Sodium in PDB 4lcz: Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex

The structure of Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex, PDB code: 4lcz was solved by T.Wan, M.Li, W.R.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.45 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	199.195, 115.097, 109.597, 90.00, 113.23, 90.00
R / Rfree (%)	25 / 25.8

The structure of Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex also contains other interesting chemical elements:

Magnesium	(Mg)	42 atoms
Zinc	(Zn)	5 atoms
Arsenic	(As)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex (pdb code 4lcz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex, PDB code: 4lcz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na320 b:42.3 occ:1.00 OD1 B:ASP211 2.1 75.0 1.0 O B:HOH444 2.2 62.0 1.0 OE2 B:GLU207 2.3 76.6 1.0 CG B:ASP211 2.8 74.8 1.0 OD2 B:ASP211 2.8 75.0 1.0 O B:HOH443 3.2 51.5 1.0 CD B:GLU207 3.3 73.3 1.0 NZ B:LYS203 3.7 62.3 1.0 OE1 B:GLU207 3.9 62.5 1.0 CG B:GLU207 4.2 66.8 1.0 CB B:ASP211 4.3 63.5 1.0 CE B:LYS203 4.8 55.9 1.0 O B:GLU207 4.8 74.4 1.0 CD B:LYS203 4.8 46.8 1.0 CA B:ASP211 4.9 60.6 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na322 b:47.5 occ:1.00 OG A:SER34 2.1 63.4 1.0 OE2 B:GLU56 2.1 75.6 1.0 O A:HOH454 2.2 46.8 1.0 CD B:GLU56 2.9 52.7 1.0 OE1 B:GLU56 3.1 53.0 1.0 CB A:SER34 3.2 40.6 1.0 O A:HOH403 3.8 31.3 1.0 O B:HOH445 4.0 38.3 1.0 CA A:SER34 4.3 29.5 1.0 CG B:GLU56 4.3 39.9 1.0 N A:TYR35 4.3 26.3 1.0 C A:SER34 4.3 42.1 1.0 CD2 A:TYR35 4.6 27.7 1.0 N A:SER34 4.7 31.2 1.0 O A:SER34 4.9 46.1 1.0 CB A:TYR35 5.0 23.2 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na320 b:60.0 occ:1.00 O C:HOH447 2.0 52.6 1.0 OE2 C:GLU207 2.4 91.3 1.0 OD1 C:ASP211 2.4 75.1 1.0 OD2 C:ASP211 2.8 73.3 1.0 O C:HOH450 2.9 54.9 1.0 CG C:ASP211 3.0 66.8 1.0 NZ C:LYS203 3.3 60.3 1.0 CD C:GLU207 3.3 82.4 1.0 OE1 C:GLU207 3.6 67.5 1.0 CE C:LYS203 4.3 63.3 1.0 CD C:LYS203 4.4 58.2 1.0 CB C:ASP211 4.5 47.5 1.0 CG C:GLU207 4.5 55.7 1.0 O C:GLU207 4.9 58.8 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na322 b:80.8 occ:0.50 OE1 C:GLU171 2.3 0.8 1.0 OE2 C:GLU171 2.3 0.2 1.0 CD C:GLU171 2.6 0.6 1.0 CG C:GLU171 4.1 82.1 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na323 b:68.2 occ:1.00 OD2 C:ASP54 2.1 42.7 1.0 O C:HOH449 2.3 52.0 1.0 CG C:ASP54 3.0 43.5 1.0 OD1 C:ASP54 3.3 49.2 1.0 O C:HOH448 3.3 60.6 1.0 O B:ALA53 4.0 22.1 1.0 ZN A:ZN320 4.0 98.5 1.0 CB C:ASP54 4.4 12.2 1.0 CD C:PRO55 4.5 27.2 1.0 C B:ALA53 4.6 20.3 1.0 CB C:GLU56 4.7 19.8 1.0 O A:HOH455 4.8 47.7 1.0 OE1 C:GLU56 4.9 91.7 1.0 CB B:ALA53 4.9 15.9 1.0 N C:GLU56 5.0 12.8 1.0

T.Wan, M.Li, X.Zhao, J.Zhang, Z.Liu, W.Chang. Crystal Structure of A Multilayer Packed Major Light-Harvesting Complex: Implications For Grana Stacking in Higher Plants Mol Plant 2014.
ISSN: ESSN 1752-9867
PubMed: 24482437
DOI: 10.1093/MP/SSU005