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Gold in PDB 3p66: Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme

Enzymatic activity of Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme

All present enzymatic activity of Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme, PDB code: 3p66 was solved by H.Wei, Z.Wang, J.Zhang, S.House, Y.-G.Gao, L.Yang, H.Robinson, L.H.Tan, H.Xing, C.Hou, I.M.Robertson, J.-M.Zuo, Y.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.36
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.543, 78.543, 37.154, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 24.3

Gold Binding Sites:

The binding sites of Gold atom in the Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme (pdb code 3p66). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 8 binding sites of Gold where determined in the Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme, PDB code: 3p66:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Gold binding site 1 out of 8 in 3p66

Go back to Gold Binding Sites List in 3p66
Gold binding site 1 out of 8 in the Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au301

b:49.0
occ:1.00
 O A:HOH2006 3.1 12.0 1.0
O A:HOH2034 3.1 18.8 1.0
O A:HOH2088 3.1 28.4 1.0
N A:THR69 3.3 13.8 1.0
O A:HOH2058 3.4 27.8 1.0
O A:THR69 3.4 13.3 1.0
N A:ARG68 3.6 12.5 1.0
CA A:GLY67 3.6 13.4 1.0
OD1 A:ASN65 3.6 14.4 1.0
C A:GLY67 3.6 13.7 1.0
OG A:SER72 3.6 15.6 1.0
N A:GLY67 3.6 11.3 1.0
C A:THR69 3.7 10.7 1.0
O A:HOH2017 3.8 15.2 1.0
CA A:THR69 3.9 14.5 1.0
CB A:THR69 4.3 10.7 1.0
O A:GLY67 4.3 15.2 1.0
OD1 A:ASP66 4.3 11.3 1.0
O A:HOH2123 4.3 22.3 1.0
C A:ARG68 4.4 15.4 1.0
CA A:ARG68 4.5 14.4 1.0
N A:PRO70 4.5 13.8 1.0
AU A:AU3307 4.5 50.8 1.0
C A:ASP66 4.8 9.7 1.0
CB A:SER72 4.8 13.3 1.0
CG A:ASN65 4.8 10.5 1.0
OG1 A:THR69 4.9 12.0 1.0
N A:ASP66 4.9 8.8 1.0
O A:HOH2021 4.9 17.1 0.5
O A:HOH2153 4.9 40.7 1.0

Gold binding site 2 out of 8 in 3p66

Go back to Gold Binding Sites List in 3p66
Gold binding site 2 out of 8 in the Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au302

b:48.5
occ:1.00
 OH A:TYR23 3.0 12.5 1.0
CE2 A:TYR23 3.7 9.0 1.0
CZ A:TYR23 3.7 10.8 1.0
CA A:GLY104 4.3 12.3 1.0
O A:ARG21 4.7 13.5 1.0
N A:GLY104 4.9 12.3 1.0
CE1 A:TYR23 4.9 12.2 1.0
CD2 A:TYR23 4.9 10.8 1.0

Gold binding site 3 out of 8 in 3p66

Go back to Gold Binding Sites List in 3p66
Gold binding site 3 out of 8 in the Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au303

b:57.1
occ:1.00
 OG A:SER24 3.1 17.0 1.0
N A:GLY26 3.2 11.4 1.0
CA A:GLY26 3.5 12.0 1.0
CB A:SER24 3.5 15.6 1.0
CA A:GLN121 3.6 14.7 1.0
CD1 A:ILE124 3.9 21.4 1.0
CB A:GLN121 3.9 19.5 1.0
N A:GLN121 4.0 15.2 1.0
CG A:GLN121 4.1 27.7 1.0
CG1 A:ILE124 4.2 18.7 1.0
N A:LEU25 4.3 13.8 1.0
C A:LEU25 4.4 12.7 1.0
O A:VAL120 4.4 13.0 1.0
C A:VAL120 4.4 12.6 1.0
CG2 A:VAL120 4.4 15.2 1.0
C A:SER24 4.4 12.2 1.0
C A:GLY26 4.5 10.1 1.0
CA A:SER24 4.6 12.6 1.0
N A:ASN27 4.7 11.7 1.0
C A:GLN121 4.8 14.7 1.0
CA A:LEU25 4.8 12.1 1.0
O A:SER24 4.9 12.0 1.0

