Atomistry » Sodium » PDB 2woi-2x2v » 2x1z
Atomistry »
  Sodium »
    PDB 2woi-2x2v »
      2x1z »

Sodium 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:

Cadmium (Cd) 8 atoms
Magnesium (Mg) 1 atom
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-D, PDB code: 2x1z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2x1z

Go back to Sodium Binding Sites List in 2x1z
Sodium binding site 1 out of 2 in the Structure of Peridinin-Chlorophyll-Protein Reconstituted with Chl-D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na1163

b:15.1
occ:1.00
CL M:CL1166 1.8 41.7 1.0
O M:HOH2102 1.9 27.9 1.0
O M:HOH2103 2.3 47.6 1.0
OD2 M:ASP55 2.3 22.4 1.0
OD1 M:ASP55 2.6 17.3 1.0
CG M:ASP55 2.8 15.1 1.0
CB M:LYS57 3.8 14.0 1.0
CB M:ASP55 4.3 9.8 1.0
CD M:LYS57 4.6 35.6 1.0
CG M:LYS57 4.6 22.9 1.0
N M:LYS57 4.8 11.1 1.0
CA M:LYS57 4.9 11.9 1.0

Sodium binding site 2 out of 2 in 2x1z

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na1164

b:19.6
occ:1.00
NZ M:LYS68 1.9 37.6 1.0
OD2 M:ASP84 2.4 11.9 1.0
O M:HOH2127 2.7 28.8 1.0
CG M:ASP84 3.1 13.2 1.0
OD1 M:ASP84 3.2 21.6 1.0
CE M:LYS68 3.4 36.3 1.0
O M:HOH2118 3.4 26.7 1.0
CG M:LYS68 3.7 18.4 1.0
CB M:SER72 4.0 12.1 1.0
CD M:LYS68 4.0 29.1 1.0
OG M:SER72 4.1 14.1 1.0
OG M:SER81 4.2 9.2 1.0
O M:HOH2132 4.3 35.9 1.0
O M:LYS68 4.3 7.9 1.0
CB M:ASP84 4.5 7.1 1.0
C M:LYS68 4.9 7.8 1.0
CB M:LYS68 5.0 9.8 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: Mon Oct 7 05:02:47 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy