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Gold in PDB 3p64: 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: 3p64 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 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.567, 78.567, 36.947, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.4

Other elements in 3p64:

The structure of Time-Dependent and Protein-Directed in Situ Growth of Gold Nanoparticles in A Single Crystal of Lysozyme also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

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 3p64). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 4 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: 3p64:
Jump to Gold binding site number: 1; 2; 3; 4;

Gold binding site 1 out of 4 in 3p64

Go back to Gold Binding Sites List in 3p64
Gold binding site 1 out of 4 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:53.2
occ:0.50
 O A:HOH2157 3.1 33.0 1.0
O A:HOH2061 3.1 26.8 1.0
O A:HOH2006 3.1 16.1 1.0
N A:THR69 3.2 17.7 1.0
O A:THR69 3.4 17.9 1.0
N A:ARG68 3.4 15.5 1.0
C A:GLY67 3.5 18.2 1.0
CA A:GLY67 3.5 20.0 1.0
O A:HOH2107 3.5 38.5 1.0
C A:THR69 3.6 14.9 1.0
OD1 A:ASN65 3.6 18.5 1.0
N A:GLY67 3.7 15.6 1.0
OG A:SER72 3.7 24.2 1.0
CA A:THR69 3.8 16.4 1.0
O A:HOH2041 3.9 19.1 1.0
O A:GLY67 4.1 21.2 1.0
CB A:THR69 4.1 12.8 1.0
C A:ARG68 4.2 18.8 1.0
OD1 A:ASP66 4.2 12.1 1.0
CA A:ARG68 4.3 14.2 1.0
N A:PRO70 4.4 21.4 1.0
O A:HOH2150 4.6 37.0 1.0
O A:HOH2227 4.7 15.3 1.0
C A:ASP66 4.7 12.5 1.0
OG1 A:THR69 4.7 14.7 1.0
CG A:ASN65 4.8 14.8 1.0
CB A:SER72 4.8 20.4 1.0
O A:HOH2023 4.9 17.8 0.5
N A:ASP66 4.9 11.1 1.0
CA A:PRO70 5.0 17.1 1.0

Gold binding site 2 out of 4 in 3p64

Go back to Gold Binding Sites List in 3p64
Gold binding site 2 out of 4 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:54.0
occ:1.00
 OH A:TYR23 3.0 13.9 1.0
O A:HOH2008 3.3 16.6 1.0
CE2 A:TYR23 3.7 12.9 1.0
CZ A:TYR23 3.7 11.0 1.0
CA A:GLY104 4.1 13.3 1.0
N A:GLY104 4.7 14.6 1.0
O A:ARG21 4.7 15.8 1.0
CE1 A:TYR23 4.9 11.9 1.0
CD2 A:TYR23 4.9 12.4 1.0

Gold binding site 3 out of 4 in 3p64

Go back to Gold Binding Sites List in 3p64
Gold binding site 3 out of 4 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:Au310

b:62.1
occ:0.50
 CL A:CL1319 1.8 26.8 1.0
NE2 A:HIS15 2.0 21.1 1.0
CE1 A:HIS15 2.9 19.8 1.0
CD2 A:HIS15 2.9 17.1 1.0
O A:HOH2116 3.3 32.8 1.0
OD1 A:ASP87 3.5 21.7 1.0
CG1 A:ILE88 3.7 18.0 1.0
N A:ILE88 3.7 17.3 1.0
CG A:ASP87 3.9 29.5 1.0
ND1 A:HIS15 3.9 30.7 1.0
CG A:HIS15 4.0 18.6 1.0
OD2 A:ASP87 4.1 38.6 1.0
OG1 A:THR89 4.2 21.8 1.0
NH1 A:ARG14 4.2 47.5 1.0
N A:THR89 4.3 15.4 1.0
CA A:ASP87 4.5 16.3 1.0
CB A:ALA11 4.5 17.7 1.0
C A:ASP87 4.5 16.0 1.0
CA A:ILE88 4.5 14.1 1.0
CB A:ILE88 4.6 14.3 1.0
C A:ILE88 4.7 13.3 1.0
CD1 A:ILE88 4.7 16.9 1.0
CB A:ASP87 4.7 19.7 1.0
O A:ALA11 4.8 18.5 1.0
O A:HOH2081 4.9 32.3 1.0

Gold binding site 4 out of 4 in 3p64

Go back to Gold Binding Sites List in 3p64
Gold binding site 4 out of 4 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:Au313

b:66.2
occ:1.00
 OG A:SER24 2.9 20.5 1.0
N A:GLY26 3.3 15.2 1.0
CB A:SER24 3.5 15.2 1.0
CA A:GLN121 3.6 17.2 1.0
CA A:GLY26 3.6 14.6 1.0
CB A:GLN121 3.9 20.0 1.0
N A:GLN121 4.0 18.2 1.0
CG A:GLN121 4.0 26.6 1.0
CD1 A:ILE124 4.1 23.5 1.0
CG2 A:VAL120 4.2 18.7 1.0
C A:VAL120 4.3 16.0 1.0
O A:VAL120 4.3 15.4 1.0
CG1 A:ILE124 4.3 21.9 1.0
N A:LEU25 4.3 17.2 1.0
C A:LEU25 4.5 14.9 1.0
C A:SER24 4.5 14.6 1.0
C A:GLY26 4.6 13.3 1.0
CA A:SER24 4.6 15.0 1.0
N A:ASN27 4.7 13.2 1.0
C A:GLN121 4.8 15.4 1.0
CA A:LEU25 4.9 15.7 1.0
O A:HOH2110 4.9 32.1 1.0
O A:SER24 5.0 16.1 1.0
O A:GLN121 5.0 17.4 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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