Magnesium in PDB 3pl9: Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution

The structure of Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution, PDB code: 3pl9 was solved by X.W.Pan, M.Li, T.Wan, L.F.Wang, C.J.Jia, Z.Q.Hou, X.L.Zhao, J.P.Zhang, W.R.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.56 / 2.80
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.793, 68.793, 425.778, 90.00, 90.00, 120.00
R / Rfree (%)	28.2 / 29.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution (pdb code 3pl9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution, PDB code: 3pl9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in the Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:62.0 occ:1.00 MG A:CLA602 0.0 62.0 1.0 NB A:CLA602 2.0 61.9 1.0 ND A:CLA602 2.0 64.1 1.0 NC A:CLA602 2.1 57.2 1.0 OE1 A:GLU96 2.2 49.9 1.0 NA A:CLA602 2.2 71.3 1.0 C4D A:CLA602 3.0 69.5 1.0 C1B A:CLA602 3.0 68.5 1.0 C4B A:CLA602 3.0 64.8 1.0 C1C A:CLA602 3.1 56.9 1.0 C1D A:CLA602 3.1 62.1 1.0 C4C A:CLA602 3.1 53.8 1.0 C4A A:CLA602 3.1 72.4 1.0 C1A A:CLA602 3.2 76.2 1.0 CD A:GLU96 3.2 45.1 1.0 CHC A:CLA602 3.4 61.5 1.0 CHB A:CLA602 3.4 73.1 1.0 CHD A:CLA602 3.5 55.6 1.0 CHA A:CLA602 3.5 73.6 1.0 CG A:GLU96 4.0 42.8 1.0 OE2 A:GLU96 4.1 43.9 1.0 C3D A:CLA602 4.2 70.2 1.0 C2B A:CLA602 4.3 69.7 1.0 NE A:ARG202 4.3 40.0 1.0 O24 A:XAT622 4.3 0.5 1.0 C3B A:CLA602 4.3 69.0 1.0 C2D A:CLA602 4.3 66.5 1.0 C2C A:CLA602 4.3 52.3 1.0 C3C A:CLA602 4.3 49.4 1.0 NH2 A:ARG202 4.4 46.3 1.0 C3A A:CLA602 4.5 72.2 1.0 C2A A:CLA602 4.5 78.9 1.0 CZ A:ARG202 4.8 42.3 1.0 C38 A:XAT622 4.8 0.3 1.0 CB A:GLU96 4.8 37.2 1.0 O2A A:CLA602 4.9 0.2 1.0

Magnesium binding site 2 out of 13 in the Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:47.8 occ:1.00 MG A:CLA603 0.0 47.8 1.0 NB A:CLA603 2.0 40.3 1.0 ND A:CLA603 2.0 51.6 1.0 NC A:CLA603 2.1 46.1 1.0 NA A:CLA603 2.2 57.2 1.0 NE2 A:HIS99 2.3 43.7 1.0 C4D A:CLA603 3.0 56.6 1.0 C4B A:CLA603 3.0 42.2 1.0 C1B A:CLA603 3.0 45.0 1.0 C1C A:CLA603 3.1 45.8 1.0 C4C A:CLA603 3.1 43.4 1.0 C1D A:CLA603 3.1 51.9 1.0 C4A A:CLA603 3.1 56.4 1.0 C1A A:CLA603 3.2 61.3 1.0 CD2 A:HIS99 3.2 42.9 1.0 CE1 A:HIS99 3.2 41.7 1.0 CHC A:CLA603 3.4 42.9 1.0 CHB A:CLA603 3.4 50.4 1.0 CHD A:CLA603 3.5 48.6 1.0 CHA A:CLA603 3.5 60.0 1.0 C7 A:CLA609 3.6 0.8 1.0 C10 A:CLA609 3.8 0.8 1.0 C8 A:CLA609 4.1 0.3 1.0 C3D A:CLA603 4.3 57.6 1.0 C3B A:CLA603 4.3 45.7 1.0 C2B A:CLA603 4.3 48.0 1.0 C2C A:CLA603 4.3 46.6 1.0 C3C A:CLA603 4.3 45.2 1.0 C2D A:CLA603 4.3 53.4 1.0 ND1 A:HIS99 4.4 40.6 1.0 CG A:HIS99 4.4 38.8 1.0 C9 A:CLA609 4.5 0.7 1.0 C3A A:CLA603 4.5 61.4 1.0 C2A A:CLA603 4.5 65.7 1.0 C6 A:CLA609 4.8 0.1 1.0 CBD A:CLA603 5.0 61.8 1.0

