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Gold in PDB 4zfp: A New Crystal Structure For the Adduct Formed in the Reaction Between AUSAC2, A Cytotoxic Homoleptic Gold(I) Compound with the Saccharinate Ligand, and the Model Protein Hen Egg White Lysozyme

Enzymatic activity of A New Crystal Structure For the Adduct Formed in the Reaction Between AUSAC2, A Cytotoxic Homoleptic Gold(I) Compound with the Saccharinate Ligand, and the Model Protein Hen Egg White Lysozyme

All present enzymatic activity of A New Crystal Structure For the Adduct Formed in the Reaction Between AUSAC2, A Cytotoxic Homoleptic Gold(I) Compound with the Saccharinate Ligand, and the Model Protein Hen Egg White Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of A New Crystal Structure For the Adduct Formed in the Reaction Between AUSAC2, A Cytotoxic Homoleptic Gold(I) Compound with the Saccharinate Ligand, and the Model Protein Hen Egg White Lysozyme, PDB code: 4zfp was solved by A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.86 / 1.96
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.584, 77.584, 37.111, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 23.5

Gold Binding Sites:

The binding sites of Gold atom in the A New Crystal Structure For the Adduct Formed in the Reaction Between AUSAC2, A Cytotoxic Homoleptic Gold(I) Compound with the Saccharinate Ligand, and the Model Protein Hen Egg White Lysozyme (pdb code 4zfp). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 3 binding sites of Gold where determined in the A New Crystal Structure For the Adduct Formed in the Reaction Between AUSAC2, A Cytotoxic Homoleptic Gold(I) Compound with the Saccharinate Ligand, and the Model Protein Hen Egg White Lysozyme, PDB code: 4zfp:
Jump to Gold binding site number: 1; 2; 3;

Gold binding site 1 out of 3 in 4zfp

Go back to Gold Binding Sites List in 4zfp
Gold binding site 1 out of 3 in the A New Crystal Structure For the Adduct Formed in the Reaction Between AUSAC2, A Cytotoxic Homoleptic Gold(I) Compound with the Saccharinate Ligand, and the Model Protein Hen Egg White Lysozyme


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of A New Crystal Structure For the Adduct Formed in the Reaction Between AUSAC2, A Cytotoxic Homoleptic Gold(I) Compound with the Saccharinate Ligand, and the Model Protein Hen Egg White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au208

b:33.1
occ:0.40
 SD A:MET105 2.4 32.0 0.5
O A:HOH397 2.5 12.5 0.4
CE A:MET105 2.6 19.0 0.5
CE A:MET105 3.0 32.5 0.5
CZ3 A:TRP28 3.2 25.7 1.0
CE3 A:TRP108 3.2 25.9 1.0
CD2 A:TRP108 3.2 25.4 1.0
CE3 A:TRP28 3.3 24.4 1.0
CZ3 A:TRP108 3.5 24.0 1.0
CE2 A:TRP108 3.5 23.9 1.0
CB A:ALA31 3.8 26.7 1.0
CH2 A:TRP108 3.8 23.9 1.0
CG A:TRP108 3.8 23.7 1.0
CZ2 A:TRP108 3.8 23.7 1.0
SD A:MET105 3.8 17.8 0.5
CG A:MET105 4.0 21.0 0.5
CH2 A:TRP28 4.1 25.7 1.0
CG A:MET105 4.2 30.9 0.5
NE1 A:TRP108 4.2 22.8 1.0
CD2 A:TRP28 4.3 22.9 1.0
CD1 A:TRP108 4.4 22.9 1.0
CB A:TRP108 4.5 24.8 1.0
CB A:MET105 4.5 21.8 0.5
CB A:MET105 4.8 29.2 0.5
CD2 A:LEU56 4.8 33.2 1.0
CA A:TRP28 5.0 20.6 1.0
CZ2 A:TRP28 5.0 25.9 1.0

Gold binding site 2 out of 3 in 4zfp

Go back to Gold Binding Sites List in 4zfp
Gold binding site 2 out of 3 in the A New Crystal Structure For the Adduct Formed in the Reaction Between AUSAC2, A Cytotoxic Homoleptic Gold(I) Compound with the Saccharinate Ligand, and the Model Protein Hen Egg White Lysozyme


