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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:

Magnesium (Mg) 1 atom
Potassium (K) 4 atoms
Chlorine (Cl) 7 atoms
Sodium (Na) 1 atom

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

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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

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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

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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

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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

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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

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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: Sat Dec 12 08:18:34 2020

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