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Cadmium in PDB 2x20: Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-B

Protein crystallography data

The structure of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-B, PDB code: 2x20 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) 43.15 / 1.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 68.570, 82.000, 75.410, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 19.6

Other elements in 2x20:

The structure of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-B also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Potassium (K) 1 atom
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-B (pdb code 2x20). 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 Chl-B, PDB code: 2x20:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 2x20

Go back to Cadmium Binding Sites List in 2x20
Cadmium binding site 1 out of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-B


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 Chl-B within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1151

b:13.8
occ:0.50
 CD M:CD1151 0.0 13.8 0.5
CD M:CD1151 1.3 19.8 0.2
O M:HOH2029 2.2 18.1 1.0
OD2 M:ASP5 2.4 9.8 1.0
O M:HOH2012 2.6 20.8 1.0
OE1 M:GLU2 2.7 26.3 1.0
O M:HOH2013 3.0 21.9 1.0
OE2 M:GLU2 3.1 24.4 1.0
CD M:GLU2 3.3 22.4 1.0
CG M:ASP5 3.3 8.4 1.0
CB M:ASP5 3.6 7.6 1.0
O M:HOH2015 4.2 10.3 1.0
CD M:CD1152 4.4 9.3 0.9
O M:HOH2022 4.4 8.1 1.0
OD1 M:ASP5 4.5 4.8 1.0
CG M:GLU2 4.8 18.5 1.0

Cadmium binding site 2 out of 8 in 2x20

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Cadmium binding site 2 out of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-B


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 Chl-B within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1151

b:19.8
occ:0.20
 CD M:CD1151 0.0 19.8 0.2
CD M:CD1151 1.3 13.8 0.5
OE2 M:GLU2 2.0 24.4 1.0
O M:HOH2013 2.0 21.9 1.0
O M:HOH2012 2.0 20.8 1.0
OE1 M:GLU2 2.2 26.3 1.0
CD M:GLU2 2.4 22.4 1.0
OD2 M:ASP5 3.1 9.8 1.0
O M:HOH2029 3.4 18.1 1.0
CG M:GLU2 3.9 18.5 1.0
O M:HOH2014 4.1 34.5 1.0
CG M:ASP5 4.1 8.4 1.0
CB M:ASP5 4.5 7.6 1.0
O M:HOH2015 4.5 10.3 1.0
CA M:GLU2 4.8 9.5 1.0
CB M:GLU2 4.8 8.4 1.0
O M:HOH2011 4.8 29.8 1.0
CD M:CD1152 4.9 9.3 0.9

Cadmium binding site 3 out of 8 in 2x20

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Cadmium binding site 3 out of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-B


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 Chl-B within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1152

b:9.3
occ:0.90
 O M:HOH2008 2.4 11.2 1.0
OD2 M:ASP5 2.4 9.8 1.0
OD1 M:ASP5 2.4 4.8 1.0
CL M:CL1157 2.4 9.5 0.9
O M:HOH2022 2.5 8.1 1.0
CG M:ASP5 2.8 8.4 1.0
O M:HOH2021 4.0 29.6 1.0
CB M:ASP5 4.3 7.6 1.0
CD M:CD1151 4.4 13.8 0.5
O M:ASP1 4.6 4.1 1.0
CB M:ALA0 4.7 9.4 1.0
CD M:CD1151 4.9 19.8 0.2

Cadmium binding site 4 out of 8 in 2x20

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Cadmium binding site 4 out of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-B


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 Chl-B within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1153

b:14.7
occ:0.50
 O M:HOH2132 2.2 25.6 1.0
O M:HOH2129 2.3 19.3 1.0
OD1 M:ASP106 2.4 9.6 1.0
OD2 M:ASP106 2.4 12.1 1.0
OD1 M:ASN102 2.6 23.8 1.0
CG M:ASP106 2.7 9.1 1.0
ND2 M:ASN102 2.9 22.9 1.0
CG M:ASN102 3.2 16.5 1.0
CB M:ASP106 4.2 6.6 1.0
O M:HOH2133 4.3 37.8 1.0
O M:ASN102 4.4 9.1 1.0
O M:HOH2070 4.6 2.0 1.0
NZ M:LYS46 4.6 21.6 1.0
CB M:ASN102 4.7 12.4 1.0

