Zinc 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
Arsenic	(As)	3 atoms
Sodium	(Na)	5 atoms

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex, PDB code: 4lcz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc 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 Zinc with other atoms in the Zn 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 A:Zn320 b:98.5 occ:1.00 O C:HOH449 2.8 52.0 1.0 OD2 A:ASP54 3.0 41.9 1.0 OD2 B:ASP54 3.0 44.0 1.0 O A:HOH455 3.2 47.7 1.0 OD2 C:ASP54 3.2 42.7 1.0 O B:HOH429 3.9 37.7 1.0 CG A:ASP54 4.0 45.3 1.0 NA C:NA323 4.0 68.2 1.0 CG B:ASP54 4.1 37.9 1.0 CG C:ASP54 4.1 43.5 1.0 O A:HOH439 4.1 40.1 1.0 CB C:ASP54 4.2 12.2 1.0 CB A:ASP54 4.3 15.5 1.0 CB B:ASP54 4.3 29.1 1.0 O A:HOH420 4.7 36.2 1.0 CA C:ASP54 4.9 31.1 1.0 CA B:ASP54 4.9 27.5 1.0 CA A:ASP54 4.9 33.8 1.0

Zinc 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 Zinc with other atoms in the Zn 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 A:Zn321 b:56.7 occ:1.00 O2 A:CAC319 1.8 81.7 1.0 C1 A:CAC319 2.4 57.5 1.0 AS A:CAC319 2.5 62.3 1.0 OE1 A:GLU107 2.7 48.3 1.0 O1 A:CAC319 3.6 59.2 1.0 CD A:GLU107 3.7 72.3 1.0 CA A:GLY108 3.8 43.8 1.0 C2 A:CAC319 3.9 68.4 1.0 OE2 A:GLU107 3.9 49.7 1.0 N A:GLY108 4.3 43.0 1.0 C A:GLU107 4.7 60.1 1.0 O A:GLU107 4.8 42.0 1.0 CG A:GLU107 5.0 65.9 1.0

Zinc 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 Zinc with other atoms in the Zn 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 A:Zn322 b:0.7 occ:1.00 OD1 A:ASP211 2.3 90.2 1.0 O A:HOH453 2.6 64.9 1.0 OE2 A:GLU207 2.6 97.0 1.0 CG A:ASP211 3.0 81.4 1.0 OD2 A:ASP211 3.1 82.5 1.0 O A:HOH452 3.6 43.1 1.0 CD A:GLU207 3.8 89.5 1.0 NZ A:LYS203 3.8 65.0 1.0 OE1 A:GLU207 4.3 72.0 1.0 CB A:ASP211 4.4 63.0 1.0 CD A:LYS203 4.8 62.1 1.0 CE A:LYS203 4.8 64.4 1.0 CA A:ASP211 5.0 65.8 1.0

Zinc 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 Zinc with other atoms in the Zn 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 B:Zn321 b:66.1 occ:1.00 O2 B:CAC319 1.8 68.6 1.0 C1 B:CAC319 2.7 62.1 1.0 OE1 B:GLU107 2.7 57.2 1.0 AS B:CAC319 2.8 59.1 1.0 CD B:GLU107 3.7 58.8 1.0 O1 B:CAC319 3.7 66.2 1.0 OE2 B:GLU107 4.0 58.1 1.0 C2 B:CAC319 4.0 97.4 1.0 CA B:GLY108 4.0 52.9 1.0 O B:GLU107 4.4 51.8 1.0 N B:GLY108 4.5 51.0 1.0 C B:GLU107 4.6 47.2 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn321 b:64.3 occ:1.00 O2 C:CAC319 1.9 63.0 1.0 OE1 C:GLU107 2.4 42.5 1.0 C1 C:CAC319 2.7 57.9 1.0 AS C:CAC319 2.8 79.2 1.0 CD C:GLU107 3.5 65.7 1.0 OE2 C:GLU107 3.8 43.8 1.0 O1 C:CAC319 3.8 65.1 1.0 CA C:GLY108 3.9 40.0 1.0 C2 C:CAC319 4.0 0.3 1.0 N C:GLY108 4.2 39.6 1.0 C C:GLU107 4.5 53.9 1.0 O C:GLU107 4.6 35.8 1.0 CG C:GLU107 4.8 60.4 1.0 CB C:GLU107 5.0 37.5 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