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 Dec 15 12:59:37 2020

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