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Gold in PDB 3p65: 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: 3p65 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 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.641, 78.641, 37.130, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 22.5

Other elements in 3p65:

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 3p65). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 5 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: 3p65:
Jump to Gold binding site number: 1; 2; 3; 4; 5;

Gold binding site 1 out of 5 in 3p65

Go back to Gold Binding Sites List in 3p65
Gold binding site 1 out of 5 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:49.9
occ:1.00
 OH A:TYR23 3.0 12.0 1.0
O A:HOH2007 3.3 13.9 1.0
CE2 A:TYR23 3.6 9.0 1.0
CZ A:TYR23 3.6 11.2 1.0
CA A:GLY104 4.1 12.8 1.0
O A:ARG21 4.6 14.0 1.0
N A:GLY104 4.7 13.1 1.0
CD2 A:TYR23 4.8 11.7 1.0
CE1 A:TYR23 4.8 12.0 1.0

Gold binding site 2 out of 5 in 3p65

Go back to Gold Binding Sites List in 3p65
Gold binding site 2 out of 5 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:65.4
occ:1.00
 O A:HOH2005 3.1 14.4 1.0
O A:HOH2058 3.2 22.6 1.0
N A:THR69 3.2 15.4 1.0
O A:THR69 3.4 15.9 1.0
O A:HOH2080 3.4 33.1 1.0
O A:HOH2076 3.4 21.6 1.0
N A:ARG68 3.5 14.1 1.0
C A:GLY67 3.5 14.9 1.0
CA A:GLY67 3.5 16.3 1.0
C A:THR69 3.6 12.4 1.0
N A:GLY67 3.6 14.2 1.0
OD1 A:ASN65 3.7 14.8 1.0
OG A:SER72 3.7 19.8 1.0
CA A:THR69 3.8 14.0 1.0
O A:HOH2026 3.9 17.0 1.0
O A:HOH2151 4.0 47.9 1.0
O A:GLY67 4.1 18.4 1.0
CB A:THR69 4.2 12.3 1.0
C A:ARG68 4.2 19.2 1.0
OD1 A:ASP66 4.3 12.0 1.0
CA A:ARG68 4.3 13.9 1.0
N A:PRO70 4.4 14.8 1.0
AU A:AU3310 4.6 48.6 0.5
C A:ASP66 4.8 10.8 1.0
OG1 A:THR69 4.8 13.7 1.0
CG A:ASN65 4.8 11.6 1.0
CB A:SER72 4.9 15.6 1.0
O A:HOH2038 4.9 18.3 0.5
N A:ASP66 4.9 10.3 1.0
CA A:PRO70 4.9 15.5 1.0

Gold binding site 3 out of 5 in 3p65

Go back to Gold Binding Sites List in 3p65
Gold binding site 3 out of 5 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:59.4
occ:1.00
 OG A:SER24 3.0 18.8 1.0
N A:GLY26 3.2 11.9 1.0
CB A:SER24 3.4 16.7 1.0
CA A:GLY26 3.5 12.6 1.0
CA A:GLN121 3.6 15.8 1.0
CB A:GLN121 4.0 19.6 1.0
CD1 A:ILE124 4.0 22.4 1.0
N A:GLN121 4.0 15.8 1.0
CG2 A:VAL120 4.2 15.8 1.0
CG A:GLN121 4.2 23.1 1.0
CG1 A:ILE124 4.3 19.6 1.0
N A:LEU25 4.3 14.1 1.0
O A:VAL120 4.3 14.3 1.0
C A:VAL120 4.4 13.6 1.0
C A:LEU25 4.4 14.3 1.0
C A:SER24 4.4 12.3 1.0
C A:GLY26 4.5 10.4 1.0
CA A:SER24 4.6 12.2 1.0
N A:ASN27 4.6 11.3 1.0
CA A:LEU25 4.8 15.7 1.0
C A:GLN121 4.9 13.2 1.0
O A:SER24 4.9 14.0 1.0

Gold binding site 4 out of 5 in 3p65

Go back to Gold Binding Sites List in 3p65
Gold binding site 4 out of 5 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:64.0
occ:0.30
 NE2 A:HIS15 2.0 20.1 1.0
CL A:CL305 2.0 25.2 1.0
CD2 A:HIS15 2.9 17.1 1.0
CE1 A:HIS15 2.9 19.7 1.0
CG1 A:ILE88 3.6 13.8 1.0
OD1 A:ASP87 3.8 22.6 1.0
N A:ILE88 3.9 14.7 1.0
ND1 A:HIS15 3.9 26.2 1.0
CG A:HIS15 4.0 16.9 1.0
CB A:ALA11 4.3 15.4 1.0
OG1 A:THR89 4.4 17.3 1.0
N A:THR89 4.5 13.7 1.0
CG A:ASP87 4.5 25.2 1.0
CD1 A:ILE88 4.6 16.3 1.0
O A:ALA11 4.7 14.6 1.0
CB A:ILE88 4.7 13.3 1.0
CA A:ILE88 4.7 13.1 1.0
C A:ASP87 4.7 13.8 1.0
CA A:ASP87 4.8 14.2 1.0
C A:ILE88 4.8 13.0 1.0
CA A:ALA11 4.9 15.8 1.0

Gold binding site 5 out of 5 in 3p65

Go back to Gold Binding Sites List in 3p65
Gold binding site 5 out of 5 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:Au310

b:48.6
occ:0.50
 O A:SER60 2.2 15.3 1.0
O A:HOH2005 2.4 14.4 1.0
O A:CYS64 2.4 11.6 1.0
O A:HOH2026 2.5 17.0 1.0
OG A:SER72 2.5 19.8 1.0
O A:ARG73 2.5 17.3 1.0
CB A:SER72 3.3 15.6 1.0
C A:SER60 3.4 14.0 1.0
C A:CYS64 3.5 11.6 1.0
C A:ARG73 3.6 17.8 1.0
CA A:ASN65 3.9 12.4 1.0
CA A:SER60 4.0 11.2 1.0
N A:ARG73 4.0 19.2 1.0
CB A:SER60 4.1 12.8 1.0
N A:ASN65 4.2 11.4 1.0
C A:SER72 4.2 21.8 1.0
CA A:ARG73 4.4 16.7 1.0
CA A:SER72 4.4 18.4 1.0
N A:ASN74 4.4 14.8 1.0
N A:ARG61 4.5 12.9 1.0
N A:CYS64 4.5 12.3 1.0
CB A:THR69 4.6 12.3 1.0
N A:ASP66 4.6 10.3 1.0
OD1 A:ASN65 4.6 14.8 1.0
C A:ARG61 4.6 15.6 1.0
AU A:AU3302 4.6 65.4 1.0
O A:SER72 4.6 20.7 1.0
O A:ARG61 4.6 18.5 1.0
CA A:CYS64 4.7 11.0 1.0
CA A:ASN74 4.7 15.1 1.0
CA A:ARG61 4.8 16.3 1.0
C A:ASN65 4.8 9.7 1.0
CB A:ASN74 4.8 14.5 1.0
CB A:ASN65 4.8 13.4 1.0
N A:TRP62 4.9 14.8 1.0
OG1 A:THR69 4.9 13.7 1.0
O A:THR69 4.9 15.9 1.0
OG A:SER60 5.0 11.8 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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