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Sodium in PDB 5ilf: The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand

Enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand

All present enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand:
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 Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand, PDB code: 5ilf was solved by A.Merlino, G.Ferraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.14 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.983, 77.983, 37.281, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 23.3

Other elements in 5ilf:

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand also contains other interesting chemical elements:

Platinum (Pt) 1 atom
Chlorine (Cl) 4 atoms

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 Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand (pdb code 5ilf). 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 Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand, PDB code: 5ilf:

Sodium binding site 1 out of 1 in 5ilf

Go back to Sodium Binding Sites List in 5ilf
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 Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand


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 Compound 4, A Platin(II) Compound Containing A O, S Bidentate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:25.7
occ:1.00
 O A:SER60 2.3 19.4 1.0
O A:HOH368 2.3 22.7 1.0
O A:HOH357 2.4 16.1 1.0
O A:ARG73 2.5 28.3 1.0
OG A:SER72 2.5 30.9 1.0
O A:CYS64 2.6 16.9 1.0
CB A:SER72 3.2 30.3 1.0
C A:SER60 3.5 18.1 1.0
C A:ARG73 3.6 27.5 1.0
C A:CYS64 3.7 16.9 1.0
CA A:ASN65 4.0 18.1 1.0
N A:ARG73 4.0 24.8 1.0
CA A:SER60 4.0 17.4 1.0
C A:SER72 4.0 29.4 1.0
CB A:SER60 4.2 17.4 1.0
CA A:SER72 4.3 30.7 1.0
N A:ASN65 4.3 16.5 1.0
CA A:ARG73 4.4 29.1 1.0
N A:ASN74 4.5 21.4 1.0
O A:SER72 4.5 26.2 1.0
N A:ARG61 4.6 20.2 1.0
N A:CYS64 4.6 16.1 1.0
OD1 A:ASN65 4.6 20.0 1.0
CA A:ASN74 4.6 20.4 1.0
N A:ASP66 4.6 16.3 1.0
CB A:THR69 4.6 21.4 1.0
C A:ARG61 4.6 23.8 1.0
CL A:CL203 4.7 28.1 1.0
O A:ARG61 4.7 27.4 1.0
CB A:ASN74 4.8 21.0 1.0
CA A:CYS64 4.8 17.9 1.0
CB A:ASN65 4.8 19.2 1.0
C A:ASN65 4.8 15.8 1.0
O A:HOH399 4.9 50.1 1.0
CA A:ARG61 4.9 23.3 1.0
N A:TRP62 4.9 21.4 1.0
O A:THR69 5.0 19.9 1.0

Reference:

J.Hildebrandt, N.Hafner, H.Gorls, D.Kritsch, G.Ferraro, M.Durst, I.B.Runnebaum, A.Merlino, W.Weigand. Platinum(II) O,S Complexes As Potential Metallodrugs Against Cisplatin Resistance. Dalton Trans V. 45 18876 2016.
ISSN: ESSN 1477-9234
PubMed: 27897281
DOI: 10.1039/C6DT01388K
Page generated: Tue Dec 15 11:06:13 2020

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