Sodium in PDB 7bdm: 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;

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

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
Ruthenium	(Ru)	1 atom

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the The Adduct of Nami-A with Hen Egg White Lysozyme at 98 Hours., PDB code: 7bdm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na201 b:14.9 occ:0.69 O A:SER60 2.3 17.6 1.0 O A:HOH382 2.4 20.5 1.0 O A:CYS64 2.4 15.3 1.0 O A:HOH366 2.4 17.1 1.0 OG A:SER72 2.5 21.9 1.0 O A:ARG73 2.5 21.2 1.0 CB A:SER72 3.3 22.2 1.0 C A:SER60 3.5 16.2 1.0 C A:CYS64 3.5 14.4 1.0 C A:ARG73 3.5 20.9 1.0 CA A:ASN65 4.0 15.4 1.0 N A:ARG73 4.0 23.2 1.0 CA A:SER60 4.0 14.7 1.0 C A:SER72 4.1 23.6 1.0 N A:ASN65 4.2 15.0 1.0 CB A:SER60 4.2 14.5 1.0 CA A:SER72 4.3 23.1 1.0 CA A:ARG73 4.4 24.2 1.0 N A:ASN74 4.4 20.6 1.0 N A:CYS64 4.5 14.9 1.0 C A:ARG61 4.6 19.1 1.0 N A:ARG61 4.6 17.1 1.0 CA A:ASN74 4.6 18.8 1.0 O A:ARG61 4.6 20.2 1.0 CA A:CYS64 4.6 14.6 1.0 CB A:THR69 4.7 17.7 1.0 O A:SER72 4.7 24.9 1.0 N A:ASP66 4.7 14.8 1.0 CL A:CL207 4.7 23.0 1.0 CB A:ASN74 4.7 18.5 1.0 OD1 A:ASN65 4.8 20.0 1.0 N A:TRP62 4.8 18.1 1.0 CB A:ASN65 4.8 17.1 1.0 CA A:ARG61 4.9 20.6 1.0 C A:ASN65 4.9 14.7 1.0 O A:THR69 4.9 20.8 1.0

Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na binding site number 2 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:Na202 b:59.2 occ:0.72 CG1 A:VAL109 2.0 26.7 1.0 OE2 A:GLU35 2.6 15.0 1.0 N A:ALA110 2.8 18.7 1.0 N A:VAL109 2.8 18.5 1.0 O A:HOH321 2.9 21.1 1.0 O A:HOH375 2.9 35.7 1.0 CB A:VAL109 3.1 24.1 1.0 CA A:VAL109 3.2 20.3 1.0 CD A:GLU35 3.4 14.2 1.0 OE1 A:GLU35 3.4 15.3 1.0 C A:VAL109 3.4 18.6 1.0 C A:TRP108 3.8 16.4 1.0 O A:HOH320 3.9 34.5 1.0 CA A:ALA110 3.9 18.7 1.0 CB A:ALA110 3.9 20.1 1.0 CA A:TRP108 4.3 14.9 1.0 CG2 A:VAL109 4.3 25.7 1.0 O A:VAL109 4.6 18.3 1.0 O A:TRP108 4.6 15.6 1.0 O A:HOH428 4.7 47.7 1.0 O A:HOH339 4.8 20.3 1.0 CG A:GLU35 4.8 14.4 1.0 CB A:TRP108 4.9 14.2 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