Cadmium in PDB 2x21: Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A
Protein crystallography data
The structure of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A, PDB code: 2x21
was solved by
T.Schulte,
R.G.Hiller,
E.Hofmann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.01 /
1.75
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.490,
81.810,
74.980,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.6 /
18.6
|
Other elements in 2x21:
The structure of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A also contains other interesting chemical elements:
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A
(pdb code 2x21). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the
Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A, PDB code: 2x21:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Cadmium binding site 1 out
of 8 in 2x21
Go back to
Cadmium Binding Sites List in 2x21
Cadmium binding site 1 out
of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Cd1151
b:9.5
occ:0.90
|
O
|
M:HOH2006
|
2.3
|
12.3
|
1.0
|
OD1
|
M:ASP5
|
2.4
|
8.2
|
1.0
|
OD2
|
M:ASP5
|
2.5
|
13.1
|
1.0
|
CL
|
M:CL1161
|
2.5
|
13.0
|
1.0
|
CG
|
M:ASP5
|
2.7
|
9.6
|
1.0
|
O
|
M:HOH2022
|
3.9
|
20.1
|
1.0
|
O
|
M:HOH2010
|
4.2
|
14.1
|
1.0
|
O
|
M:HOH2025
|
4.3
|
35.7
|
1.0
|
CB
|
M:ASP5
|
4.3
|
7.6
|
1.0
|
CD
|
M:CD1152
|
4.4
|
9.0
|
0.5
|
O
|
M:ASP1
|
4.6
|
8.5
|
1.0
|
CD
|
M:CD1152
|
4.7
|
11.9
|
0.2
|
O
|
M:HOH2024
|
4.7
|
42.5
|
1.0
|
CB
|
M:ALA0
|
4.7
|
9.2
|
1.0
|
|
Cadmium binding site 2 out
of 8 in 2x21
Go back to
Cadmium Binding Sites List in 2x21
Cadmium binding site 2 out
of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Cd1152
b:9.0
occ:0.50
|
CD
|
M:CD1152
|
0.0
|
9.0
|
0.5
|
CD
|
M:CD1152
|
0.9
|
11.9
|
0.2
|
O
|
M:HOH2025
|
1.9
|
35.7
|
1.0
|
O
|
M:HOH2034
|
2.2
|
18.5
|
1.0
|
OD2
|
M:ASP5
|
2.4
|
13.1
|
1.0
|
CL
|
M:CL1160
|
2.4
|
19.6
|
0.5
|
OE1
|
M:GLU2
|
2.6
|
24.3
|
1.0
|
OE2
|
M:GLU2
|
3.0
|
24.0
|
1.0
|
CD
|
M:GLU2
|
3.2
|
15.7
|
1.0
|
O
|
M:HOH2014
|
3.4
|
25.5
|
1.0
|
CG
|
M:ASP5
|
3.4
|
9.6
|
1.0
|
CB
|
M:ASP5
|
3.7
|
7.6
|
1.0
|
CD
|
M:CD1151
|
4.4
|
9.5
|
0.9
|
O
|
M:HOH2011
|
4.4
|
20.2
|
1.0
|
OD1
|
M:ASP5
|
4.5
|
8.2
|
1.0
|
O
|
M:HOH2010
|
4.7
|
14.1
|
1.0
|
CG
|
M:GLU2
|
4.7
|
15.8
|
1.0
|
O
|
M:HOH2006
|
5.0
|
12.3
|
1.0
|
|
Cadmium binding site 3 out
of 8 in 2x21
Go back to
Cadmium Binding Sites List in 2x21
Cadmium binding site 3 out
of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Cd1152
b:11.9
occ:0.20
|
CD
|
M:CD1152
|
0.0
|
11.9
|
0.2
|
CD
|
M:CD1152
|
0.9
|
9.0
|
0.5
|
OE1
|
M:GLU2
|
2.0
|
24.3
|
1.0
|
CL
|
M:CL1160
|
2.2
|
19.6
|
0.5
|
OE2
|
M:GLU2
|
2.2
|
24.0
|
1.0
|
CD
|
M:GLU2
|
2.4
|
15.7
|
1.0
|
O
|
M:HOH2025
|
2.7
|
35.7
|
1.0
|
O
|
M:HOH2014
|
2.8
|
25.5
|
1.0
|
OD2
|
M:ASP5
|
2.8
|
13.1
|
1.0
|
O
|
M:HOH2034
|
2.9
|
18.5
|
1.0
|
CG
|
M:ASP5
|
3.8
|
9.6
|
1.0
|
CG
|
M:GLU2
|
3.9
|
15.8
|
1.0
|
CB
|
M:ASP5
|
4.1
|
7.6
|
1.0
|
O
|
M:HOH2010
|
4.2
|
14.1
|
1.0
|
O
|
M:HOH2011
|
4.4
|
20.2
|
1.0
|
O
|
M:HOH2013
|
4.7
|
31.5
|
1.0
|
CD
|
M:CD1151
|
4.7
|
9.5
|
0.9
|
CA
|
M:GLU2
|
4.7
|
9.5
|
1.0
|
CB
|
M:GLU2
|
4.7
|
10.4
|
1.0
|
O
|
M:HOH2006
|
4.9
|
12.3
|
1.0
|
OD1
|
M:ASP5
|
4.9
|
8.2
|
1.0
|
|
Cadmium binding site 4 out
of 8 in 2x21
Go back to
Cadmium Binding Sites List in 2x21
Cadmium binding site 4 out
of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Cd1153
b:12.1
occ:1.00
|
O
|
M:HOH2182
|
2.1
|
11.6
|
1.0
|
O
|
M:HOH2184
|
2.3
|
11.8
|
1.0
|
OD2
|
M:ASP116
|
2.4
|
8.9
|
1.0
|
CL
|
M:CL1162
|
2.6
|
19.1
|
1.0
|
CL
|
M:CL1158
|
2.6
|
16.5
|
1.0
|
CG
|
M:ASP116
|
3.2
|
8.2
|
1.0
|
OD1
|
M:ASP116
|
3.4
|
8.0
|
1.0
|
CD
|
M:CD1157
|
3.7
|
10.5
|
0.6
|
O
|
M:HOH2190
|
4.0
|
25.5
|
1.0
|
O
|
M:HOH2183
|
4.1
|
31.4
|
1.0
|
O
|
M:HOH2185
|
4.5
|
18.9
|
1.0
|
CD
|
M:LYS118
|
4.6
|
14.6
|
1.0
|
CB
|
M:ASP116
|
4.7
|
8.7
|
1.0
|
CE
|
M:LYS118
|
4.7
|
21.0
|
1.0
|
NZ
|
M:LYS118
|
4.7
|
23.1
|
1.0
|
O
|
M:HOH2096
|
5.0
|
15.4
|
1.0
|
|
Cadmium binding site 5 out
of 8 in 2x21
Go back to
Cadmium Binding Sites List in 2x21
Cadmium binding site 5 out
of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Cd1154
b:15.2
occ:0.80
|
OD1
|
M:ASP106
|
2.3
|
10.2
|
1.0
|
O
|
M:HOH2164
|
2.4
|
13.3
|
1.0
|
OD1
|
M:ASN102
|
2.4
|
16.0
|
1.0
|
OD2
|
M:ASP106
|
2.5
|
12.3
|
1.0
|
CG
|
M:ASP106
|
2.7
|
10.0
|
1.0
|
CG
|
M:ASN102
|
3.3
|
18.3
|
1.0
|
ND2
|
M:ASN102
|
3.5
|
16.4
|
1.0
|
O
|
M:HOH2165
|
3.8
|
25.5
|
1.0
|
O
|
M:HOH2167
|
4.2
|
21.1
|
1.0
|
CB
|
M:ASP106
|
4.2
|
8.3
|
1.0
|
O
|
M:ASN102
|
4.4
|
10.5
|
1.0
|
NZ
|
M:LYS46
|
4.4
|
22.4
|
1.0
|
CB
|
M:ASN102
|
4.7
|
14.0
|
1.0
|
O
|
M:HOH2172
|
4.9
|
21.5
|
1.0
|
O
|
M:HOH2168
|
5.0
|
10.8
|
1.0
|
|
Cadmium binding site 6 out
of 8 in 2x21
Go back to
Cadmium Binding Sites List in 2x21
Cadmium binding site 6 out
of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Cd1155
b:18.0
occ:0.50
|
O
|
M:HOH2088
|
2.1
|
30.7
|
1.0
|
OE1
|
M:GLU39
|
2.3
|
27.6
|
1.0
|
CL
|
M:CL1159
|
2.5
|
16.0
|
0.5
|
OE2
|
M:GLU39
|
2.8
|
29.8
|
1.0
|
CD
|
M:GLU39
|
2.9
|
27.4
|
1.0
|
CG
|
M:GLU39
|
4.3
|
18.0
|
1.0
|
CB
|
M:GLN36
|
4.3
|
13.4
|
1.0
|
CB
|
M:LEU38
|
4.4
|
16.7
|
1.0
|
CD
|
M:CD1156
|
4.4
|
20.1
|
0.2
|
N
|
M:GLU39
|
4.6
|
12.2
|
1.0
|
CG
|
M:LEU38
|
4.8
|
16.2
|
1.0
|
CD1
|
M:LEU38
|
4.8
|
25.8
|
1.0
|
CA
|
M:GLN36
|
4.8
|
13.2
|
1.0
|
N
|
M:LEU38
|
4.9
|
12.5
|
1.0
|
CB
|
M:GLU39
|
4.9
|
12.7
|
1.0
|
|
Cadmium binding site 7 out
of 8 in 2x21
Go back to
Cadmium Binding Sites List in 2x21
Cadmium binding site 7 out
of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Cd1156
b:20.1
occ:0.25
|
O
|
M:HOH2092
|
2.2
|
29.8
|
1.0
|
OE2
|
M:GLU39
|
2.7
|
29.8
|
1.0
|
O
|
M:HOH2088
|
3.2
|
30.7
|
1.0
|
CD
|
M:GLU39
|
3.5
|
27.4
|
1.0
|
CG
|
M:GLU39
|
3.9
|
18.0
|
1.0
|
NZ
|
M:LYS113
|
4.3
|
30.6
|
1.0
|
OE1
|
M:GLU39
|
4.4
|
27.6
|
1.0
|
CD
|
M:CD1155
|
4.4
|
18.0
|
0.5
|
NZ
|
M:LYS42
|
4.5
|
30.1
|
1.0
|
CE
|
M:LYS113
|
4.7
|
26.0
|
1.0
|
O
|
M:HOH2177
|
4.9
|
24.1
|
1.0
|
|
Cadmium binding site 8 out
of 8 in 2x21
Go back to
Cadmium Binding Sites List in 2x21
Cadmium binding site 8 out
of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Bchl-A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Cd1157
b:10.5
occ:0.60
|
O
|
M:HOH2096
|
2.5
|
15.4
|
1.0
|
CL
|
M:CL1158
|
2.5
|
16.5
|
1.0
|
O
|
M:HOH2079
|
2.7
|
8.7
|
1.0
|
CL
|
M:CL1162
|
2.8
|
19.1
|
1.0
|
CD
|
M:CD1153
|
3.7
|
12.1
|
1.0
|
O
|
M:HOH2190
|
4.3
|
25.5
|
1.0
|
O
|
M:HOH2184
|
4.5
|
11.8
|
1.0
|
NZ
|
M:LYS34
|
5.0
|
35.8
|
1.0
|
CE
|
M:LYS34
|
5.0
|
37.2
|
1.0
|
|
Reference:
T.Schulte,
R.G.Hiller,
E.Hofmann.
X-Ray Structures of the Peridinin-Chlorophyll-Protein Reconstituted with Different Chlorophylls. Febs Lett. V. 584 973 2010.
ISSN: ISSN 0014-5793
PubMed: 20102711
DOI: 10.1016/J.FEBSLET.2010.01.041
Page generated: Fri Jul 19 15:25:31 2024
|