Atomistry » Sodium » PDB 5iaj-5imz » 5ii3
Atomistry »
  Sodium »
    PDB 5iaj-5imz »
      5ii3 »

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 Oct 7 21:36:28 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy