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Sodium in PDB 5ii3: The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 3, 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 3, 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 3, 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 3, A Platin(II) Compound Containing A O, S Bidentate Ligand, PDB code: 5ii3 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) 55.30 / 1.78
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.206, 78.206, 37.005, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 19

Other elements in 5ii3:

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Hen Egg White Lysozyme and Compound 3, A Platin(II) Compound Containing A O, S Bidentate Ligand also contains other interesting chemical elements:

Platinum (Pt) 1 atom
Chlorine (Cl) 5 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 3, A Platin(II) Compound Containing A O, S Bidentate Ligand (pdb code 5ii3). 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 3, A Platin(II) Compound Containing A O, S Bidentate Ligand, PDB code: 5ii3:

Sodium binding site 1 out of 1 in 5ii3

Go back to Sodium Binding Sites List in 5ii3
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 3, 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 3, A Platin(II) Compound Containing A O, S Bidentate Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:15.6
occ:1.00
 O A:SER60 2.3 15.4 1.0
O A:HOH380 2.4 15.6 1.0
O A:CYS64 2.4 14.7 1.0
O A:HOH361 2.4 13.7 1.0
O A:ARG73 2.5 19.4 1.0
OG A:SER72 2.6 19.7 1.0
CB A:SER72 3.2 19.2 1.0
C A:SER60 3.4 16.7 1.0
C A:CYS64 3.5 13.0 1.0
C A:ARG73 3.5 20.2 1.0
CA A:ASN65 3.8 13.6 1.0
N A:ARG73 4.0 19.2 1.0
CA A:SER60 4.0 13.5 1.0
N A:ASN65 4.1 13.2 1.0
C A:SER72 4.1 20.7 1.0
CB A:SER60 4.2 14.2 1.0
CA A:SER72 4.3 20.2 1.0
CA A:ARG73 4.4 21.0 1.0
N A:ASN74 4.4 17.7 1.0
N A:CYS64 4.4 13.6 1.0
O A:ARG61 4.5 21.1 1.0
N A:ASP66 4.5 13.0 1.0
N A:ARG61 4.6 16.8 1.0
C A:ARG61 4.6 19.8 1.0
CA A:CYS64 4.6 12.7 1.0
CA A:ASN74 4.6 19.0 1.0
O A:SER72 4.6 18.5 1.0
OD1 A:ASN65 4.6 17.5 1.0
O A:HOH412 4.7 31.1 1.0
CL A:CL207 4.7 19.7 1.0
CB A:THR69 4.7 18.9 1.0
CB A:ASN74 4.7 18.3 1.0
C A:ASN65 4.7 12.2 1.0
CB A:ASN65 4.8 15.1 1.0
CA A:ARG61 4.8 20.1 1.0
N A:TRP62 4.9 19.8 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: Mon Aug 18 00:16:38 2025

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