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Ruthenium in PDB 7bdm: The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours.

Enzymatic activity of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours.

All present enzymatic activity of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours.:
3.2.1.17;

Protein crystallography data

The structure of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours., PDB code: 7bdm 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) 33.93 / 1.07
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.022, 79.022, 37.567, 90, 90, 90
R / Rfree (%) 17 / 20.1

Other elements in 7bdm:

The structure of The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours. also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Sodium (Na) 2 atoms

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours. (pdb code 7bdm). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total only one binding site of Ruthenium was determined in the The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours., PDB code: 7bdm:

Ruthenium binding site 1 out of 1 in 7bdm

Go back to Ruthenium Binding Sites List in 7bdm
Ruthenium binding site 1 out of 1 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 98 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 98 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru209

b:45.4
occ:0.79
O A:HOH332 2.3 38.6 0.8
O A:HOH343 2.3 23.2 0.8
NE2 A:HIS15 2.3 27.0 1.0
NH1 A:ARG14 2.5 29.4 0.2
O A:HOH401 2.6 24.3 0.8
CE1 A:HIS15 3.2 26.9 1.0
OD1 A:ASP87 3.4 43.3 1.0
CD2 A:HIS15 3.4 26.2 1.0
CZ A:ARG14 3.7 29.0 0.2
CD A:ARG14 4.2 27.3 0.2
NE A:ARG14 4.3 28.4 0.2
ND1 A:HIS15 4.3 26.8 1.0
CG A:HIS15 4.5 25.1 1.0
CG A:ASP87 4.6 40.2 1.0
NH2 A:ARG14 4.6 29.2 0.2
OG1 A:THR89 4.9 24.5 1.0
CG1 A:ILE88 5.0 19.8 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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