Magnesium binding site 3 out of 13 in the Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:38.0 occ:1.00 MG A:CLA604 0.0 38.0 1.0 ND A:CLA604 2.0 40.5 1.0 NB A:CLA604 2.1 40.6 1.0 NC A:CLA604 2.1 43.9 1.0 NA A:CLA604 2.1 40.0 1.0 O A:HOH307 2.2 47.0 1.0 C4D A:CLA604 3.0 43.8 1.0 C4B A:CLA604 3.1 41.7 1.0 C1D A:CLA604 3.1 44.3 1.0 C1C A:CLA604 3.1 43.7 1.0 C1B A:CLA604 3.1 39.0 1.0 C4C A:CLA604 3.1 44.8 1.0 C4A A:CLA604 3.1 36.3 1.0 C1A A:CLA604 3.2 40.9 1.0 CHC A:CLA604 3.4 41.6 1.0 CHD A:CLA604 3.4 46.5 1.0 CHB A:CLA604 3.5 38.9 1.0 CHA A:CLA604 3.5 44.4 1.0 O23 A:NEX623 3.6 35.1 1.0 C24 A:NEX623 3.8 33.8 1.0 O A:HOH244 3.8 31.6 1.0 C3D A:CLA604 4.2 43.8 1.0 C23 A:NEX623 4.3 34.7 1.0 C2D A:CLA604 4.3 45.5 1.0 C3B A:CLA604 4.3 42.4 1.0 C2B A:CLA604 4.3 40.6 1.0 C2C A:CLA604 4.3 43.1 1.0 C3C A:CLA604 4.3 44.9 1.0 C3A A:CLA604 4.4 30.9 1.0 C2A A:CLA604 4.5 31.0 1.0 CE2 A:TYR135 4.6 46.1 1.0 O A:GLY109 4.6 19.3 1.0 CA A:GLY109 4.7 19.4 1.0 C4 A:XAT622 4.9 35.2 1.0 C A:GLY109 4.9 17.3 1.0 CBD A:CLA604 5.0 39.4 1.0 C25 A:NEX623 5.0 35.2 1.0

Magnesium binding site 4 out of 13 in the Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:29.5 occ:1.00 MG A:CHL606 0.0 29.5 1.0 ND A:CHL606 2.0 28.4 1.0 NB A:CHL606 2.0 32.2 1.0 NC A:CHL606 2.1 32.1 1.0 NA A:CHL606 2.2 38.2 1.0 O A:HOH248 2.3 20.8 1.0 C4D A:CHL606 2.9 33.2 1.0 C1D A:CHL606 3.0 29.0 1.0 C4B A:CHL606 3.1 28.6 1.0 C1B A:CHL606 3.1 27.1 1.0 C1C A:CHL606 3.1 33.4 1.0 C4C A:CHL606 3.1 34.0 1.0 C4A A:CHL606 3.2 31.0 1.0 C1A A:CHL606 3.2 38.9 1.0 CHD A:CHL606 3.4 32.1 1.0 CHC A:CHL606 3.4 30.3 1.0 CHB A:CHL606 3.5 24.4 1.0 CHA A:CHL606 3.5 35.9 1.0 O A:HOH305 3.8 27.0 1.0 OE2 A:GLU151 3.9 33.6 1.0 C3D A:CHL606 4.2 36.3 1.0 C2D A:CHL606 4.3 31.5 1.0 C3B A:CHL606 4.3 23.7 1.0 C2B A:CHL606 4.3 28.8 1.0 C3C A:CHL606 4.3 34.4 1.0 C2C A:CHL606 4.3 35.9 1.0 C38 A:NEX623 4.4 35.7 1.0 C3A A:CHL606 4.5 35.4 1.0 O1A A:CLA604 4.5 49.2 1.0 C2A A:CHL606 4.5 40.8 1.0 CD A:GLU151 4.8 24.6 1.0 CBC A:CHL607 5.0 49.4 1.0 CBD A:CHL606 5.0 36.3 1.0

