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Sodium in PDB 7bcx: The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.

Enzymatic activity of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.

All present enzymatic activity of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours.:
3.2.1.17;

Protein crystallography data

The structure of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours., PDB code: 7bcx 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) 27.07 / 1.06
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.211, 78.211, 37.507, 90, 90, 90
R / Rfree (%) 16.1 / 18.5

Other elements in 7bcx:

The structure of The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. also contains other interesting chemical elements:

Ruthenium (Ru) 3 atoms
Chlorine (Cl) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours. (pdb code 7bcx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 Hours., PDB code: 7bcx:

Sodium binding site 1 out of 1 in 7bcx

Go back to Sodium Binding Sites List in 7bcx
Sodium binding site 1 out of 1 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 8 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 8 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:13.5
occ:0.87
O A:SER60 2.3 15.1 1.0
O A:HOH388 2.4 18.4 1.0
O A:CYS64 2.4 12.7 1.0
O A:ARG73 2.4 18.1 1.0
OG A:SER72 2.5 20.5 1.0
O A:HOH366 2.5 14.0 1.0
CB A:SER72 3.3 20.6 1.0
C A:SER60 3.5 14.0 1.0
C A:CYS64 3.5 11.9 1.0
C A:ARG73 3.5 18.5 1.0
CA A:ASN65 3.9 13.1 1.0
N A:ARG73 3.9 21.1 1.0
CA A:SER60 4.1 12.5 1.0
C A:SER72 4.1 22.1 1.0
N A:ASN65 4.1 12.6 1.0
CB A:SER60 4.2 12.8 1.0
CA A:ARG73 4.3 21.1 1.0
CA A:SER72 4.3 21.0 1.0
N A:ASN74 4.4 17.5 1.0
N A:CYS64 4.4 12.5 1.0
O A:HOH393 4.5 31.8 1.0
CA A:ASN74 4.6 16.6 1.0
N A:ARG61 4.6 15.5 1.0
C A:ARG61 4.6 18.2 1.0
CA A:CYS64 4.6 12.5 1.0
O A:SER72 4.6 23.7 1.0
CB A:ASN74 4.7 16.1 1.0
O A:ARG61 4.7 19.3 1.0
N A:ASP66 4.7 12.4 1.0
CB A:THR69 4.7 14.3 1.0
OD1 A:ASN65 4.7 17.5 1.0
CL A:CL204 4.7 16.6 0.8
CB A:ASN65 4.8 15.1 1.0
N A:TRP62 4.8 17.7 1.0
CA A:ARG61 4.8 18.0 1.0
C A:ASN65 4.9 12.3 1.0
O A:THR69 5.0 17.6 1.0
N A:TRP63 5.0 13.5 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 17:20:15 2021

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