Sodium in PDB 7bd0: 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;

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

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

Ruthenium	(Ru)	3 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the The Adduct of Nami-A with Hen Egg White Lysozyme at 26 Hours., PDB code: 7bd0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium 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 Sodium with other atoms in the Na 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:Na203 b:55.5 occ:1.00 O A:HOH435 2.4 45.0 1.0 NZ A:LYS13 2.5 35.2 1.0 CE A:LYS13 3.6 33.5 1.0 OXT A:LEU129 3.6 68.0 1.0 C A:LEU129 4.8 67.0 1.0 CD A:LYS13 4.9 30.5 1.0 CB A:LEU129 4.9 62.2 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na204 b:13.5 occ:0.80 O A:SER60 2.3 14.9 1.0 O A:HOH386 2.4 18.4 1.0 O A:CYS64 2.4 13.3 1.0 O A:ARG73 2.4 22.5 1.0 OG A:SER72 2.5 20.7 1.0 O A:HOH356 2.5 14.8 1.0 CB A:SER72 3.3 21.1 1.0 C A:CYS64 3.5 12.5 1.0 C A:SER60 3.5 14.7 1.0 C A:ARG73 3.5 24.3 1.0 CA A:ASN65 3.9 13.6 1.0 N A:ARG73 3.9 27.0 1.0 CA A:SER60 4.1 12.9 1.0 N A:ASN65 4.1 13.1 1.0 C A:SER72 4.1 24.2 1.0 CB A:SER60 4.2 12.8 1.0 CA A:ARG73 4.3 30.7 1.0 CA A:SER72 4.3 22.1 1.0 N A:CYS64 4.4 12.8 1.0 N A:ASN74 4.4 20.4 1.0 N A:ARG61 4.5 17.0 1.0 C A:ARG61 4.6 18.9 1.0 O A:HOH387 4.6 32.6 1.0 CA A:ASN74 4.6 17.4 1.0 CA A:CYS64 4.6 12.9 1.0 O A:ARG61 4.6 19.2 1.0 O A:SER72 4.6 25.0 1.0 N A:ASP66 4.7 12.6 1.0 CB A:ASN74 4.7 16.4 1.0 CB A:THR69 4.7 14.8 1.0 O A:HOH399 4.7 12.9 1.0 OD1 A:ASN65 4.8 19.7 1.0 CB A:ASN65 4.8 16.4 1.0 CA A:ARG61 4.8 20.7 1.0 N A:TRP62 4.8 18.4 1.0 C A:ASN65 4.8 12.8 1.0 O A:HOH388 5.0 44.3 1.0 O A:THR69 5.0 17.7 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na205 b:36.9 occ:1.00 O A:LYS13 2.8 21.5 1.0 N A:ASP18 2.9 21.9 1.0 CA A:GLY16 3.2 21.2 1.0 CB A:ASP18 3.2 27.0 1.0 C A:GLY16 3.3 20.5 1.0 N A:LEU17 3.4 19.8 1.0 CA A:ASP18 3.6 23.9 1.0 C A:LYS13 3.6 21.4 1.0 CA A:LYS13 3.6 20.8 1.0 N A:GLY16 3.6 21.9 1.0 O A:ASP18 3.8 23.2 1.0 O A:GLY16 3.9 20.2 1.0 CG A:LYS13 3.9 26.5 1.0 C A:LEU17 4.0 20.4 1.0 C A:ASP18 4.2 23.0 1.0 O A:MET12 4.2 17.2 1.0 CA A:LEU17 4.2 19.6 1.0 CB A:LYS13 4.3 23.1 1.0 CG A:ASP18 4.6 31.2 1.0 N A:LYS13 4.7 18.8 1.0 N A:ARG14 4.9 23.3 1.0 C A:MET12 4.9 17.2 1.0 OD2 A:ASP18 5.0 34.0 1.0 C A:HIS15 5.0 22.8 1.0

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