Atomistry » Gold » PDB 3l47-5ix6 » 3p68
Atomistry »
  Gold »
    PDB 3l47-5ix6 »
      3p68 »

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

Go back to Gold Binding Sites List in 3p68
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: Sat Dec 12 01:53:50 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