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Ruthenium in PDB 7bd0: The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours.

Enzymatic activity of The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours.

All present enzymatic activity of The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours.:
3.2.1.17;

Protein crystallography data

The structure of The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours., PDB code: 7bd0 was solved by L.Chiniadis, P.Giastas, I.Bratsos, A.Papakyriakou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.09 / 1.06
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.298, 78.298, 37.571, 90, 90, 90
R / Rfree (%) 16.4 / 18.5

Other elements in 7bd0:

The structure of The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours. also contains other interesting chemical elements:

Sodium (Na) 3 atoms
Chlorine (Cl) 2 atoms

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours. (pdb code 7bd0). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 3 binding sites of Ruthenium where determined in the The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours., PDB code: 7bd0:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in 7bd0

Go back to Ruthenium Binding Sites List in 7bd0
Ruthenium binding site 1 out of 3 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours.


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru207

b:30.5
occ:0.82
N1 A:IMD206 2.1 32.9 0.8
O A:HOH357 2.3 21.9 0.8
O A:HOH403 2.4 14.6 0.8
O A:HOH440 2.4 24.7 0.8
O A:HOH400 2.4 19.0 0.8
CL A:CL208 2.5 28.6 0.8
C5 A:IMD206 3.1 32.9 0.8
C2 A:IMD206 3.1 32.2 0.8
O A:HOH302 3.7 57.2 1.0
NZ A:LYS33 4.2 21.0 1.0
C4 A:IMD206 4.2 32.2 0.8
N3 A:IMD206 4.2 31.0 0.8
C4 A:IMD209 4.5 28.7 0.4
CE2 A:PHE38 5.0 16.1 1.0

Ruthenium binding site 2 out of 3 in 7bd0

Go back to Ruthenium Binding Sites List in 7bd0
Ruthenium binding site 2 out of 3 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours.


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru210

b:15.6
occ:0.43
N1 A:IMD209 2.0 28.3 0.4
O A:HOH430 2.3 10.3 0.4
O A:HOH379 2.4 12.3 0.4
O A:HOH384 2.4 9.0 0.4
CL A:CL211 2.4 17.4 0.4
O A:HOH394 2.4 10.6 0.4
C5 A:IMD209 2.9 28.9 0.4
C2 A:IMD209 3.1 28.5 0.4
C4 A:IMD209 4.1 28.7 0.4
N3 A:IMD209 4.2 28.3 0.4
C4 A:IMD212 4.7 21.6 0.6

Ruthenium binding site 3 out of 3 in 7bd0

Go back to Ruthenium Binding Sites List in 7bd0
Ruthenium binding site 3 out of 3 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours.


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru213

b:24.0
occ:0.64
N1 A:IMD212 2.1 22.3 0.6
O A:HOH383 2.3 16.0 0.6
O A:HOH438 2.3 17.9 0.6
O A:HOH401 2.4 18.4 0.6
O A:HOH389 2.4 18.2 0.6
O A:HOH393 2.4 17.3 0.6
C2 A:IMD212 3.0 22.2 0.6
C5 A:IMD212 3.2 21.8 0.6
N3 A:IMD212 4.2 22.0 0.6
C4 A:IMD212 4.3 21.6 0.6
CA A:GLY4 4.8 20.7 1.0
N A:ARG5 5.0 21.0 1.0
N A:CYS6 5.0 20.1 1.0

Reference:

L.Chiniadis, P.Giastas, I.Bratsos, A.Papakyriakou. Insights Into the Protein Ruthenation Mechanism By Antimetastatic Metallodrugs: High-Resolution X-Ray Structures of the Adduct Formed Between Hen Egg-White Lysozyme and Nami-A at Various Time Points. Inorg.Chem. V. 60 10729 2021.
ISSN: ISSN 0020-1669
PubMed: 34197115
DOI: 10.1021/ACS.INORGCHEM.1C01441
Page generated: Sat Aug 21 17:33:20 2021

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