Atomistry » Cadmium » PDB 2wxt-3a05 » 2x1z
Atomistry »
  Cadmium »
    PDB 2wxt-3a05 »
      2x1z »

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

Go back to Cadmium Binding Sites List in 2x1z
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

Go back to Cadmium Binding Sites List in 2x1z
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

Go back to Cadmium Binding Sites List in 2x1z
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

Go back to Cadmium Binding Sites List in 2x1z
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

Go back to Cadmium Binding Sites List in 2x1z
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

Go back to Cadmium Binding Sites List in 2x1z
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: Thu Jul 10 12:11:11 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy