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Gold in PDB 3p68: 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: 3p68 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 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.400, 78.400, 37.224, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.5

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 3p68). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 7 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: 3p68:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7;

Gold binding site 1 out of 7 in 3p68

Go back to Gold Binding Sites List in 3p68
Gold binding site 1 out of 7 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:Au1301

b:62.5
occ:1.00
 OH A:TYR23 3.0 16.7 1.0
O A:HOH2007 3.4 22.6 1.0
CE2 A:TYR23 3.8 12.7 1.0
CZ A:TYR23 3.8 11.4 1.0
CA A:GLY104 4.2 14.8 1.0
O A:ARG21 4.7 16.5 1.0
N A:GLY104 4.8 13.5 1.0
CD2 A:TYR23 5.0 14.3 1.0
CE1 A:TYR23 5.0 13.3 1.0

Gold binding site 2 out of 7 in 3p68

Go back to Gold Binding Sites List in 3p68
Gold binding site 2 out of 7 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:Au1302

b:61.0
occ:1.00
 O A:HOH2092 3.0 24.1 1.0
O A:HOH2015 3.2 15.7 1.0
O A:HOH2027 3.3 26.0 1.0
N A:THR69 3.3 17.8 1.0
O A:THR69 3.4 15.4 1.0
OG A:SER72 3.6 16.8 1.0
C A:GLY67 3.6 17.9 1.0
N A:ARG68 3.6 15.5 1.0
CA A:GLY67 3.7 15.3 1.0
OD1 A:ASN65 3.7 16.6 1.0
C A:THR69 3.7 13.8 1.0
N A:GLY67 3.8 12.9 1.0
O A:HOH2005 3.9 16.7 1.0
CA A:THR69 4.0 15.1 1.0
O A:GLY67 4.1 20.4 1.0
CB A:THR69 4.3 15.7 1.0
C A:ARG68 4.4 20.0 1.0
OD1 A:ASP66 4.4 13.5 1.0
CA A:ARG68 4.4 15.9 1.0
N A:PRO70 4.4 15.2 1.0
CB A:SER72 4.7 16.8 1.0
AU A:AU31307 4.7 48.0 0.5
O A:HOH2033 4.8 18.8 0.5
C A:ASP66 4.9 15.6 1.0
CG A:ASN65 4.9 13.8 1.0
OG1 A:THR69 4.9 18.6 1.0
CA A:PRO70 4.9 18.4 1.0

Gold binding site 3 out of 7 in 3p68

Go back to Gold Binding Sites List in 3p68
Gold binding site 3 out of 7 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:Au1303

b:71.4
occ:1.00
 ND2 A:ASN65 3.0 17.4 1.0
O A:HOH2076 3.5 39.6 1.0
CA A:GLY67 3.7 15.3 1.0
N A:GLY67 4.1 12.9 1.0
CG A:ASN65 4.1 13.8 1.0
OD1 A:ASN65 4.2 16.6 1.0
O A:HOH2027 4.6 26.0 1.0
C A:ASP66 4.7 15.6 1.0
O A:HOH2095 4.9 29.2 1.0
O A:ASP66 4.9 16.9 1.0

Gold binding site 4 out of 7 in 3p68

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Gold binding site 4 out of 7 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:Au1304

b:70.8
occ:1.00
 OG A:SER24 3.1 22.2 1.0
N A:GLY26 3.2 17.2 1.0
CA A:GLY26 3.6 18.4 1.0
CD1 A:ILE124 3.6 34.0 1.0
CB A:SER24 3.6 21.0 1.0
CA A:GLN121 3.7 18.4 1.0
CG1 A:ILE124 4.0 20.8 1.0
N A:GLN121 4.1 17.3 1.0
CG A:GLN121 4.1 33.6 1.0
CB A:GLN121 4.1 28.7 1.0
N A:LEU25 4.2 14.4 1.0
O A:VAL120 4.4 16.8 1.0
C A:LEU25 4.4 16.3 1.0
C A:VAL120 4.4 17.7 1.0
C A:SER24 4.5 14.9 1.0
CG2 A:VAL120 4.5 23.4 1.0
C A:GLY26 4.6 14.7 1.0
CA A:SER24 4.7 16.5 1.0
N A:ASN27 4.8 16.3 1.0
CA A:LEU25 4.8 17.3 1.0
C A:GLN121 4.8 19.6 1.0
O A:SER24 5.0 17.6 1.0

