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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: Tue Dec 15 05:58:43 2020

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