Palladium in PDB 2z5p: Apo-Fr with Low Content of Pd Ions
Protein crystallography data
The structure of Apo-Fr with Low Content of Pd Ions, PDB code: 2z5p
was solved by
T.Ueno,
K.Hirata,
M.Abe,
M.Suzuki,
S.Abe,
N.Shimizu,
M.Yamamoto,
M.Takata,
Y.Watanabe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.79 /
1.65
|
Space group
|
F 4 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
180.790,
180.790,
180.790,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.9 /
18.8
|
Other elements in 2z5p:
The structure of Apo-Fr with Low Content of Pd Ions also contains other interesting chemical elements:
Palladium Binding Sites:
The binding sites of Palladium atom in the Apo-Fr with Low Content of Pd Ions
(pdb code 2z5p). This binding sites where shown within
5.0 Angstroms radius around Palladium atom.
In total 6 binding sites of Palladium where determined in the
Apo-Fr with Low Content of Pd Ions, PDB code: 2z5p:
Jump to Palladium binding site number:
1;
2;
3;
4;
5;
6;
Palladium binding site 1 out
of 6 in 2z5p
Go back to
Palladium Binding Sites List in 2z5p
Palladium binding site 1 out
of 6 in the Apo-Fr with Low Content of Pd Ions
Mono view
Stereo pair view
|
A full contact list of Palladium with other atoms in the Pd binding
site number 1 of Apo-Fr with Low Content of Pd Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pd201
b:28.3
occ:0.30
|
CD
|
A:GLU130
|
1.9
|
25.0
|
0.3
|
OE1
|
A:GLU130
|
2.2
|
25.2
|
0.3
|
CG
|
A:GLU130
|
2.3
|
25.2
|
0.3
|
OE2
|
A:GLU130
|
2.4
|
24.4
|
0.3
|
SG
|
A:CYS126
|
2.5
|
28.1
|
0.5
|
NE2
|
A:HIS114
|
2.6
|
26.0
|
0.9
|
O
|
A:CYS126
|
3.1
|
27.2
|
0.6
|
PD
|
A:PD204
|
3.2
|
0.9
|
0.2
|
CD2
|
A:HIS114
|
3.2
|
25.6
|
0.9
|
PD
|
A:PD202
|
3.2
|
46.1
|
0.3
|
C
|
A:CYS126
|
3.6
|
27.2
|
0.6
|
CB
|
A:CYS126
|
3.7
|
27.6
|
0.5
|
CE1
|
A:HIS114
|
3.7
|
25.7
|
0.7
|
CB
|
A:CYS126
|
3.7
|
27.3
|
0.5
|
CB
|
A:GLU130
|
3.8
|
25.1
|
0.3
|
CA
|
A:CYS126
|
4.0
|
27.2
|
0.5
|
CA
|
A:CYS126
|
4.0
|
27.4
|
0.5
|
CG
|
A:HIS114
|
4.4
|
24.0
|
0.9
|
N
|
A:ASP127
|
4.5
|
27.1
|
1.0
|
ND1
|
A:HIS114
|
4.6
|
25.5
|
0.8
|
CA
|
A:GLU130
|
4.7
|
25.1
|
0.6
|
N
|
A:GLU130
|
4.8
|
24.5
|
0.6
|
SG
|
A:CYS126
|
4.8
|
29.9
|
0.5
|
CD1
|
A:LEU134
|
5.0
|
23.1
|
1.0
|
|
Palladium binding site 2 out
of 6 in 2z5p
Go back to
Palladium Binding Sites List in 2z5p
Palladium binding site 2 out
of 6 in the Apo-Fr with Low Content of Pd Ions
Mono view
Stereo pair view
|
A full contact list of Palladium with other atoms in the Pd binding
site number 2 of Apo-Fr with Low Content of Pd Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pd202