Gold binding site 5 out of 7 in 3p68

Go back to Gold Binding Sites List in 3p68
Gold binding site 5 out of 7 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:Au1305

b:45.6
occ:0.50
 OG1 A:THR51 2.7 12.6 1.0
OD2 A:ASP66 2.8 14.2 1.0
O A:GLY49 2.8 16.1 1.0
NE A:ARG68 3.0 32.8 1.0
OG1 A:THR69 3.0 18.6 1.0
N A:THR51 3.3 13.9 1.0
CB A:THR51 3.5 11.8 1.0
C A:SER50 3.5 15.6 1.0
CG A:ARG68 3.6 19.2 1.0
CA A:SER50 3.6 14.7 1.0
CG A:ASP66 3.7 14.4 1.0
OG A:SER60 3.7 15.4 1.0
CD A:ARG68 3.7 18.9 1.0
O A:ARG68 3.8 20.5 1.0
NE A:ARG45 3.8 41.9 1.0
C A:GLY49 3.8 15.7 1.0
OD1 A:ASP66 3.8 13.5 1.0
CZ A:ARG68 3.9 42.2 1.0
CA A:THR51 4.0 12.4 1.0
NH2 A:ARG45 4.1 17.9 1.0
O A:SER50 4.1 13.4 1.0
NH2 A:ARG68 4.1 21.0 1.0
CZ A:ARG45 4.1 40.7 1.0
N A:SER50 4.2 14.9 1.0
C A:ARG68 4.2 20.0 1.0
OH A:TYR53 4.3 14.4 1.0
CB A:THR69 4.3 15.7 1.0
CD A:ARG45 4.6 26.3 1.0
CB A:ARG68 4.6 14.7 1.0
CB A:SER60 4.7 16.0 1.0
N A:THR69 4.7 17.8 1.0
CA A:THR69 4.8 15.1 1.0
CG2 A:THR51 4.8 16.6 1.0
CG2 A:THR69 4.8 17.4 1.0
CB A:SER50 4.8 12.3 1.0
CA A:ARG68 5.0 15.9 1.0
CB A:ASP66 5.0 14.3 1.0

Gold binding site 6 out of 7 in 3p68

Go back to Gold Binding Sites List in 3p68
Gold binding site 6 out of 7 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:Au1306

b:79.5
occ:1.00
 O A:HOH2095 3.1 29.2 1.0
O A:HOH2089 3.2 19.9 1.0
ND2 A:ASN65 3.3 17.4 1.0
CB A:PRO79 3.8 16.5 1.0
CA A:PRO79 3.8 14.9 1.0
CB A:ASN65 3.9 15.7 1.0
N A:PRO79 4.0 17.3 1.0
CG A:ASN65 4.1 13.8 1.0
CD A:PRO79 4.2 16.3 1.0
O A:ASN65 4.4 14.0 1.0
CG A:PRO79 4.5 18.6 1.0
C A:ILE78 4.5 15.9 1.0
O A:ILE78 4.8 15.1 1.0
ND2 A:ASN74 4.8 18.9 1.0
O A:HOH2113 4.9 43.4 1.0
O A:HOH2076 5.0 39.6 1.0
CA A:ASN65 5.0 14.3 1.0
C A:ASN65 5.0 13.0 1.0

Gold binding site 7 out of 7 in 3p68

Go back to Gold Binding Sites List in 3p68
Gold binding site 7 out of 7 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:Au1307

b:48.0
occ:0.50
 O A:CYS64 2.3 13.2 1.0
O A:ARG73 2.3 15.7 1.0
O A:SER60 2.4 15.5 1.0
O A:HOH2005 2.5 16.7 1.0
OG A:SER72 2.5 16.8 1.0
O A:HOH2015 2.5 15.7 1.0
CB A:SER72 3.3 16.8 1.0
C A:CYS64 3.4 15.7 1.0
C A:ARG73 3.4 19.4 1.0
C A:SER60 3.5 14.2 1.0
CA A:ASN65 3.9 14.3 1.0
N A:ARG73 4.0 20.5 1.0
N A:ASN65 4.1 15.5 1.0
CA A:SER60 4.1 14.5 1.0
C A:SER72 4.2 21.6 1.0
CB A:SER60 4.3 16.0 1.0
CA A:ARG73 4.3 18.7 1.0
N A:CYS64 4.3 15.4 1.0
N A:ASN74 4.3 18.0 1.0
CA A:SER72 4.4 21.2 1.0
CA A:ASN74 4.5 15.8 1.0
CA A:CYS64 4.5 15.5 1.0
C A:ARG61 4.5 16.7 1.0
O A:ARG61 4.6 21.5 1.0
N A:ASP66 4.6 12.8 1.0
N A:ARG61 4.6 14.9 1.0
O A:SER72 4.7 25.3 1.0
CB A:ASN74 4.7 13.2 1.0
AU A:AU31302 4.7 61.0 1.0
OD1 A:ASN65 4.8 16.6 1.0
CB A:ASN65 4.8 15.7 1.0
C A:ASN65 4.8 13.0 1.0
N A:TRP62 4.8 14.0 1.0
CB A:THR69 4.8 15.7 1.0
CA A:ARG61 4.9 19.8 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: Mon Jul 7 01:26:10 2025

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