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: Wed Jul 10 14:19:12 2024
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