Magnesium binding site 5 out of 13 in the Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:48.8 occ:1.00 MG A:CHL607 0.0 48.8 1.0 ND A:CHL607 2.0 52.3 1.0 NB A:CHL607 2.0 50.4 1.0 NC A:CHL607 2.1 52.7 1.0 NA A:CHL607 2.2 50.3 1.0 O A:HOH245 2.2 12.0 1.0 C4D A:CHL607 3.0 52.1 1.0 C1B A:CHL607 3.0 46.3 1.0 C4B A:CHL607 3.1 47.6 1.0 C1C A:CHL607 3.1 52.7 1.0 C1D A:CHL607 3.1 52.1 1.0 C4C A:CHL607 3.1 51.5 1.0 C4A A:CHL607 3.1 51.4 1.0 C1A A:CHL607 3.2 52.8 1.0 CHC A:CHL607 3.4 47.4 1.0 CHB A:CHL607 3.4 49.9 1.0 CHD A:CHL607 3.5 53.0 1.0 CHA A:CHL607 3.5 52.6 1.0 C10 A:CHL607 4.1 0.6 1.0 OMC A:CHL606 4.2 35.9 1.0 C3D A:CHL607 4.3 52.5 1.0 C2B A:CHL607 4.3 45.1 1.0 C3B A:CHL607 4.3 45.6 1.0 C2D A:CHL607 4.3 50.3 1.0 C8 A:CHL607 4.3 0.4 1.0 C2C A:CHL607 4.3 53.1 1.0 C3C A:CHL607 4.3 48.5 1.0 C3A A:CHL607 4.5 55.1 1.0 C2A A:CHL607 4.5 59.1 1.0 C9 A:CHL607 4.5 0.5 1.0 C12 A:CHL607 4.7 0.1 1.0 CMC A:CHL606 4.8 40.0 1.0 C11 A:CHL607 5.0 0.5 1.0

Magnesium binding site 6 out of 13 in the Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg608 b:58.1 occ:1.00 MG A:CHL608 0.0 58.1 1.0 NB A:CHL608 2.0 58.1 1.0 ND A:CHL608 2.0 64.0 1.0 NC A:CHL608 2.1 67.2 1.0 NA A:CHL608 2.2 51.4 1.0 O A:HOH247 2.3 19.1 1.0 C4D A:CHL608 3.0 61.8 1.0 C4B A:CHL608 3.0 61.0 1.0 C1B A:CHL608 3.0 57.0 1.0 C1C A:CHL608 3.1 69.7 1.0 C1D A:CHL608 3.1 64.5 1.0 C4C A:CHL608 3.1 68.2 1.0 C4A A:CHL608 3.2 50.9 1.0 CZ A:PHE178 3.2 70.5 1.0 C1A A:CHL608 3.2 50.2 1.0 CHC A:CHL608 3.4 65.8 1.0 CHB A:CHL608 3.5 55.5 1.0 CHD A:CHL608 3.5 67.3 1.0 CG2 A:ILE158 3.5 30.3 1.0 CE1 A:PHE178 3.5 72.7 1.0 CHA A:CHL608 3.5 58.4 1.0 CE2 A:PHE178 4.2 72.2 1.0 C3B A:CHL608 4.3 58.6 1.0 C2B A:CHL608 4.3 58.0 1.0 C3D A:CHL608 4.3 61.4 1.0 C2D A:CHL608 4.3 63.2 1.0 C2C A:CHL608 4.4 72.8 1.0 C3C A:CHL608 4.4 71.8 1.0 C3A A:CHL608 4.5 46.5 1.0 C2A A:CHL608 4.5 41.5 1.0 CD1 A:PHE178 4.7 68.8 1.0 O A:ILE158 4.8 25.3 1.0 CB A:ARG162 4.8 50.9 1.0 O A:HOH246 4.9 26.9 1.0 CB A:ILE158 5.0 28.0 1.0

