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Cadmium in PDB 2x1z: Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-D

Protein crystallography data

The structure of Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-D, PDB code: 2x1z 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) 43.11 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 68.580, 81.990, 75.240, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 18.3

Other elements in 2x1z:

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

Magnesium (Mg) 1 atom
Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-D (pdb code 2x1z). 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-D, PDB code: 2x1z:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 2x1z

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Cadmium binding site 1 out of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-D


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-D within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1171

b:10.4
occ:0.50
 CD M:CD1171 0.0 10.4 0.5
CD M:CD1171 1.2 22.3 0.2
O M:HOH2021 1.8 21.9 1.0
O M:HOH2028 2.2 18.3 1.0
OD2 M:ASP5 2.4 13.0 1.0
OE1 M:GLU2 2.5 20.9 1.0
O M:HOH2011 2.6 21.4 1.0
OE2 M:GLU2 3.0 21.3 1.0
O M:HOH2013 3.1 26.8 1.0
CD M:GLU2 3.1 20.2 1.0
CG M:ASP5 3.4 12.9 1.0
CB M:ASP5 3.7 8.6 1.0
O M:HOH2010 4.2 15.8 1.0
CD M:CD1172 4.4 8.9 0.9
OD1 M:ASP5 4.5 8.8 1.0
O M:HOH2009 4.6 13.4 1.0
CG M:GLU2 4.7 16.6 1.0
O M:HOH2007 5.0 10.0 1.0

Cadmium binding site 2 out of 8 in 2x1z

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


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-D within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1171

b:22.3
occ:0.20
 CD M:CD1171 0.0 22.3 0.2
CD M:CD1171 1.2 10.4 0.5
OE1 M:GLU2 2.0 20.9 1.0
OE2 M:GLU2 2.0 21.3 1.0
O M:HOH2011 2.1 21.4 1.0
O M:HOH2013 2.2 26.8 1.0
CD M:GLU2 2.3 20.2 1.0
O M:HOH2021 3.0 21.9 1.0
OD2 M:ASP5 3.2 13.0 1.0
O M:HOH2028 3.3 18.3 1.0
CG M:GLU2 3.8 16.6 1.0
O M:HOH2009 4.1 13.4 1.0
CG M:ASP5 4.2 12.9 1.0
O M:HOH2010 4.4 15.8 1.0
CB M:ASP5 4.6 8.6 1.0
CB M:GLU2 4.7 10.6 1.0
CA M:GLU2 4.8 8.9 1.0

Cadmium binding site 3 out of 8 in 2x1z

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


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-D within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1172

b:8.9
occ:0.90
 O M:HOH2007 2.4 10.0 1.0
OD1 M:ASP5 2.4 8.8 1.0
CL M:CL1161 2.5 10.5 0.9
OD2 M:ASP5 2.5 13.0 1.0
CG M:ASP5 2.8 12.9 1.0
O M:HOH2020 4.0 27.8 1.0
O M:HOH2021 4.1 21.9 1.0
O M:HOH2009 4.3 13.4 1.0
CB M:ASP5 4.3 8.6 1.0
CD M:CD1171 4.4 10.4 0.5
O M:ASP1 4.7 7.0 1.0
CB M:ALA0 4.7 8.8 1.0
O M:HOH2026 4.9 55.1 1.0

Cadmium binding site 4 out of 8 in 2x1z

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


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-D within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1173

b:25.5
occ:0.50
 O M:HOH2148 1.7 27.6 1.0
OD2 M:ASP106 2.3 13.6 1.0
OD1 M:ASP106 2.4 14.7 1.0
ND2 M:ASN102 2.4 17.8 0.5
O M:HOH2093 2.5 32.5 1.0
CG M:ASP106 2.7 12.5 1.0
OD1 M:ASN102 3.0 22.9 0.5
CG M:ASN102 3.1 13.3 0.5
O M:HOH2151 3.6 42.6 1.0
CB M:ASP106 4.2 8.0 1.0
OD1 M:ASN102 4.2 21.4 0.5
O M:ASN102 4.3 10.9 0.5
O M:HOH2153 4.3 41.5 1.0
O M:ASN102 4.5 10.9 0.5
NZ M:LYS46 4.6 31.2 1.0
CB M:ASN102 4.6 12.0 0.5
O M:HOH2149 4.7 38.7 1.0
CB M:ASN102 4.8 12.7 0.5
O M:HOH2152 4.9 14.0 1.0
CA M:ASP106 5.0 9.0 1.0
CG M:ASN102 5.0 15.2 0.5

