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Gold in PDB 6sex: X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H Exposure of Protein Crystals to Compound 1

Enzymatic activity of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H Exposure of Protein Crystals to Compound 1

All present enzymatic activity of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H 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 21H Exposure of Protein Crystals to Compound 1, PDB code: 6sex 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) 34.78 / 1.78
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.735, 76.735, 38.981, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 22.4

Gold Binding Sites:

The binding sites of Gold atom in the X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H Exposure of Protein Crystals to Compound 1 (pdb code 6sex). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 4 binding sites of Gold where determined in the X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H Exposure of Protein Crystals to Compound 1, PDB code: 6sex:
Jump to Gold binding site number: 1; 2; 3; 4;

Gold binding site 1 out of 4 in 6sex

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Gold binding site 1 out of 4 in the X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H 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 21H Exposure of Protein Crystals to Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au212

b:17.1
occ:0.25
 O A:HOH459 2.3 0.5 0.2
CE A:MET105 2.4 8.0 0.5
SD A:MET105 2.5 27.9 0.5
CZ3 A:TRP28 2.9 18.0 1.0
CE A:MET105 3.0 27.0 0.5
CE3 A:TRP28 3.1 16.6 1.0
CE3 A:TRP108 3.2 15.5 1.0
CD2 A:TRP108 3.2 15.2 1.0
CE2 A:TRP108 3.5 15.0 1.0
CZ3 A:TRP108 3.6 15.5 1.0
CB A:ALA31 3.7 13.3 1.0
SD A:MET105 3.8 7.6 0.5
CH2 A:TRP108 3.8 15.5 1.0
CZ2 A:TRP108 3.8 15.1 1.0
CG A:TRP108 3.8 14.6 1.0
CH2 A:TRP28 3.9 18.0 1.0
CG A:MET105 4.1 9.4 0.5
CD2 A:TRP28 4.1 15.3 1.0
CD2 A:LEU56 4.1 19.9 0.8
NE1 A:TRP108 4.2 16.1 1.0
CG A:MET105 4.3 22.7 0.5
CD1 A:TRP108 4.4 15.9 1.0
CD2 A:LEU56 4.4 15.0 0.2
CB A:TRP108 4.5 14.1 1.0
CB A:MET105 4.6 10.0 0.5
CB A:MET105 4.8 18.9 0.5
CZ2 A:TRP28 4.8 16.7 1.0
CE2 A:TRP28 4.9 15.7 1.0
CG A:LEU56 4.9 15.1 0.2
CA A:TRP28 5.0 12.8 1.0

Gold binding site 2 out of 4 in 6sex

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Gold binding site 2 out of 4 in the X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H 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 21H Exposure of Protein Crystals to Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au213

b:22.5
occ:0.40
 AU A:AU213 0.0 22.5 0.4
ND1 A:HIS15 2.3 27.3 1.0
AU A:AU213 2.5 51.5 0.4
OD1 A:ASN93 2.7 16.7 0.5
CG A:HIS15 3.0 23.9 1.0
CB A:HIS15 3.1 22.7 1.0
CE1 A:HIS15 3.3 29.6 1.0
CG1 A:VAL92 3.5 17.0 1.0
CG A:ASN93 3.6 18.3 0.5
CB A:VAL92 3.7 15.6 1.0
O A:HIS15 3.8 23.3 1.0
CA A:HIS15 3.8 21.6 1.0
O A:THR89 3.9 17.9 1.0
ND2 A:ASN93 3.9 20.7 0.5
CA A:THR89 4.0 19.1 1.0
CG2 A:THR89 4.0 22.9 1.0
CD2 A:HIS15 4.2 23.3 1.0
O A:HOH443 4.2 25.1 0.4
C A:HIS15 4.3 21.2 1.0
NE2 A:HIS15 4.3 23.2 1.0
CB A:THR89 4.4 20.4 1.0
C A:THR89 4.5 18.2 1.0
N A:ASN93 4.5 16.3 0.5
OG1 A:THR89 4.5 22.1 1.0
N A:ASN93 4.6 16.4 0.5
CG2 A:VAL92 4.6 15.1 1.0
NZ A:LYS96 4.8 20.6 1.0
CB A:ASN93 4.9 17.7 0.5
CA A:VAL92 4.9 15.8 1.0
C A:VAL92 4.9 16.4 1.0
N A:THR89 5.0 18.1 1.0

Gold binding site 3 out of 4 in 6sex

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Gold binding site 3 out of 4 in the X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H 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 21H Exposure of Protein Crystals to Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au213

b:51.5
occ:0.40
 AU A:AU213 0.0 51.5 0.4
O A:HOH443 1.9 25.1 0.4
AU A:AU213 2.5 22.5 0.4
ND1 A:HIS15 2.7 27.3 1.0
CE1 A:HIS15 3.4 29.6 1.0
CG A:HIS15 3.6 23.9 1.0
CA A:HIS15 3.7 21.6 1.0
CB A:HIS15 3.9 22.7 1.0
O A:HIS15 4.2 23.3 1.0
OD1 A:ASN93 4.2 16.7 0.5
O A:HOH328 4.3 38.0 1.0
C A:HIS15 4.4 21.2 1.0
NE2 A:HIS15 4.5 23.2 1.0
CD2 A:HIS15 4.6 23.3 1.0
CG2 A:THR89 4.7 22.9 1.0
O A:HOH304 4.8 41.9 1.0
N A:HIS15 4.8 21.9 1.0
O A:ARG14 4.8 20.8 1.0
ND2 A:ASN93 4.9 20.7 0.5
OG1 A:THR89 5.0 22.1 1.0

Gold binding site 4 out of 4 in 6sex

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Gold binding site 4 out of 4 in the X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H 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 4 of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H Exposure of Protein Crystals to Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au214

b:22.8
occ:0.30
 O A:HOH435 2.1 0.5 0.3
NE2 A:HIS15 2.1 23.2 1.0
O A:HOH306 2.8 21.1 0.7
CD2 A:HIS15 2.9 23.3 1.0
NH2 A:ARG14 3.2 25.4 1.0
CE1 A:HIS15 3.2 29.6 1.0
CG1 A:ILE88 3.3 17.7 1.0
OD1 A:ASP87 3.8 25.6 0.5
N A:ILE88 3.8 17.3 1.0
OD1 A:ASP87 3.9 19.0 0.5
CG A:HIS15 4.0 23.9 1.0
CB A:ALA11 4.1 16.1 1.0
CZ A:ARG14 4.1 25.2 1.0
CG A:ASP87 4.2 24.1 0.5
ND1 A:HIS15 4.2 27.3 1.0
CD1 A:ILE88 4.2 18.8 1.0
NH1 A:ARG14 4.3 28.8 1.0
OD2 A:ASP87 4.3 24.1 0.5
N A:THR89 4.3 18.1 1.0
CB A:ILE88 4.4 17.8 1.0
CA A:ILE88 4.4 17.9 1.0
OG1 A:THR89 4.5 22.1 1.0
C A:ILE88 4.6 18.0 1.0
O A:ALA11 4.7 17.8 1.0
C A:ASP87 4.8 16.8 0.5
CA A:ALA11 4.8 16.1 1.0
C A:ASP87 4.8 18.2 0.5
CA A:ASP87 4.9 20.2 0.5
CG A:ASP87 4.9 19.2 0.5
CG2 A:ILE88 4.9 19.1 1.0
CA A:ASP87 5.0 18.0 0.5

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 14:39:53 2024

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