Gold binding site 4 out of 8 in 3p66

Go back to Gold Binding Sites List in 3p66
Gold binding site 4 out of 8 in the Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au304

b:63.9
occ:1.00
 ND2 A:ASN65 3.1 14.2 1.0
O A:HOH2174 3.2 43.0 1.0
CA A:GLY67 3.7 13.4 1.0
N A:GLY67 4.1 11.3 1.0
CG A:ASN65 4.2 10.5 1.0
OD1 A:ASN65 4.5 14.4 1.0
O A:HOH2088 4.6 28.4 1.0
C A:ASP66 4.7 9.7 1.0
O A:HOH2102 4.8 39.9 1.0
O A:ASP66 4.9 11.5 1.0

Gold binding site 5 out of 8 in 3p66

Go back to Gold Binding Sites List in 3p66
Gold binding site 5 out of 8 in the Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au305

b:55.6
occ:0.50
 OG1 A:THR51 2.6 9.5 1.0
OD2 A:ASP66 2.8 11.0 1.0
NE A:ARG68 2.8 20.9 1.0
O A:GLY49 2.9 15.4 1.0
OG1 A:THR69 3.3 12.0 1.0
NE A:ARG45 3.4 26.9 1.0
CB A:THR51 3.4 7.9 1.0
CG A:ARG68 3.4 14.0 1.0
N A:THR51 3.4 9.0 1.0
C A:SER50 3.6 9.7 1.0
CD A:ARG68 3.6 15.3 1.0
CZ A:ARG68 3.7 23.2 1.0
CG A:ASP66 3.7 10.3 1.0
CZ A:ARG45 3.7 23.9 1.0
NH2 A:ARG68 3.7 17.6 1.0
NH2 A:ARG45 3.8 14.1 1.0
CA A:SER50 3.8 11.8 1.0
O A:ARG68 3.8 17.4 1.0
OD1 A:ASP66 3.9 11.3 1.0
OG A:SER60 4.0 10.0 1.0
C A:GLY49 4.0 13.8 1.0
CA A:THR51 4.1 10.2 1.0
CD A:ARG45 4.1 15.1 1.0
O A:SER50 4.2 10.8 1.0
OH A:TYR53 4.3 10.1 1.0
C A:ARG68 4.3 15.4 1.0
N A:SER50 4.4 12.5 1.0
CB A:ARG68 4.6 11.2 1.0
CB A:THR69 4.6 10.7 1.0
CG2 A:THR51 4.6 10.5 1.0
NH1 A:ARG45 4.7 48.0 1.0
N A:THR69 4.9 13.8 1.0
NH1 A:ARG68 4.9 19.0 1.0
CB A:SER60 4.9 10.2 1.0
O A:HOH2107 5.0 31.6 1.0
CB A:ASP66 5.0 11.0 1.0
CA A:ARG68 5.0 14.4 1.0
CA A:THR69 5.0 14.5 1.0

Gold binding site 6 out of 8 in 3p66

Go back to Gold Binding Sites List in 3p66
Gold binding site 6 out of 8 in the Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au306

b:75.9
occ:1.00
 O A:HOH2104 3.0 32.3 1.0
O A:HOH2060 3.0 19.6 1.0
ND2 A:ASN65 3.5 14.2 1.0
CB A:PRO79 3.8 11.2 1.0
CA A:PRO79 3.8 11.0 1.0
CB A:ASN65 3.9 10.7 1.0
N A:PRO79 3.9 11.2 1.0
CG A:ASN65 4.2 10.5 1.0
CD A:PRO79 4.3 11.8 1.0
C A:ILE78 4.4 11.3 1.0
O A:ASN65 4.5 10.7 1.0
CG A:PRO79 4.6 15.0 1.0
O A:HOH2102 4.6 39.9 1.0
O A:ILE78 4.7 11.6 1.0
ND2 A:ASN74 4.7 14.5 1.0