b:46.1
occ:0.30
|
SG
|
A:CYS126
|
2.6
|
28.1
|
0.5
|
PD
|
A:PD201
|
3.2
|
28.3
|
0.3
|
CG
|
A:GLU130
|
3.2
|
25.2
|
0.3
|
OE2
|
A:GLU130
|
3.4
|
24.4
|
0.3
|
CA
|
A:ASP127
|
3.4
|
26.7
|
1.0
|
N
|
A:ASP127
|
3.4
|
27.1
|
1.0
|
C
|
A:CYS126
|
3.6
|
27.2
|
0.6
|
CD
|
A:GLU130
|
3.7
|
25.0
|
0.3
|
O
|
A:CYS126
|
3.7
|
27.2
|
0.6
|
CB
|
A:ASP127
|
3.9
|
26.7
|
0.3
|
CB
|
A:CYS126
|
4.0
|
27.3
|
0.5
|
CB
|
A:GLU130
|
4.2
|
25.1
|
0.3
|
CB
|
A:CYS126
|
4.2
|
27.6
|
0.5
|
OD1
|
A:ASP127
|
4.2
|
27.5
|
0.3
|
CA
|
A:CYS126
|
4.5
|
27.2
|
0.5
|
CA
|
A:CYS126
|
4.5
|
27.4
|
0.5
|
PD
|
A:PD204
|
4.6
|
0.9
|
0.2
|
CG
|
A:ASP127
|
4.6
|
27.0
|
0.3
|
C
|
A:ASP127
|
4.7
|
26.2
|
1.0
|
OE1
|
A:GLU130
|
4.7
|
25.2
|
0.3
|
O
|
A:PRO123
|
5.0
|
24.0
|
0.9
|
O
|
A:ASP127
|
5.0
|
26.2
|
0.6
|
|
Palladium binding site 3 out
of 6 in 2z5p
Go back to
Palladium Binding Sites List in 2z5p
Palladium binding site 3 out
of 6 in the Apo-Fr with Low Content of Pd Ions
Mono view
Stereo pair view
|
A full contact list of Palladium with other atoms in the Pd binding
site number 3 of Apo-Fr with Low Content of Pd Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pd203
b:65.4
occ:0.30
|
OE1
|
A:GLU45
|
2.2
|
16.4
|
0.5
|
PD
|
A:PD206
|
2.5
|
0.5
|
0.2
|
SG
|
A:CYS48
|
2.5
|
13.5
|
1.0
|
O
|
A:HOH1194
|
2.6
|
37.9
|
1.0
|
OD1
|
A:ASP38
|
3.2
|
13.0
|
1.0
|
CD
|
A:GLU45
|
3.5
|
17.2
|
0.5
|
CB
|
A:CYS48
|
3.5
|
11.3
|
1.0
|
CG
|
A:ASP38
|
3.6
|
11.4
|
1.0
|
CB
|
A:ASP38
|
3.6
|
9.3
|
1.0
|
OE2
|
A:GLU45
|
4.2
|
17.9
|
0.5
|
OD2
|
A:ASP38
|
4.5
|
11.5
|
1.0
|
CG
|
A:GLU45
|
4.5
|
14.7
|
0.5
|
CA
|
A:ASP38
|
4.5
|
9.1
|
1.0
|
O
|
A:HOH1223
|
4.6
|
56.6
|
1.0
|
CG
|
A:GLU45
|
4.7
|
14.7
|
0.5
|
CB
|
A:GLU45
|
4.8
|
13.0
|
0.5
|
CA
|
A:CYS48
|
4.9
|
11.2
|
1.0
|
CD
|
A:ARG52
|
4.9
|
20.1
|
1.0
|
O
|
A:GLU45
|
5.0
|
12.3
|
1.0
|
|
Palladium binding site 4 out
of 6 in 2z5p
Go back to
Palladium Binding Sites List in 2z5p
Palladium binding site 4 out
of 6 in the Apo-Fr with Low Content of Pd Ions
Mono view
Stereo pair view
|
A full contact list of Palladium with other atoms in the Pd binding
site number 4 of Apo-Fr with Low Content of Pd Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pd204
b:0.9
occ:0.20
|
O
|
A:HOH1218
|
2.4
|
58.0
|
1.0
|
SG
|
A:CYS126
|
2.5
|
28.1
|
0.5
|
NE2
|
A:HIS114
|
2.5
|
26.0
|
0.9
|
CE1
|
A:HIS114
|
2.6
|
25.7
|
0.7
|
PD
|
A:PD201
|
3.2
|
28.3
|
0.3
|
CB
|
A:CYS126
|
3.2
|
27.6
|
0.5
|
CB
|
A:CYS126
|
3.2
|
27.3
|
0.5
|
SG
|
A:CYS126
|
3.3
|
29.9
|
0.5
|
CD2
|
A:HIS114
|
3.8
|
25.6
|
0.9
|
ND1
|
A:HIS114
|
3.8
|
25.5
|
0.8
|
CA
|
A:CYS126
|
