Atomistry » Cadmium » PDB 2wxt-3a05 » 2x20
Atomistry »
  Cadmium »
    PDB 2wxt-3a05 »
      2x20 »

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

Go back to Cadmium Binding Sites List in 2x20
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

Go back to Cadmium Binding Sites List in 2x20
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

Go back to Cadmium Binding Sites List in 2x20
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

Go back to Cadmium Binding Sites List in 2x20
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy