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Sodium in PDB 6set: X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 3 Days Exposure of Protein Crystals to Compound 1

Enzymatic activity of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 3 Days Exposure of Protein Crystals to Compound 1

All present enzymatic activity of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 3 Days 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 3 Days Exposure of Protein Crystals to Compound 1, PDB code: 6set 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) 30.86 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.448, 77.448, 37.316, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 21.5

Other elements in 6set:

The structure of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 3 Days Exposure of Protein Crystals to Compound 1 also contains other interesting chemical elements:

Gold (Au) 5 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 3 Days Exposure of Protein Crystals to Compound 1 (pdb code 6set). 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 3 Days Exposure of Protein Crystals to Compound 1, PDB code: 6set:

Sodium binding site 1 out of 1 in 6set

Go back to Sodium Binding Sites List in 6set
Sodium binding site 1 out of 1 in the X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 3 Days 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 3 Days Exposure of Protein Crystals to Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na213

b:49.2
occ:1.00
O A:HOH383 2.2 15.2 1.0
O A:HOH312 2.6 21.2 1.0
OE1 A:GLU35 2.9 20.9 1.0
O A:GLU35 3.9 25.1 1.0
CD A:GLU35 4.1 23.3 1.0
CA A:GLU35 4.2 20.7 1.0
OE1 A:GLN57 4.4 21.9 1.0
CG A:GLN57 4.4 23.6 1.0
O A:PHE34 4.5 24.3 1.0
O A:HOH364 4.5 28.2 1.0
C A:GLU35 4.6 23.0 1.0
O A:HOH330 4.6 25.1 1.0
OE2 A:GLU35 4.8 24.2 1.0
ND2 A:ASN44 4.8 24.9 1.0
CB A:GLN57 4.9 21.8 1.0
CD A:GLN57 4.9 23.1 1.0
CB A:GLU35 5.0 21.4 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 12:59:35 2020

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