4.4
|
27.2
|
0.5
|
CG
|
A:HIS114
|
4.4
|
24.0
|
0.9
|
CA
|
A:CYS126
|
4.4
|
27.4
|
0.5
|
PD
|
A:PD202
|
4.6
|
46.1
|
0.3
|
CB
|
A:SER118
|
4.9
|
27.0
|
1.0
|
OG
|
A:SER118
|
4.9
|
27.4
|
0.6
|
CD
|
A:GLU130
|
5.0
|
25.0
|
0.3
|
|
Palladium binding site 5 out
of 6 in 2z5p
Go back to
Palladium Binding Sites List in 2z5p
Palladium binding site 5 out
of 6 in the Apo-Fr with Low Content of Pd Ions
Mono view
Stereo pair view
|
A full contact list of Palladium with other atoms in the Pd binding
site number 5 of Apo-Fr with Low Content of Pd Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pd205
b:0.9
occ:0.20
|
NE2
|
A:HIS49
|
2.0
|
13.7
|
0.5
|
CD2
|
A:HIS49
|
2.9
|
13.4
|
0.5
|
CE1
|
A:HIS49
|
3.1
|
13.8
|
0.5
|
O
|
A:HOH1224
|
3.4
|
45.8
|
1.0
|
CG
|
A:GLU53
|
3.5
|
14.5
|
0.5
|
CD
|
A:GLU53
|
3.9
|
18.9
|
0.5
|
OE1
|
A:GLU53
|
4.0
|
22.1
|
0.5
|
CG
|
A:HIS49
|
4.1
|
11.4
|
0.5
|
ND1
|
A:HIS49
|
4.2
|
14.5
|
0.5
|
CG
|
A:GLU53
|
4.3
|
16.0
|
0.5
|
OE2
|
A:GLU53
|
4.7
|
21.0
|
0.5
|
CB
|
A:GLU53
|
4.8
|
13.1
|
0.5
|
CB
|
A:GLU53
|
4.8
|
12.8
|
0.5
|
|
Palladium binding site 6 out
of 6 in 2z5p
Go back to
Palladium Binding Sites List in 2z5p
Palladium binding site 6 out
of 6 in the Apo-Fr with Low Content of Pd Ions
Mono view
Stereo pair view
|
A full contact list of Palladium with other atoms in the Pd binding
site number 6 of Apo-Fr with Low Content of Pd Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Pd206
b:0.5
occ:0.20
|
SG
|
A:CYS48
|
2.4
|
13.5
|
1.0
|
PD
|
A:PD203
|
2.5
|
65.4
|
0.3
|
O
|
A:HOH1223
|
3.2
|
56.6
|
1.0
|
N
|
A:HIS49
|
3.3
|
10.8
|
1.0
|
CB
|
A:CYS48
|
3.3
|
11.3
|
1.0
|
C
|
A:CYS48
|
3.5
|
11.1
|
1.0
|
CA
|
A:HIS49
|
3.6
|
10.5
|
1.0
|
CD
|
A:ARG52
|
3.8
|
20.1
|
1.0
|
O
|
A:HOH1194
|
3.9
|
37.9
|
1.0
|
CB
|
A:HIS49
|
4.0
|
10.9
|
1.0
|
O
|
A:CYS48
|
4.0
|
11.3
|
1.0
|
CA
|
A:CYS48
|
4.1
|
11.2
|
1.0
|
OE1
|
A:GLU45
|
4.1
|
16.4
|
0.5
|
O
|
A:GLU45
|
4.1
|
12.3
|
1.0
|
CG
|
A:ARG52
|
4.4
|
15.4
|
1.0
|
NH2
|
A:ARG52
|
4.6
|
26.2
|
0.7
|
CG
|
A:GLU45
|
4.8
|
14.7
|
0.5
|
ND1
|
A:HIS49
|
4.9
|
14.5
|
0.5
|
CB
|
A:ARG52
|
4.9
|
12.6
|
1.0
|
CG
|
A:HIS49
|
4.9
|
11.4
|
0.5
|
NE
|
A:ARG52
|
5.0
|
22.5
|
0.8
|
|
Reference:
T.Ueno,
M.Abe,
K.Hirata,
S.Abe,
M.Suzuki,
N.Shimizu,
M.Yamamoto,
M.Takata,
Y.Watanabe.
Process of Accumulation of Metal Ions on the Interior Surface of Apo-Ferritin: Crystal Structures of A Series of Apo-Ferritins Containing Variable Quantities of Pd(II) Ions. J.Am.Chem.Soc. V. 131 5094 2009.
ISSN: ISSN 0002-7863
PubMed: 19317403
DOI: 10.1021/JA806688S
Page generated: Thu Oct 10 10:17:10 2024
|