 out of 2 in the X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of X-Ray Structure of the Adduct Formed Between Hen Egg White Lysozyme and Nami-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru202

b:62.0
occ:0.40
O A:HOH419 1.8 25.8 0.4
O A:HOH417 2.2 29.5 0.4
O A:HOH351 2.3 25.2 0.4
OD1 A:ASP101 2.3 59.3 1.0
O A:HOH352 2.6 29.7 0.4
OD2 A:ASP101 2.9 59.4 1.0
CG A:ASP101 3.0 55.1 1.0
CB A:ASP101 4.5 45.1 1.0
O A:ASP101 4.5 44.2 1.0

Reference:

L.Messori, A.Merlino. Ruthenium Metalation of Proteins: the X-Ray Structure of the Complex Formed Between Nami-A and Hen Egg White Lysozyme. Dalton Trans V. 43 6128 2014.
ISSN: ISSN 1477-9226
PubMed: 24553967
DOI: 10.1039/C3DT53582G
Page generated: Wed Dec 16 02:08:21 2020

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