Cadmium binding site 5 out of 8 in 2x20

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Cadmium binding site 5 out of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-B


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 Chl-B within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1154

b:7.0
occ:0.50
 CD M:CD1154 0.0 7.0 0.5
CD M:CD1154 1.6 10.3 0.5
CL M:CL1159 2.0 8.2 0.5
OD2 M:ASP116 2.4 9.3 1.0
CG M:ASP116 3.2 9.3 1.0
OD1 M:ASP116 3.4 6.6 1.0
O M:HOH2149 3.5 37.2 1.0
O M:HOH2150 4.5 18.7 1.0
CB M:ASP116 4.6 8.2 1.0
CD M:LYS118 4.8 19.4 1.0
CE M:LYS118 4.9 24.6 1.0
NZ M:LYS118 5.0 32.9 1.0

Cadmium binding site 6 out of 8 in 2x20

Go back to Cadmium Binding Sites List in 2x20
Cadmium binding site 6 out of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-B


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 Chl-B within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1154

b:10.3
occ:0.50
 CD M:CD1154 0.0 10.3 0.5
CD M:CD1154 1.6 7.0 0.5
OD2 M:ASP116 2.4 9.3 1.0
OD1 M:ASP116 2.5 6.6 1.0
CG M:ASP116 2.8 9.3 1.0
CL M:CL1159 2.8 8.2 0.5
CD M:LYS118 4.2 19.4 1.0
CD M:PRO117 4.3 9.9 1.0
CB M:ASP116 4.3 8.2 1.0
CE M:LYS118 4.3 24.6 1.0
CG M:LYS118 4.4 14.4 1.0
CG M:PRO117 4.4 10.6 1.0
O M:HOH2150 4.6 18.7 1.0
O M:HOH2149 4.7 37.2 1.0
N M:PRO117 4.8 9.4 1.0
CB M:LYS118 4.8 9.9 1.0
N M:LYS118 4.8 9.7 1.0
NZ M:LYS118 4.9 32.9 1.0

Cadmium binding site 7 out of 8 in 2x20

Go back to Cadmium Binding Sites List in 2x20
Cadmium binding site 7 out of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-B


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 Chl-B within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1155

b:16.6
occ:0.40
 O M:HOH2072 2.0 30.4 1.0
OE1 M:GLU39 2.3 28.2 1.0
CL M:CL1158 2.4 34.3 1.0
O M:HOH2073 2.5 28.2 1.0
OE2 M:GLU39 2.7 31.4 1.0
CD M:GLU39 2.8 24.7 1.0
CD M:CD1156 3.8 32.6 0.2
CG M:GLU39 4.3 17.8 1.0
CB M:LEU38 4.3 12.1 1.0
CD1 M:LEU38 4.4 20.2 1.0
CB M:GLN36 4.4 13.1 1.0
O M:HOH2075 4.6 37.9 1.0
N M:GLU39 4.6 9.7 1.0
CG M:LEU38 4.7 15.1 1.0
CA M:GLN36 4.9 13.2 1.0
CB M:GLU39 4.9 9.7 1.0
N M:LEU38 4.9 8.2 1.0
CG M:GLN36 5.0 15.8 1.0

Cadmium binding site 8 out of 8 in 2x20

Go back to Cadmium Binding Sites List in 2x20
Cadmium binding site 8 out of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-B


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 Chl-B within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1156

b:32.6
occ:0.25
 OE2 M:GLU39 2.2 31.4 1.0
O M:HOH2073 2.7 28.2 1.0
O M:HOH2075 2.8 37.9 1.0
CD M:GLU39 3.1 24.7 1.0
CG M:GLU39 3.8 17.8 1.0
CD M:CD1155 3.8 16.6 0.4
OE1 M:GLU39 4.0 28.2 1.0
NZ M:LYS113 4.5 37.8 1.0
O M:HOH2072 4.7 30.4 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 15:24:30 2024

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