Magnesium 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:

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

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 42 binding sites of Magnesium where determined in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex, PDB code: 4lcz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 42 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg305 b:31.5 occ:1.00 MG A:CHL305 0.0 31.5 1.0 NB A:CHL305 2.0 31.6 1.0 ND A:CHL305 2.0 25.0 1.0 NC A:CHL305 2.1 26.1 1.0 O A:TYR24 2.2 29.8 1.0 NA A:CHL305 2.3 20.8 1.0 C4D A:CHL305 2.9 20.6 1.0 C1B A:CHL305 3.0 25.3 1.0 C4B A:CHL305 3.0 33.4 1.0 C4C A:CHL305 3.1 28.0 1.0 C1C A:CHL305 3.1 27.9 1.0 C1D A:CHL305 3.1 27.9 1.0 C1A A:CHL305 3.2 19.4 1.0 C4A A:CHL305 3.2 34.6 1.0 C A:TYR24 3.4 25.2 1.0 CHA A:CHL305 3.5 19.1 1.0 CHB A:CHL305 3.5 22.2 1.0 CHC A:CHL305 3.5 33.4 1.0 CHD A:CHL305 3.6 25.3 1.0 C3D A:CHL305 4.2 22.4 1.0 C10 A:LHG304 4.2 43.9 1.0 C8 A:LHG304 4.2 22.6 1.0 C2B A:CHL305 4.3 32.4 1.0 CA A:TYR24 4.3 31.4 1.0 C3B A:CHL305 4.3 33.0 1.0 N A:LEU25 4.3 22.0 1.0 C2D A:CHL305 4.3 22.1 1.0 C3C A:CHL305 4.3 28.8 1.0 CA A:LEU25 4.4 22.9 1.0 C2C A:CHL305 4.4 40.7 1.0 C2A A:CHL305 4.5 21.3 1.0 C3A A:CHL305 4.6 24.2 1.0 CB A:TYR24 4.8 23.5 1.0 CBD A:CHL305 4.9 17.8 1.0 C9 A:LHG304 4.9 31.5 1.0 C A:LEU25 4.9 35.5 1.0

Magnesium binding site 2 out of 42 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg306 b:17.4 occ:1.00 MG A:CLA306 0.0 17.4 1.0 NB A:CLA306 2.0 36.6 1.0 ND A:CLA306 2.0 31.5 1.0 OE1 A:GLU65 2.1 13.4 1.0 NC A:CLA306 2.2 16.9 1.0 NA A:CLA306 2.2 27.2 1.0 C4D A:CLA306 3.0 22.0 1.0 C1B A:CLA306 3.0 19.1 1.0 C4B A:CLA306 3.0 14.9 1.0 C1C A:CLA306 3.1 19.5 1.0 CD A:GLU65 3.2 23.9 1.0 C4C A:CLA306 3.2 17.1 1.0 C1D A:CLA306 3.2 18.3 1.0 C1A A:CLA306 3.2 29.0 1.0 C4A A:CLA306 3.2 33.8 1.0 CHB A:CLA306 3.5 25.9 1.0 CHA A:CLA306 3.5 20.7 1.0 CHC A:CLA306 3.6 24.5 1.0 CHD A:CLA306 3.6 28.3 1.0 C38 A:LUT302 3.7 13.0 1.0 OE2 A:GLU65 3.8 14.5 1.0 NE A:ARG185 4.1 21.7 1.0 NH2 A:ARG185 4.1 21.7 1.0 CG A:GLU65 4.2 14.9 1.0 C3D A:CLA306 4.2 31.7 1.0 C2B A:CLA306 4.3 14.3 1.0 C3B A:CLA306 4.3 14.3 1.0 CZ A:ARG185 4.3 25.5 1.0 C2D A:CLA306 4.4 19.4 1.0 C2C A:CLA306 4.4 17.5 1.0 C3C A:CLA306 4.4 24.7 1.0 C3A A:CLA306 4.5 21.1 1.0 C2A A:CLA306 4.5 17.4 1.0 CD A:ARG185 4.9 17.3 1.0 CBD A:CLA306 4.9 32.9 1.0 C28 A:LUT302 5.0 22.4 1.0

