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Gold 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:

Sodium (Na) 1 atom

Gold Binding Sites:

The binding sites of Gold 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 Gold atom.
In total 3 binding sites of Gold where determined in the X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 24H Exposure of Protein Crystals to Compound 1, PDB code: 6sez:
Jump to Gold binding site number: 1; 2; 3;

Gold binding site 1 out of 3 in 6sez

Go back to Gold Binding Sites List in 6sez
Gold binding site 1 out of 3 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 Gold with other atoms in the Au 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:Au207

b:59.0
occ:0.40
 ND1 A:HIS15 2.8 46.2 1.0
OD1 A:ASN93 2.9 43.8 1.0
CB A:HIS15 3.0 39.7 1.0
CG A:HIS15 3.2 40.7 1.0
O A:HIS15 3.5 38.0 1.0
CG1 A:VAL92 3.5 27.2 1.0
CA A:HIS15 3.7 38.5 1.0
O A:THR89 3.7 32.1 1.0
O A:HOH338 3.8 39.4 0.6
CG A:ASN93 3.8 46.0 1.0
CB A:VAL92 3.9 28.0 1.0
CA A:THR89 3.9 33.6 1.0
CE1 A:HIS15 3.9 48.0 1.0
CG2 A:THR89 4.1 32.0 1.0
C A:HIS15 4.1 36.4 1.0
OG1 A:THR89 4.3 38.4 1.0
C A:THR89 4.3 32.0 1.0
ND2 A:ASN93 4.3 48.4 1.0
CB A:THR89 4.3 33.4 1.0
CD2 A:HIS15 4.4 41.1 1.0
O A:HOH332 4.6 53.9 1.0
N A:ASN93 4.7 34.5 1.0
CG2 A:VAL92 4.7 24.9 1.0
NE2 A:HIS15 4.8 41.2 1.0
O A:HOH326 4.8 41.4 1.0
NZ A:LYS96 4.9 43.6 1.0
CB A:ASN93 5.0 41.6 1.0

Gold binding site 2 out of 3 in 6sez

Go back to Gold Binding Sites List in 6sez
Gold binding site 2 out of 3 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 Gold with other atoms in the Au binding site number 2 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:Au208

b:56.0
occ:0.30
 CZ3 A:TRP28 3.0 28.2 1.0
CE3 A:TRP28 3.2 25.1 1.0
SD A:MET105 3.2 35.3 1.0
CE3 A:TRP108 3.2 27.3 1.0
CD2 A:TRP108 3.3 27.2 1.0
CZ3 A:TRP108 3.4 27.3 1.0
CE2 A:TRP108 3.7 27.9 1.0
CH2 A:TRP108 3.8 29.5 1.0
CB A:ALA31 3.8 24.0 1.0
CH2 A:TRP28 3.9 29.2 1.0
CG A:MET105 3.9 35.6 1.0
CZ2 A:TRP108 3.9 29.9 1.0
CG A:TRP108 4.0 27.5 1.0
CD2 A:TRP28 4.1 27.5 1.0
CE A:MET105 4.1 42.5 1.0
CD2 A:LEU56 4.3 31.9 1.0
CB A:MET105 4.3 32.2 1.0
NE1 A:TRP108 4.5 28.5 1.0
CD1 A:TRP108 4.6 28.4 1.0
CB A:TRP108 4.6 27.3 1.0
CZ2 A:TRP28 4.7 29.0 1.0
CE2 A:TRP28 4.8 27.8 1.0
CA A:TRP28 4.8 26.1 1.0
CA A:MET105 4.9 31.0 1.0

Gold binding site 3 out of 3 in 6sez

Go back to Gold Binding Sites List in 6sez
Gold binding site 3 out of 3 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 Gold with other atoms in the Au binding site number 3 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:Au209

b:55.3
occ:0.25
 O A:HOH380 1.9 0.5 0.2
NE2 A:HIS15 2.5 41.2 1.0
CD2 A:HIS15 3.2 41.1 1.0
CG1 A:ILE88 3.4 39.7 1.0
OD1 A:ASP87 3.5 42.7 1.0
NH2 A:ARG14 3.5 64.8 1.0
CE1 A:HIS15 3.6 48.0 1.0
O A:HOH348 3.6 45.9 1.0
N A:ILE88 3.9 35.5 1.0
CD1 A:ILE88 4.3 38.9 1.0
CB A:ALA11 4.3 35.4 1.0
CG A:HIS15 4.5 40.7 1.0
CB A:ILE88 4.5 37.2 1.0
CZ A:ARG14 4.6 63.2 1.0
CG A:ASP87 4.6 46.1 1.0
ND1 A:HIS15 4.6 46.2 1.0
CA A:ASP87 4.6 37.9 1.0
N A:THR89 4.6 34.7 1.0
CA A:ILE88 4.7 37.1 1.0
OG1 A:THR89 4.7 38.4 1.0
C A:ASP87 4.7 35.8 1.0
C A:ILE88 4.9 37.2 1.0
CG2 A:ILE88 4.9 35.1 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: Wed Jul 10 14:39:55 2024

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