Atomistry » Sodium » PDB 6s08-6sez » 6sez
Atomistry »
  Sodium »
    PDB 6s08-6sez »
      6sez »

Sodium in PDB 6sez: X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 24H Exposure of Protein Crystals to Compound 1

Enzymatic activity of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 24H Exposure of Protein Crystals to Compound 1

All present enzymatic activity of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 24H Exposure of Protein Crystals to Compound 1:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 24H Exposure of Protein Crystals to Compound 1, PDB code: 6sez was solved by G.Ferraro, A.Giorgio, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.78 / 2.22
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.844, 77.844, 37.459, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 24.9

Other elements in 6sez:

The structure of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 24H Exposure of Protein Crystals to Compound 1 also contains other interesting chemical elements:

Gold (Au) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 24H Exposure of Protein Crystals to Compound 1 (pdb code 6sez). 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 X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 24H Exposure of Protein Crystals to Compound 1, PDB code: 6sez:

Sodium binding site 1 out of 1 in 6sez

Go back to Sodium Binding Sites List in 6sez
Sodium binding site 1 out of 1 in the X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 24H Exposure of Protein Crystals to Compound 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 24H Exposure of Protein Crystals to Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:42.6
occ:1.00
 O A:SER60 2.2 31.1 1.0
O A:CYS64 2.3 29.6 1.0
OG A:SER72 2.4 43.1 1.0
O A:HOH329 2.4 37.1 1.0
O A:ARG73 2.5 36.7 0.5
O A:ARG73 2.5 36.8 0.5
O1 A:NO3203 2.7 39.0 1.0
O3 A:NO3203 3.4 46.2 1.0
CB A:SER72 3.4 44.0 1.0
C A:SER60 3.4 33.1 1.0
N A:NO3203 3.5 41.8 1.0
C A:CYS64 3.5 26.1 1.0
C A:ARG73 3.6 37.9 0.5
C A:ARG73 3.6 38.0 0.5
N A:ARG73 3.9 42.6 0.5
CA A:ASN65 3.9 30.8 1.0
N A:ARG73 4.0 42.7 0.5
C A:SER72 4.0 44.6 1.0
N A:ASN65 4.1 28.7 1.0
CA A:SER60 4.1 29.8 1.0
CA A:SER72 4.3 45.4 1.0
CA A:ARG73 4.4 42.1 0.5
CA A:ARG73 4.4 42.3 0.5
O A:HOH302 4.4 57.8 1.0
O A:SER72 4.4 41.5 1.0
CB A:SER60 4.4 30.9 1.0
N A:ASN74 4.5 36.2 1.0
N A:CYS64 4.5 26.4 1.0
N A:ARG61 4.5 33.8 1.0
C A:ARG61 4.5 36.4 1.0
CB A:THR69 4.6 38.0 1.0
CA A:CYS64 4.6 27.3 1.0
N A:TRP62 4.6 33.5 1.0
CA A:ASN74 4.6 35.1 1.0
O A:ARG61 4.7 39.2 1.0
CB A:ASN74 4.7 33.4 1.0
O A:THR69 4.7 37.4 1.0
CB A:ASN65 4.7 32.3 1.0
CA A:ARG61 4.8 37.3 1.0
O2 A:NO3203 4.8 36.7 1.0
CG2 A:THR69 4.9 34.7 1.0
N A:ASP66 4.9 29.2 1.0
N A:TRP63 5.0 30.7 1.0

Reference:

G.Ferraro, A.Giorgio, A.M.Mansour, A.Merlino. Protein-Mediated Disproportionation of Au(I): Insights From the Structures of Adducts of Au(III) Compounds Bearing N,N-Pyridylbenzimidazole Derivatives with Lysozyme. Dalton Trans V. 48 14027 2019.
ISSN: ESSN 1477-9234
PubMed: 31490509
DOI: 10.1039/C9DT02729G
Page generated: Tue Oct 8 13:27:27 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