Cadmium binding site 5 out of 8 in 2x1z

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


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-D within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1174

b:11.0
occ:0.40
 CD M:CD1174 0.0 11.0 0.4
CD M:CD1174 1.5 8.2 0.6
CL M:CL1167 1.8 11.0 0.5
OD2 M:ASP116 2.3 9.2 1.0
CG M:ASP116 3.2 8.9 1.0
OD1 M:ASP116 3.3 6.5 1.0
O M:HOH2070 4.1 38.7 1.0
O M:HOH2165 4.6 20.3 1.0
CB M:ASP116 4.6 7.0 1.0
CD M:LYS118 4.8 17.2 1.0

Cadmium binding site 6 out of 8 in 2x1z

Go back to Cadmium Binding Sites List in 2x1z
Cadmium binding site 6 out of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-D


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-D within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1174

b:8.2
occ:0.60
 CD M:CD1174 0.0 8.2 0.6
CD M:CD1174 1.5 11.0 0.4
OD2 M:ASP116 2.4 9.2 1.0
OD1 M:ASP116 2.4 6.5 1.0
CL M:CL1167 2.6 11.0 0.5
CG M:ASP116 2.7 8.9 1.0
CD M:LYS118 4.2 17.2 1.0
CG M:LYS118 4.2 14.1 1.0
CB M:ASP116 4.3 7.0 1.0
CD M:PRO117 4.3 9.1 1.0
CG M:PRO117 4.5 12.7 1.0
CE M:LYS118 4.6 23.9 1.0
O M:HOH2165 4.7 20.3 1.0
CB M:LYS118 4.8 11.9 1.0
N M:LYS118 4.8 8.6 1.0
N M:PRO117 4.8 7.9 1.0
CA M:ASP116 5.0 8.0 1.0

Cadmium binding site 7 out of 8 in 2x1z

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Cadmium binding site 7 out of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-D


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-D within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1175

b:12.7
occ:0.40
 O M:HOH2080 1.9 32.8 1.0
OE1 M:GLU39 2.3 25.0 1.0
CL M:CL1162 2.4 31.7 1.0
OE2 M:GLU39 2.8 32.3 1.0
CD M:GLU39 2.9 28.5 1.0
CD M:CD1176 3.9 22.0 0.2
CB M:LEU38 4.1 11.9 0.5
CG M:GLU39 4.4 18.0 1.0
CB M:GLN36 4.4 9.8 1.0
O M:HOH2085 4.6 33.8 1.0
CB M:LEU38 4.7 11.9 0.5
N M:GLU39 4.7 10.0 1.0
CD2 M:LEU38 4.8 14.9 0.5
CA M:GLN36 4.8 11.6 1.0
CG M:LEU38 4.8 13.9 0.5
CG M:LEU38 4.8 13.3 0.5
NE2 M:GLN36 4.9 18.7 1.0
CD1 M:LEU38 4.9 13.0 0.5
CG M:GLN36 4.9 13.8 1.0
CB M:GLU39 5.0 10.9 1.0
N M:LEU38 5.0 10.4 0.5
C M:GLN36 5.0 10.3 1.0

Cadmium binding site 8 out of 8 in 2x1z

Go back to Cadmium Binding Sites List in 2x1z
Cadmium binding site 8 out of 8 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-D


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-D within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd1176

b:22.0
occ:0.25
 OE2 M:GLU39 2.1 32.3 1.0
O M:HOH2080 2.8 32.8 1.0
O M:HOH2085 2.9 33.8 1.0
CD M:GLU39 3.2 28.5 1.0
CG M:GLU39 3.9 18.0 1.0
CD M:CD1175 3.9 12.7 0.4
OE1 M:GLU39 4.0 25.0 1.0
NZ M:LYS113 5.0 27.0 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 15:23:46 2024

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