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of A New Crystal Structure For the Adduct Formed in the Reaction Between AUSAC2, A Cytotoxic Homoleptic Gold(I) Compound with the Saccharinate Ligand, and the Model Protein Hen Egg White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au209

b:44.6
occ:0.85
 NE2 A:HIS15 2.1 29.4 1.0
O3 A:NO3207 2.3 36.0 0.8
CD2 A:HIS15 2.8 29.8 1.0
N A:NO3207 3.2 34.2 0.8
O1 A:NO3207 3.2 38.6 0.8
NH1 A:ARG14 3.2 43.3 1.0
CE1 A:HIS15 3.3 34.2 1.0
CG1 A:ILE88 3.7 34.5 1.0
O A:HOH376 3.8 57.5 1.0
CZ A:ARG14 4.0 42.5 1.0
CG A:HIS15 4.1 29.8 1.0
OD1 A:ASP87 4.1 36.1 1.0
CB A:ALA11 4.2 30.4 1.0
ND1 A:HIS15 4.2 32.7 1.0
CD1 A:ILE88 4.3 37.6 1.0
OG1 A:THR89 4.3 31.3 1.0
O A:ALA11 4.4 30.1 1.0
CD A:ARG14 4.4 46.0 1.0
NE A:ARG14 4.5 46.2 1.0
O2 A:NO3207 4.5 44.8 0.8
N A:ILE88 4.7 32.2 1.0
CG A:ARG14 4.7 45.1 1.0
NH2 A:ARG14 4.7 46.1 1.0
CA A:ALA11 4.8 30.3 1.0
N A:THR89 4.8 28.4 1.0
C A:ALA11 4.9 29.5 1.0
CB A:ILE88 5.0 32.3 1.0

Gold binding site 3 out of 3 in 4zfp

Go back to Gold Binding Sites List in 4zfp
Gold binding site 3 out of 3 in the A New Crystal Structure For the Adduct Formed in the Reaction Between AUSAC2, A Cytotoxic Homoleptic Gold(I) Compound with the Saccharinate Ligand, and the Model Protein Hen Egg White Lysozyme


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of A New Crystal Structure For the Adduct Formed in the Reaction Between AUSAC2, A Cytotoxic Homoleptic Gold(I) Compound with the Saccharinate Ligand, and the Model Protein Hen Egg White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au210

b:50.4
occ:0.35
 ND1 A:HIS15 1.9 32.7 1.0
O A:HOH403 2.3 22.8 0.3
CE1 A:HIS15 2.9 34.2 1.0
CG A:HIS15 2.9 29.8 1.0
CB A:HIS15 3.3 29.6 1.0
CA A:HIS15 3.7 32.1 1.0
OD1 A:ASN93 3.7 42.8 1.0
O A:HOH305 4.0 55.7 1.0
NE2 A:HIS15 4.0 29.4 1.0
CD2 A:HIS15 4.0 29.8 1.0
CG2 A:THR89 4.1 30.7 1.0
O A:HIS15 4.2 32.1 1.0
C A:HIS15 4.5 29.9 1.0
ND2 A:ASN93 4.5 42.5 1.0
CG A:ASN93 4.5 41.5 1.0
OG1 A:THR89 4.5 31.3 1.0
O A:HOH316 4.6 38.1 1.0
O A:HOH421 4.6 19.7 0.3
CB A:THR89 4.8 31.4 1.0
CG1 A:VAL92 4.8 25.1 1.0
NZ A:LYS96 4.9 29.1 1.0
CA A:THR89 4.9 29.1 1.0
N A:HIS15 4.9 33.4 1.0

Reference:

G.Ferraro, L.Massai, L.Messori, M.A.Cinellu, A.Merlino. Structural Evidences For A Secondary Gold Binding Site in the Hydrophobic Box of Lysozyme. Biometals V. 28 745 2015.
ISSN: ISSN 1572-8773
PubMed: 26054833
DOI: 10.1007/S10534-015-9863-7
Page generated: Wed Jul 10 14:27:01 2024

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