Magnesium binding site 7 out of 13 in the Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution


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 Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg609 b:52.8 occ:1.00 MG A:CLA609 0.0 52.8 1.0 ND A:CLA609 2.0 50.6 1.0 NC A:CLA609 2.1 52.4 1.0 NB A:CLA609 2.1 54.9 1.0 NA A:CLA609 2.1 56.4 1.0 OE1 A:GLU159 2.2 39.0 1.0 C4D A:CLA609 3.0 55.7 1.0 C1D A:CLA609 3.1 51.0 1.0 C1C A:CLA609 3.1 49.2 1.0 C4B A:CLA609 3.1 56.7 1.0 C1B A:CLA609 3.1 58.0 1.0 C4C A:CLA609 3.1 49.2 1.0 C4A A:CLA609 3.1 56.7 1.0 C1A A:CLA609 3.2 56.4 1.0 CD A:GLU159 3.2 37.0 1.0 CHC A:CLA609 3.4 51.5 1.0 CHD A:CLA609 3.4 51.5 1.0 CHA A:CLA609 3.5 56.2 1.0 CHB A:CLA609 3.5 61.3 1.0 CG A:GLU159 3.8 37.1 1.0 C3D A:CLA609 4.2 53.3 1.0 C2D A:CLA609 4.3 51.5 1.0 C2B A:CLA609 4.3 61.2 1.0 C2C A:CLA609 4.3 48.6 1.0 C3C A:CLA609 4.3 46.1 1.0 C3B A:CLA609 4.3 61.4 1.0 OE2 A:GLU159 4.3 31.6 1.0 C2A A:CLA609 4.5 53.5 1.0 C3A A:CLA609 4.5 51.4 1.0 CMD A:CLA603 4.5 50.2 1.0 CB A:GLU159 4.6 31.4 1.0 NH2 A:ARG162 4.8 33.2 1.0 CBD A:CLA609 4.9 51.6 1.0

Magnesium binding site 8 out of 13 in the Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg610 b:41.6 occ:1.00 MG A:CLA610 0.0 41.6 1.0 ND A:CLA610 2.0 43.1 1.0 NB A:CLA610 2.0 40.4 1.0 NC A:CLA610 2.1 43.5 1.0 OE1 A:GLU197 2.1 30.8 1.0 NA A:CLA610 2.1 43.5 1.0 C4D A:CLA610 3.0 47.6 1.0 C4B A:CLA610 3.0 41.6 1.0 C1C A:CLA610 3.1 38.1 1.0 C1B A:CLA610 3.1 39.7 1.0 C1D A:CLA610 3.1 45.5 1.0 C4C A:CLA610 3.1 40.6 1.0 C4A A:CLA610 3.1 45.6 1.0 C1A A:CLA610 3.2 43.6 1.0 CD A:GLU197 3.2 31.8 1.0 CHC A:CLA610 3.4 37.6 1.0 CHD A:CLA610 3.4 43.6 1.0 CHA A:CLA610 3.5 47.9 1.0 CHB A:CLA610 3.5 42.9 1.0 NH1 A:ARG101 3.7 37.8 1.0 CG A:GLU197 4.0 29.6 1.0 OE2 A:GLU197 4.0 39.1 1.0 C38 A:LUT620 4.2 34.8 1.0 C3D A:CLA610 4.2 49.8 1.0 C3B A:CLA610 4.3 41.4 1.0 C2D A:CLA610 4.3 50.0 1.0 C2B A:CLA610 4.3 39.6 1.0 C2C A:CLA610 4.3 39.3 1.0 C3C A:CLA610 4.3 37.6 1.0 C2A A:CLA610 4.4 40.2 1.0 C3A A:CLA610 4.4 45.4 1.0 CD A:ARG101 4.7 40.7 1.0 CZ A:ARG101 4.7 43.7 1.0 C28 A:LUT620 4.9 33.1 1.0 CB A:GLU197 4.9 25.5 1.0 CBD A:CLA610 4.9 54.0 1.0