Magnesium binding site 3 out of 42 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg307 b:18.3 occ:1.00 MG A:CLA307 0.0 18.3 1.0 ND A:CLA307 2.0 12.6 1.0 NB A:CLA307 2.0 14.3 1.0 NC A:CLA307 2.2 21.7 1.0 NA A:CLA307 2.2 19.0 1.0 NE2 A:HIS68 2.3 9.1 1.0 C4D A:CLA307 2.9 11.9 1.0 C1B A:CLA307 3.0 11.3 1.0 C4B A:CLA307 3.0 12.6 1.0 C1A A:CLA307 3.1 11.8 1.0 C4A A:CLA307 3.2 33.6 1.0 C1C A:CLA307 3.2 13.9 1.0 C1D A:CLA307 3.2 18.7 1.0 C4C A:CLA307 3.2 17.5 1.0 CE1 A:HIS68 3.2 24.2 1.0 CD2 A:HIS68 3.4 9.6 1.0 CHB A:CLA307 3.4 10.7 1.0 CHA A:CLA307 3.5 19.1 1.0 CHC A:CLA307 3.6 21.5 1.0 C9 A:CHL313 3.6 16.6 1.0 CHD A:CLA307 3.7 18.5 1.0 C3D A:CLA307 4.1 12.4 1.0 C2B A:CLA307 4.3 31.6 1.0 C10 A:CHL313 4.3 38.7 1.0 C3B A:CLA307 4.3 23.0 1.0 C8 A:CHL313 4.3 40.0 1.0 C2D A:CLA307 4.3 13.2 1.0 ND1 A:HIS68 4.4 10.1 1.0 C7 A:CHL313 4.4 39.0 1.0 C2A A:CLA307 4.5 20.9 1.0 C2C A:CLA307 4.5 15.8 1.0 C3C A:CLA307 4.5 15.1 1.0 C3A A:CLA307 4.5 17.1 1.0 CG A:HIS68 4.5 10.2 1.0 C11 A:CHL313 4.8 31.0 1.0 CBD A:CLA307 4.9 27.9 1.0

Magnesium binding site 4 out of 42 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 A:Mg308 b:29.8 occ:1.00 MG A:CLA308 0.0 29.8 1.0 NC A:CLA308 2.0 42.0 1.0 O A:HOH433 2.0 25.0 1.0 NB A:CLA308 2.0 28.8 1.0 ND A:CLA308 2.0 33.5 1.0 NA A:CLA308 2.4 30.1 1.0 C4D A:CLA308 3.0 34.8 1.0 C1C A:CLA308 3.0 28.6 1.0 C1B A:CLA308 3.0 25.7 1.0 C4C A:CLA308 3.1 32.4 1.0 C4B A:CLA308 3.1 26.2 1.0 C1D A:CLA308 3.2 35.2 1.0 C1A A:CLA308 3.3 43.5 1.0 C4A A:CLA308 3.4 42.1 1.0 CHC A:CLA308 3.5 26.9 1.0 CHA A:CLA308 3.6 34.4 1.0 CHB A:CLA308 3.6 27.9 1.0 CHD A:CLA308 3.6 34.8 1.0 C24 A:NEX303 4.0 36.1 1.0 O A:GLY78 4.1 23.0 1.0 O23 A:NEX303 4.2 38.7 1.0 C3D A:CLA308 4.2 37.4 1.0 C2C A:CLA308 4.3 29.8 1.0 C3C A:CLA308 4.3 32.2 1.0 C2B A:CLA308 4.3 25.9 1.0 C2D A:CLA308 4.3 37.8 1.0 C3B A:CLA308 4.4 33.0 1.0 C22 A:NEX303 4.4 35.1 1.0 CA A:GLY78 4.4 21.5 1.0 C23 A:NEX303 4.5 36.8 1.0 C A:GLY78 4.7 21.6 1.0 C3A A:CLA308 4.7 29.2 1.0 C2A A:CLA308 4.7 31.9 1.0 O A:HOH418 4.8 23.5 1.0 C18 A:LUT302 4.8 25.0 1.0 CG A:PRO82 4.8 39.1 1.0 CBD A:CLA308 5.0 37.0 1.0

