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Gold in PDB 6seu: X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H Exposure of Protein Crystals to Compound 2

Enzymatic activity of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H Exposure of Protein Crystals to Compound 2

All present enzymatic activity of X-Ray Structure of the Gold/Lysozyme Adduct Formed Upon 21H Exposure of Protein Crystals to Compound 2:
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 2, PDB code: 6seu 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) 34.73 / 1.95
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.953, 76.953, 38.889, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 26

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 2 (pdb code 6seu). 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 2, PDB code: 6seu:
Jump to Gold binding site number: 1; 2; 3; 4;

Gold binding site 1 out of 4 in 6seu

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au207

b:37.5
occ:0.20
 CE A:MET105 2.6 14.1 0.5
CE3 A:TRP108 3.0 20.1 1.0
CZ3 A:TRP28 3.0 18.1 1.0
CD2 A:TRP108 3.0 21.9 1.0
CE3 A:TRP28 3.1 18.3 1.0
CZ3 A:TRP108 3.2 21.3 1.0
SD A:MET105 3.4 24.4 0.5
CE2 A:TRP108 3.4 20.9 1.0
CH2 A:TRP108 3.6 20.4 1.0
CZ2 A:TRP108 3.7 20.6 1.0
CG A:TRP108 3.7 20.1 1.0
CG A:MET105 3.8 22.6 0.5
CB A:ALA31 3.8 17.6 1.0
CH2 A:TRP28 3.9 17.5 1.0
SD A:MET105 4.0 14.7 0.5
CG A:MET105 4.2 15.7 0.5
NE1 A:TRP108 4.2 21.6 1.0
CD2 A:TRP28 4.2 17.5 1.0
CD2 A:LEU56 4.3 23.0 1.0
CD1 A:TRP108 4.3 22.1 1.0
CB A:MET105 4.4 21.0 0.5
CB A:TRP108 4.4 19.2 1.0
CB A:MET105 4.6 16.0 0.5
CZ2 A:TRP28 4.9 17.7 1.0
CE A:MET105 4.9 24.0 0.5
CE2 A:TRP28 5.0 16.9 1.0

Gold binding site 2 out of 4 in 6seu

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au208

b:35.3
occ:0.40
 AU A:AU208 0.0 35.3 0.4
ND1 A:HIS15 2.3 27.9 1.0
AU A:AU208 2.8 62.7 0.2
ND2 A:ASN93 2.8 30.4 1.0
CG A:HIS15 3.1 25.7 1.0
CB A:HIS15 3.2 25.1 1.0
CE1 A:HIS15 3.3 29.2 1.0
CG1 A:VAL92 3.5 20.1 1.0
CG A:ASN93 3.8 31.3 1.0
O A:HIS15 3.8 25.3 1.0
CB A:VAL92 3.8 20.2 1.0
O A:THR89 3.8 22.3 1.0
CA A:HIS15 3.9 22.9 1.0
CA A:THR89 4.0 22.8 1.0
OD1 A:ASN93 4.0 38.5 1.0
CG2 A:THR89 4.1 25.5 1.0
CD2 A:HIS15 4.2 26.3 1.0
NE2 A:HIS15 4.4 28.8 1.0
C A:HIS15 4.4 24.1 1.0
C A:THR89 4.4 22.6 1.0
CB A:THR89 4.5 24.6 1.0
O A:HOH309 4.5 41.1 1.0
N A:ASN93 4.6 21.1 1.0
OG1 A:THR89 4.6 24.3 1.0
CG2 A:VAL92 4.6 20.1 1.0
NZ A:LYS96 4.7 21.5 1.0
O A:HOH337 4.9 40.0 1.0
CA A:VAL92 4.9 19.3 1.0
C A:VAL92 5.0 19.8 1.0
CB A:ASN93 5.0 26.8 1.0

Gold binding site 3 out of 4 in 6seu

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au208

b:62.7
occ:0.25
 AU A:AU208 0.0 62.7 0.2
ND1 A:HIS15 2.7 27.9 1.0
AU A:AU208 2.8 35.3 0.4
CE1 A:HIS15 3.4 29.2 1.0
CG A:HIS15 3.6 25.7 1.0
CA A:HIS15 3.8 22.9 1.0
CB A:HIS15 4.0 25.1 1.0
O A:HIS15 4.3 25.3 1.0
NE2 A:HIS15 4.4 28.8 1.0
C A:HIS15 4.5 24.1 1.0
CD2 A:HIS15 4.5 26.3 1.0
O A:ARG14 4.6 23.8 1.0
ND2 A:ASN93 4.8 30.4 1.0
O A:HOH337 4.8 40.0 1.0
N A:HIS15 4.8 23.7 1.0

Gold binding site 4 out of 4 in 6seu

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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 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au209

b:50.0
occ:0.40
 O A:HOH394 2.1 10.6 0.4
NE2 A:HIS15 2.5 28.8 1.0
CD2 A:HIS15 3.0 26.3 1.0
O A:HOH310 3.0 31.6 1.0
CG1 A:ILE88 3.3 20.9 1.0
NH2 A:ARG14 3.3 29.2 1.0
CE1 A:HIS15 3.6 29.2 1.0
OD2 A:ASP87 3.9 32.2 1.0
NH1 A:ARG14 3.9 34.6 1.0
N A:ILE88 3.9 20.0 1.0
CZ A:ARG14 4.0 31.6 1.0
CB A:ALA11 4.0 21.4 1.0
CD1 A:ILE88 4.2 21.7 1.0
CG A:HIS15 4.3 25.7 1.0
CG A:ASP87 4.3 28.1 1.0
OD1 A:ASP87 4.4 26.1 1.0
CB A:ILE88 4.4 20.3 1.0
ND1 A:HIS15 4.5 27.9 1.0
CA A:ILE88 4.6 20.5 1.0
N A:THR89 4.6 22.6 1.0
CA A:ALA11 4.7 21.3 1.0
OG1 A:THR89 4.7 24.3 1.0
C A:ASP87 4.8 20.5 1.0
O A:ALA11 4.8 23.2 1.0
CA A:ASP87 4.8 22.1 1.0
C A:ILE88 4.9 21.2 1.0
CG2 A:ILE88 5.0 22.3 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 14:38:54 2024

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