Gold binding site 7 out of 8 in 3p66

Go back to Gold Binding Sites List in 3p66
Gold binding site 7 out of 8 in the Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 7 of Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au307

b:50.8
occ:1.00
 O A:SER60 2.3 12.2 1.0
O A:HOH2006 2.3 12.0 1.0
O A:CYS64 2.3 10.4 1.0
OG A:SER72 2.4 15.6 1.0
O A:HOH2017 2.4 15.2 1.0
O A:ARG73 2.5 14.2 1.0
CB A:SER72 3.2 13.3 1.0
C A:SER60 3.4 12.5 1.0
C A:CYS64 3.5 9.4 1.0
C A:ARG73 3.5 15.2 1.0
CA A:ASN65 3.9 10.1 1.0
CA A:SER60 4.0 9.4 1.0
N A:ARG73 4.0 16.6 1.0
C A:SER72 4.2 19.0 1.0
N A:ASN65 4.2 10.0 1.0
CB A:SER60 4.2 10.2 1.0
CA A:SER72 4.3 17.2 1.0
CA A:ARG73 4.4 15.0 1.0
N A:ASN74 4.4 13.1 1.0
N A:CYS64 4.4 11.1 1.0
AU A:AU3301 4.5 49.0 1.0
N A:ARG61 4.5 12.3 1.0
OD1 A:ASN65 4.6 14.4 1.0
N A:ASP66 4.6 8.8 1.0
C A:ARG61 4.6 13.4 1.0
CB A:THR69 4.6 10.7 1.0
CA A:CYS64 4.6 9.7 1.0
O A:SER72 4.6 17.1 1.0
O A:ARG61 4.6 17.0 1.0
CA A:ASN74 4.7 13.8 1.0
O A:HOH2172 4.7 33.8 1.0
CB A:ASN74 4.8 13.6 1.0
CB A:ASN65 4.8 10.7 1.0
C A:ASN65 4.8 7.3 1.0
CA A:ARG61 4.9 13.5 1.0
N A:TRP62 4.9 11.2 1.0
O A:THR69 4.9 13.3 1.0
OG1 A:THR69 5.0 12.0 1.0

Gold binding site 8 out of 8 in 3p66

Go back to Gold Binding Sites List in 3p66
Gold binding site 8 out of 8 in the Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 8 of Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au308

b:59.3
occ:1.00
 OG1 A:THR43 2.7 16.2 1.0
O A:GLN41 2.8 13.2 1.0
N A:THR43 3.1 11.2 1.0
CB A:THR43 3.5 10.1 1.0
CG2 A:THR43 3.6 11.5 1.0
C A:ALA42 3.8 9.9 1.0
CA A:THR43 3.8 11.0 1.0
C A:GLN41 3.9 13.8 1.0
CA A:ALA42 4.0 9.8 1.0
O A:THR43 4.3 15.7 1.0
N A:ALA42 4.4 10.2 1.0
C A:THR43 4.5 11.5 1.0
O A:ALA42 4.7 8.5 1.0

Reference:

H.Wei, Z.Wang, J.Zhang, S.House, Y.G.Gao, L.Yang, H.Robinson, L.H.Tan, H.Xing, C.Hou, I.M.Robertson, J.M.Zuo, Y.Lu. Time-Dependent, Protein-Directed Growth of Gold Nanoparticles Within A Single Crystal of Lysozyme. Nat Nanotechnol V. 6 93 2011.
ISSN: ISSN 1748-3387
PubMed: 21278750
DOI: 10.1038/NNANO.2010.280
Page generated: Wed Jul 10 14:19:12 2024

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