Magnesium binding site 5 out of 42 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 A:Mg309 b:45.2 occ:1.00 MG A:CHL309 0.0 45.2 1.0 O A:VAL119 2.0 34.1 1.0 NB A:CHL309 2.0 47.4 1.0 ND A:CHL309 2.0 43.2 1.0 NC A:CHL309 2.1 61.5 1.0 NA A:CHL309 2.3 50.4 1.0 C4D A:CHL309 2.9 45.4 1.0 C1B A:CHL309 3.0 50.6 1.0 C4B A:CHL309 3.0 46.0 1.0 C1C A:CHL309 3.1 40.3 1.0 C4C A:CHL309 3.1 38.2 1.0 C1D A:CHL309 3.1 40.4 1.0 C A:VAL119 3.1 33.5 1.0 C1A A:CHL309 3.2 51.4 1.0 C4A A:CHL309 3.2 53.1 1.0 CHA A:CHL309 3.5 48.9 1.0 CHC A:CHL309 3.5 44.5 1.0 CHB A:CHL309 3.5 53.4 1.0 CHD A:CHL309 3.6 37.8 1.0 CA A:VAL119 3.8 32.8 1.0 C3D A:CHL309 4.2 43.9 1.0 N A:HIS120 4.3 37.9 1.0 C2B A:CHL309 4.3 51.5 1.0 C3B A:CHL309 4.3 48.7 1.0 C2D A:CHL309 4.3 40.5 1.0 C2C A:CHL309 4.4 37.1 1.0 C3C A:CHL309 4.4 35.7 1.0 C A:HIS120 4.4 37.6 1.0 C2A A:CHL309 4.5 54.9 1.0 C3A A:CHL309 4.5 56.0 1.0 N A:ALA121 4.6 36.6 1.0 CB A:HIS120 4.6 43.0 1.0 O A:HIS120 4.7 39.3 1.0 CA A:HIS120 4.7 39.3 1.0 CG1 A:VAL119 4.7 27.0 1.0 N A:VAL119 4.7 35.4 1.0 CA A:ALA121 4.9 34.9 1.0 CBD A:CHL309 4.9 49.5 1.0 CB A:VAL119 4.9 29.4 1.0

Magnesium binding site 6 out of 42 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg310 b:32.9 occ:1.00 MG A:CHL310 0.0 32.9 1.0 O A:HOH422 2.0 26.2 1.0 NB A:CHL310 2.0 27.9 1.0 ND A:CHL310 2.0 34.8 1.0 NC A:CHL310 2.0 30.7 1.0 NA A:CHL310 2.4 32.2 1.0 C4D A:CHL310 2.9 36.5 1.0 C1B A:CHL310 3.0 27.2 1.0 C4B A:CHL310 3.0 26.4 1.0 C4C A:CHL310 3.0 32.4 1.0 C1C A:CHL310 3.0 28.8 1.0 C1D A:CHL310 3.1 36.0 1.0 C1A A:CHL310 3.3 34.4 1.0 C4A A:CHL310 3.3 39.6 1.0 CHC A:CHL310 3.5 27.4 1.0 CHD A:CHL310 3.5 35.0 1.0 CHB A:CHL310 3.5 28.4 1.0 CHA A:CHL310 3.6 36.6 1.0 O A:HOH421 3.9 40.4 1.0 C38 A:NEX303 4.2 32.2 1.0 C3D A:CHL310 4.2 39.0 1.0 C2B A:CHL310 4.3 29.1 1.0 C3B A:CHL310 4.3 29.6 1.0 C2D A:CHL310 4.3 58.7 1.0 C3C A:CHL310 4.3 31.6 1.0 C2C A:CHL310 4.3 36.9 1.0 OE1 A:GLN131 4.4 32.8 1.0 CG2 A:ILE127 4.6 27.2 1.0 C2A A:CHL310 4.6 42.0 1.0 C3A A:CHL310 4.7 32.2 1.0 O2A A:CLA308 5.0 35.4 1.0 CBD A:CHL310 5.0 39.4 1.0

