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Sodium in PDB 5nj1: The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Arsenoplatin-1

Enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Arsenoplatin-1

All present enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Arsenoplatin-1:
3.2.1.17;

Protein crystallography data

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Arsenoplatin-1, PDB code: 5nj1 was solved by G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.22 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.512, 79.512, 35.906, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 24.2

Other elements in 5nj1:

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Arsenoplatin-1 also contains other interesting chemical elements:

Arsenic (As) 1 atom
Platinum (Pt) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Arsenoplatin-1 (pdb code 5nj1). 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 X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Arsenoplatin-1, PDB code: 5nj1:

Sodium binding site 1 out of 1 in 5nj1

Go back to Sodium Binding Sites List in 5nj1
Sodium binding site 1 out of 1 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Arsenoplatin-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Arsenoplatin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:33.2
occ:1.00
OG A:SER72 2.2 33.3 1.0
O A:SER60 2.3 32.8 1.0
O A:CYS64 2.4 25.2 1.0
O A:ARG73 2.5 36.5 1.0
O A:HOH313 2.7 36.5 1.0
O3 A:NO3205 2.7 31.7 1.0
CB A:SER72 3.2 41.0 1.0
C A:SER60 3.4 29.4 1.0
C A:ARG73 3.4 32.8 1.0
C A:CYS64 3.5 27.8 1.0
N A:NO3205 3.7 40.5 1.0
O2 A:NO3205 3.8 44.6 1.0
N A:ARG73 3.8 36.3 1.0
CA A:ASN65 4.0 33.7 1.0
C A:SER72 4.1 39.5 1.0
CA A:SER60 4.1 31.1 1.0
N A:ASN65 4.1 28.8 1.0
CA A:ARG73 4.2 33.8 1.0
CB A:SER60 4.3 30.1 1.0
CA A:SER72 4.3 40.9 1.0
N A:ASN74 4.4 29.5 1.0
O A:ARG61 4.4 31.8 1.0
N A:CYS64 4.4 27.9 1.0
C A:ARG61 4.4 32.7 1.0
N A:ARG61 4.5 29.9 1.0
CA A:CYS64 4.6 26.6 1.0
O A:SER72 4.6 39.6 1.0
CA A:ASN74 4.6 33.2 1.0
CB A:THR69 4.7 30.3 1.0
CA A:ARG61 4.7 34.5 1.0
N A:TRP62 4.8 31.8 1.0
O1 A:NO3205 4.8 35.2 1.0
O A:THR69 4.9 31.6 1.0
OG A:SER60 4.9 27.7 1.0
N A:ASP66 4.9 27.6 1.0
CB A:ASN65 4.9 33.3 1.0
CB A:ASN74 5.0 31.9 1.0
N A:TRP63 5.0 29.5 1.0
C A:ASN65 5.0 27.3 1.0

Reference:

D.Miodragovic, A.Merlino, E.P.Swindell, A.Bogachkov, R.W.Ahn, S.Abuhadba, G.Ferraro, T.Marzo, A.P.Mazar, L.Messori, T.V.O'halloran. Arsenoplatin-1 Is A Dual Pharmacophore Anticancer Agent. J.Am.Chem.Soc. V. 141 6453 2019.
ISSN: ESSN 1520-5126
PubMed: 30943017
DOI: 10.1021/JACS.8B13681
Page generated: Tue Dec 15 11:21:03 2020

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