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Gold 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:

Chlorine (Cl) 1 atom
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 3 Days Exposure of Protein Crystals to Compound 1 (pdb code 6set). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 5 binding sites of Gold where 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:
Jump to Gold binding site number: 1; 2; 3; 4; 5;

Gold binding site 1 out of 5 in 6set

Go back to Gold Binding Sites List in 6set
Gold binding site 1 out of 5 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 Gold with other atoms in the Au 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:Au210

b:37.1
occ:0.35
 AU A:AU210 0.0 37.1 0.3
AU A:AU210 1.8 32.8 0.1
O A:PHE34 3.1 24.3 1.0
O A:GLU35 3.9 25.1 1.0
C A:PHE34 4.0 20.9 1.0
C A:GLU35 4.2 23.0 1.0
OD1 A:ASN37 4.3 29.7 0.4
O A:HOH312 4.5 21.2 1.0
N A:SER36 4.5 23.2 1.0
O A:LYS33 4.6 20.3 1.0
N A:ASN37 4.7 24.9 0.6
N A:ASN37 4.7 25.4 0.4
N A:GLU35 4.7 22.0 1.0
CA A:PHE34 4.7 20.7 1.0
CA A:GLU35 4.8 20.7 1.0
CA A:SER36 4.9 23.9 1.0
C A:SER36 5.0 24.5 1.0

Gold binding site 2 out of 5 in 6set

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Gold binding site 2 out of 5 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 Gold with other atoms in the Au binding site number 2 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:Au210

b:32.8
occ:0.15
 AU A:AU210 0.0 32.8 0.1
AU A:AU210 1.8 37.1 0.3
O A:PHE34 3.2 24.3 1.0
OD1 A:ASN37 3.3 29.7 0.4
O A:LYS33 3.8 20.3 1.0
C A:PHE34 3.8 20.9 1.0
CA A:PHE34 3.9 20.7 1.0
CG A:ASN37 4.3 29.1 0.4
NH1 A:ARG114 4.5 23.7 1.0
N A:ASN37 4.6 24.9 0.6
N A:ASN37 4.6 25.4 0.4
C A:LYS33 4.7 21.4 1.0
CB A:ASN37 4.8 26.1 0.6
N A:PHE34 4.8 20.8 1.0
N A:GLU35 4.8 22.0 1.0
CD1 A:PHE34 4.8 24.1 1.0
CB A:ASN37 4.9 28.0 0.4
CB A:PHE34 5.0 23.4 1.0

Gold binding site 3 out of 5 in 6set

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Gold binding site 3 out of 5 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 Gold with other atoms in the Au binding site number 3 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:Au211

b:27.7
occ:0.30
 AU A:AU211 0.0 27.7 0.3
AU A:AU211 1.8 40.6 0.2
O A:HOH306 3.0 33.7 1.0
O1 A:NO3207 3.1 43.6 1.0
O A:ASN19 3.2 26.9 1.0
O2 A:NO3207 3.2 39.3 1.0
N A:NO3207 3.6 41.0 1.0
O A:HOH441 3.8 49.8 1.0
ND2 A:ASN19 4.0 45.3 1.0
C A:ASN19 4.3 29.2 1.0
N A:ARG21 4.4 28.3 1.0
CA A:TYR20 4.7 25.8 1.0
CG A:ASN19 4.8 43.5 1.0
N A:GLY22 4.8 26.0 1.0
N A:TYR20 4.9 25.3 1.0
O3 A:NO3207 4.9 44.7 1.0
O A:HOH346 5.0 31.3 1.0
CB A:ASN19 5.0 37.4 1.0

Gold binding site 4 out of 5 in 6set

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Gold binding site 4 out of 5 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 Gold with other atoms in the Au binding site number 4 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:Au211

b:40.6
occ:0.20
 AU A:AU211 0.0 40.6 0.2
AU A:AU211 1.8 27.7 0.3
ND2 A:ASN19 2.3 45.3 1.0
O1 A:NO3207 2.7 43.6 1.0
O A:ASN19 2.7 26.9 1.0
CG A:ASN19 3.3 43.5 1.0
N A:NO3207 3.6 41.0 1.0
CB A:ASN19 3.8 37.4 1.0
C A:ASN19 3.9 29.2 1.0
O2 A:NO3207 4.0 39.3 1.0
OD1 A:ASN19 4.2 46.9 1.0
N A:GLY22 4.4 26.0 1.0
CA A:ASN19 4.5 32.3 1.0
O A:HOH306 4.5 33.7 1.0
O A:HOH313 4.6 29.2 1.0
CA A:GLY22 4.7 23.9 1.0
O3 A:NO3207 4.9 44.7 1.0
N A:TYR20 4.9 25.3 1.0
N A:ARG21 5.0 28.3 1.0

Gold binding site 5 out of 5 in 6set

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Gold binding site 5 out of 5 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 Gold with other atoms in the Au binding site number 5 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:Au212

b:42.9
occ:0.30
 O A:THR118 3.0 28.0 1.0
O A:HOH378 3.1 33.9 1.0
C A:THR118 4.1 29.9 1.0
N A:THR118 4.2 27.7 1.0
N A:GLY117 4.2 24.9 1.0
CG2 A:VAL120 4.3 30.3 1.0
CA A:GLY117 4.4 27.9 1.0
C A:GLY117 4.4 30.1 1.0
O A:HOH393 4.6 49.3 1.0
CG1 A:VAL120 4.7 28.5 1.0
N A:VAL120 4.8 30.7 1.0
CA A:THR118 4.9 29.5 1.0
O A:CYS115 5.0 23.2 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 14:38:26 2024

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