Magnesium binding site 7 out of 42 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg311 b:37.6 occ:1.00 MG A:CHL311 0.0 37.6 1.0 ND A:CHL311 2.0 32.6 1.0 O A:HOH412 2.0 26.7 1.0 NB A:CHL311 2.1 38.4 1.0 NC A:CHL311 2.1 39.9 1.0 NA A:CHL311 2.3 24.9 1.0 C4D A:CHL311 2.9 28.4 1.0 C1B A:CHL311 3.0 25.8 1.0 C4C A:CHL311 3.1 27.2 1.0 C1C A:CHL311 3.1 24.6 1.0 C4B A:CHL311 3.1 30.6 1.0 C1D A:CHL311 3.1 29.1 1.0 C1A A:CHL311 3.2 45.0 1.0 C4A A:CHL311 3.2 30.8 1.0 CHB A:CHL311 3.5 22.1 1.0 CHA A:CHL311 3.5 43.9 1.0 CHC A:CHL311 3.5 31.0 1.0 CHD A:CHL311 3.5 46.0 1.0 C18 C:CHL305 3.7 63.6 1.0 CMC A:CHL310 4.1 39.3 1.0 OMC A:CHL310 4.1 34.3 1.0 C3D A:CHL311 4.2 30.4 1.0 C20 C:CHL305 4.2 43.8 1.0 C2B A:CHL311 4.3 36.2 1.0 C2D A:CHL311 4.3 30.9 1.0 C19 C:CHL305 4.3 66.0 1.0 C3C A:CHL311 4.4 31.9 1.0 C2C A:CHL311 4.4 33.7 1.0 C3B A:CHL311 4.4 24.4 1.0 O A:HOH436 4.4 36.1 1.0 C16 C:CHL305 4.5 89.1 1.0 C2A A:CHL311 4.6 37.6 1.0 C3A A:CHL311 4.6 33.6 1.0 C17 C:CHL305 4.8 79.1 1.0 CBD A:CHL311 4.9 35.3 1.0

Magnesium binding site 8 out of 42 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg312 b:28.5 occ:1.00 MG A:CHL312 0.0 28.5 1.0 ND A:CHL312 2.0 26.6 1.0 NB A:CHL312 2.0 38.1 1.0 O A:HOH425 2.1 15.9 1.0 NC A:CHL312 2.1 29.8 1.0 NA A:CHL312 2.3 27.7 1.0 C4D A:CHL312 2.9 53.3 1.0 C1B A:CHL312 3.0 31.9 1.0 C4B A:CHL312 3.0 36.2 1.0 C1C A:CHL312 3.1 41.0 1.0 C4C A:CHL312 3.1 35.1 1.0 C1D A:CHL312 3.1 29.6 1.0 C1A A:CHL312 3.2 29.9 1.0 C4A A:CHL312 3.3 33.2 1.0 CZ A:PHE161 3.3 40.6 1.0 CE2 A:PHE161 3.5 49.6 1.0 CHA A:CHL312 3.5 25.0 1.0 CHC A:CHL312 3.5 39.5 1.0 CHB A:CHL312 3.5 31.6 1.0 CHD A:CHL312 3.6 27.7 1.0 C3D A:CHL312 4.2 24.1 1.0 O A:HOH426 4.2 16.4 1.0 CE1 A:PHE161 4.3 39.2 1.0 C2B A:CHL312 4.3 53.1 1.0 C3B A:CHL312 4.3 38.9 1.0 C2D A:CHL312 4.4 24.9 1.0 C3C A:CHL312 4.4 31.0 1.0 C2C A:CHL312 4.4 40.9 1.0 O A:VAL138 4.5 23.2 1.0 C2A A:CHL312 4.6 30.2 1.0 C3A A:CHL312 4.6 35.6 1.0 CD2 A:PHE161 4.6 38.6 1.0 CB A:VAL138 4.9 32.8 1.0 CBD A:CHL312 4.9 24.9 1.0

Magnesium binding site 9 out of 42 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg313 b:30.8 occ:1.00 MG A:CHL313 0.0 30.8 1.0 ND A:CHL313 2.0 15.8 1.0 NB A:CHL313 2.0 28.9 1.0 NC A:CHL313 2.1 19.9 1.0 OE1 A:GLU139 2.1 17.0 1.0 NA A:CHL313 2.3 19.1 1.0 C4D A:CHL313 2.9 15.0 1.0 C1B A:CHL313 3.0 18.4 1.0 C4B A:CHL313 3.0 33.0 1.0 C1D A:CHL313 3.1 19.2 1.0 C4C A:CHL313 3.1 24.6 1.0 C1C A:CHL313 3.1 20.5 1.0 C1A A:CHL313 3.2 25.4 1.0 C4A A:CHL313 3.2 19.8 1.0 CD A:GLU139 3.3 18.7 1.0 CHB A:CHL313 3.5 17.8 1.0 CHA A:CHL313 3.5 16.3 1.0 CHC A:CHL313 3.5 25.5 1.0 CHD A:CHL313 3.6 18.5 1.0 CG A:GLU139 3.8 19.7 1.0 NH2 A:ARG142 4.1 22.5 1.0 C3D A:CHL313 4.2 14.5 1.0 C2B A:CHL313 4.3 19.7 1.0 C2D A:CHL313 4.3 14.8 1.0 C3B A:CHL313 4.3 24.8 1.0 OE2 A:GLU139 4.3 19.6 1.0 CMD A:CLA307 4.4 14.0 1.0 C3C A:CHL313 4.4 22.4 1.0 C2C A:CHL313 4.4 23.7 1.0 O A:HOH430 4.4 20.2 1.0 C2 C:CHL305 4.5 47.6 1.0 C2A A:CHL313 4.6 15.6 1.0 C3A A:CHL313 4.6 19.4 1.0 CB A:GLU139 4.7 27.9 1.0 CBA A:CHL313 4.8 15.9 1.0 CBD A:CHL313 4.9 17.9 1.0

Magnesium binding site 10 out of 42 in the Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of A Multilayer-Packed Major Light-Harvesting Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg314 b:26.9 occ:1.00 MG A:CLA314 0.0 26.9 1.0 NB A:CLA314 2.0 27.4 1.0 ND A:CLA314 2.0 27.5 1.0 NC A:CLA314 2.1 25.6 1.0 NA A:CLA314 2.3 38.9 1.0 OE1 A:GLU180 2.3 32.8 1.0 C4D A:CLA314 3.0 28.8 1.0 C1B A:CLA314 3.0 36.7 1.0 C4B A:CLA314 3.1 26.8 1.0 CD A:GLU180 3.1 40.7 1.0 C1C A:CLA314 3.1 25.2 1.0 C4C A:CLA314 3.1 29.7 1.0 C1D A:CLA314 3.2 26.4 1.0 C4A A:CLA314 3.2 30.3 1.0 C1A A:CLA314 3.2 30.9 1.0 CHB A:CLA314 3.5 29.8 1.0 CHA A:CLA314 3.5 30.5 1.0 CHC A:CLA314 3.6 25.6 1.0 CHD A:CLA314 3.6 35.5 1.0 CG A:GLU180 3.8 28.3 1.0 OE2 A:GLU180 3.9 37.8 1.0 NE A:ARG70 4.0 18.6 1.0 C3D A:CLA314 4.2 28.9 1.0 C38 A:LUT301 4.2 31.6 1.0 C2B A:CLA314 4.3 28.7 1.0 NH2 A:ARG70 4.3 20.4 1.0 C3B A:CLA314 4.3 27.6 1.0 C2D A:CLA314 4.3 29.8 1.0 C2C A:CLA314 4.4 24.4 1.0 C3C A:CLA314 4.4 24.3 1.0 CZ A:ARG70 4.5 19.2 1.0 C3A A:CLA314 4.5 32.1 1.0 C2A A:CLA314 4.6 33.1 1.0 CB A:GLU180 4.7 29.3 1.0 CD A:ARG70 4.9 17.6 1.0 CBA A:CLA314 4.9 40.9 1.0 CBD A:CLA314 4.9 31.8 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