Magnesium binding site 9 out of 13 in the Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg611 b:19.8 occ:1.00 MG A:CLA611 0.0 19.8 1.0 ND A:CLA611 2.0 25.2 1.0 NB A:CLA611 2.0 18.5 1.0 NC A:CLA611 2.1 21.3 1.0 NA A:CLA611 2.2 28.9 1.0 O3P A:G3P630 2.6 72.3 1.0 O2P A:G3P630 2.8 80.3 1.0 P A:G3P630 3.0 82.0 1.0 C4D A:CLA611 3.0 25.0 1.0 C1B A:CLA611 3.1 16.5 1.0 C4B A:CLA611 3.1 16.6 1.0 C1D A:CLA611 3.1 19.9 1.0 C1C A:CLA611 3.1 23.9 1.0 C4C A:CLA611 3.1 22.9 1.0 C4A A:CLA611 3.2 29.5 1.0 C1A A:CLA611 3.2 31.2 1.0 CHC A:CLA611 3.4 22.8 1.0 CHB A:CLA611 3.5 20.5 1.0 CHD A:CLA611 3.5 21.1 1.0 CHA A:CLA611 3.5 25.8 1.0 O1P A:G3P630 3.6 83.0 1.0 CMD A:CLA612 3.9 32.2 1.0 C3D A:CLA611 4.2 21.3 1.0 C2B A:CLA611 4.3 15.4 1.0 C3B A:CLA611 4.3 13.5 1.0 C2D A:CLA611 4.3 21.2 1.0 C2C A:CLA611 4.3 24.4 1.0 C3C A:CLA611 4.3 24.6 1.0 NZ A:LYS199 4.5 43.1 1.0 O4P A:G3P630 4.5 81.0 1.0 C3A A:CLA611 4.5 34.3 1.0 C2A A:CLA611 4.6 37.5 1.0 C3 A:G3P630 4.6 76.6 1.0 CBD A:CLA611 5.0 22.6 1.0

Magnesium binding site 10 out of 13 in the Crystal Structure of Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution


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 Spinach Minor Light-Harvesting Complex CP29 at 2.80 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg612 b:37.9 occ:1.00 MG A:CLA612 0.0 37.9 1.0 ND A:CLA612 2.0 38.7 1.0 NB A:CLA612 2.0 34.3 1.0 NC A:CLA612 2.1 27.9 1.0 NE2 A:HIS200 2.1 33.9 1.0 NA A:CLA612 2.2 39.3 1.0 C4D A:CLA612 3.0 45.7 1.0 C4B A:CLA612 3.1 37.5 1.0 C1C A:CLA612 3.1 26.5 1.0 C1B A:CLA612 3.1 33.8 1.0 CE1 A:HIS200 3.1 32.1 1.0 C1D A:CLA612 3.1 34.7 1.0 C4C A:CLA612 3.1 31.5 1.0 CD2 A:HIS200 3.1 34.6 1.0 C4A A:CLA612 3.2 40.1 1.0 C1A A:CLA612 3.2 48.5 1.0 CHC A:CLA612 3.4 30.7 1.0 CHB A:CLA612 3.5 38.3 1.0 CHD A:CLA612 3.5 30.9 1.0 CHA A:CLA612 3.5 52.6 1.0 ND1 A:HIS200 4.2 29.0 1.0 C3D A:CLA612 4.2 48.0 1.0 C2B A:CLA612 4.3 34.8 1.0 CG A:HIS200 4.3 30.4 1.0 C3B A:CLA612 4.3 40.4 1.0 C2C A:CLA612 4.3 24.6 1.0 C2D A:CLA612 4.3 37.2 1.0 C3C A:CLA612 4.3 28.9 1.0 C3A A:CLA612 4.5 46.2 1.0 C2A A:CLA612 4.5 54.3 1.0 CBD A:CLA612 4.9 66.4 1.0

X.Pan, M.Li, T.Wan, L.Wang, C.Jia, Z.Hou, X.Zhao, J.Zhang, W.Chang. Structural Insights Into Energy Regulation of Light-Harvesting Complex CP29 From Spinach. Nat.Struct.Mol.Biol. V. 18 309 2011.
ISSN: ESSN 1545-9985
PubMed: 21297637
DOI: 10.1038/NSMB.2008