Atomistry » Gold » PDB 5jjo-7mq6 » 6sex
Atomistry »
  Gold »
    PDB 5jjo-7mq6 »
      6sex »

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

Go back to Gold Binding Sites List in 6sex
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

Go back to Gold Binding Sites List in 6sex
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

Go back to Gold Binding Sites List in 6sex
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

Go back to Gold Binding Sites List in 6sex
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: Sat Dec 12 01:54:48 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy