Magnesium in PDB 2c9e: Peridinin-Chlorophyll A Protein, High-Salt Form

The structure of Peridinin-Chlorophyll A Protein, High-Salt Form, PDB code: 2c9e was solved by T.Schulte, F.P.Sharples, R.G.Hiller, E.Hofmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.95 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.576, 62.673, 63.345, 90.00, 100.89, 90.00
R / Rfree (%)	17.4 / 21.9

The binding sites of Magnesium atom in the Peridinin-Chlorophyll A Protein, High-Salt Form (pdb code 2c9e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Peridinin-Chlorophyll A Protein, High-Salt Form, PDB code: 2c9e:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Peridinin-Chlorophyll A Protein, High-Salt Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Peridinin-Chlorophyll A Protein, High-Salt Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1327 b:19.4 occ:1.00 MG A:CLA1327 0.0 19.4 1.0 ND A:CLA1327 2.1 19.9 1.0 NC A:CLA1327 2.1 18.9 1.0 NB A:CLA1327 2.1 19.1 1.0 O A:HOH2076 2.2 14.1 1.0 NA A:CLA1327 2.2 18.3 1.0 C4D A:CLA1327 3.0 18.3 1.0 C1C A:CLA1327 3.1 19.1 1.0 C4C A:CLA1327 3.1 20.1 1.0 C1D A:CLA1327 3.1 17.4 1.0 C4B A:CLA1327 3.1 18.7 1.0 C1B A:CLA1327 3.1 18.7 1.0 C4A A:CLA1327 3.2 20.3 1.0 C1A A:CLA1327 3.3 19.1 1.0 CHC A:CLA1327 3.5 17.3 1.0 CHD A:CLA1327 3.5 19.0 1.0 CHB A:CLA1327 3.5 18.1 1.0 CHA A:CLA1327 3.6 18.0 1.0 NE2 A:HIS70 4.0 21.7 1.0 C19 A:CLA1328 4.1 26.5 1.0 C3D A:CLA1327 4.3 17.8 1.0 C2C A:CLA1327 4.3 19.6 1.0 C3C A:CLA1327 4.3 20.0 1.0 C2D A:CLA1327 4.3 18.8 1.0 C3B A:CLA1327 4.3 18.6 1.0 C2B A:CLA1327 4.4 17.8 1.0 C19 A:PID1331 4.5 16.3 1.0 CAA A:DGD1332 4.5 22.8 1.0 C3A A:CLA1327 4.5 18.1 1.0 C2A A:CLA1327 4.6 21.1 1.0 CBA A:DGD1332 4.6 21.1 1.0 CE1 A:HIS70 4.8 23.9 1.0 CD2 A:HIS70 4.8 22.4 1.0 CM5 A:PID1331 4.8 16.0 1.0 CD1 A:LEU97 4.8 17.8 1.0 C17 A:PID1331 5.0 18.9 1.0

Magnesium binding site 2 out of 3 in the Peridinin-Chlorophyll A Protein, High-Salt Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Peridinin-Chlorophyll A Protein, High-Salt Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1328 b:18.9 occ:1.00 MG A:CLA1328 0.0 18.9 1.0 ND A:CLA1328 2.0 16.8 1.0 NB A:CLA1328 2.1 18.0 1.0 NC A:CLA1328 2.1 18.2 1.0 O A:HOH2211 2.1 17.6 1.0 NA A:CLA1328 2.2 15.0 1.0 C4D A:CLA1328 3.0 19.0 1.0 C1B A:CLA1328 3.1 17.1 1.0 C4B A:CLA1328 3.1 20.1 1.0 C1D A:CLA1328 3.1 18.5 1.0 C1C A:CLA1328 3.1 19.6 1.0 C4C A:CLA1328 3.1 20.2 1.0 C4A A:CLA1328 3.2 17.9 1.0 C1A A:CLA1328 3.2 18.8 1.0 CHB A:CLA1328 3.5 15.8 1.0 CHC A:CLA1328 3.5 20.5 1.0 CHD A:CLA1328 3.5 19.4 1.0 CHA A:CLA1328 3.5 17.5 1.0 NE2 A:HIS244 4.0 21.7 1.0 CCA A:DGD1336 4.0 25.5 1.0 C3D A:CLA1328 4.2 18.4 1.0 C2D A:CLA1328 4.3 18.2 1.0 C2B A:CLA1328 4.3 19.9 1.0 CBA A:DGD1336 4.3 24.5 1.0 C3B A:CLA1328 4.3 20.3 1.0 C2C A:CLA1328 4.4 18.9 1.0 C3C A:CLA1328 4.4 20.1 1.0 C3A A:CLA1328 4.5 16.3 1.0 C2A A:CLA1328 4.5 19.4 1.0 C19 A:PID1335 4.7 22.8 1.0 CD2 A:HIS244 4.7 18.9 1.0 CM5 A:PID1335 4.8 17.7 1.0 CE1 A:HIS244 4.9 21.1 1.0 CD1 A:LEU271 4.9 20.0 1.0

Magnesium binding site 3 out of 3 in the Peridinin-Chlorophyll A Protein, High-Salt Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Peridinin-Chlorophyll A Protein, High-Salt Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1337 b:27.1 occ:1.00 OG A:SER71 2.4 30.5 1.0 OD1 A:ASP75 2.5 38.8 1.0 OD1 A:ASP223 2.5 29.4 1.0 O A:SER71 2.5 28.3 1.0 OD2 A:ASP223 2.6 27.1 1.0 O A:HOH2081 2.7 41.6 1.0 O A:HOH2201 2.7 39.7 1.0 CG A:ASP223 2.9 28.2 1.0 CG A:ASP75 3.1 37.5 1.0 C A:SER71 3.2 27.8 1.0 OD2 A:ASP75 3.3 38.5 1.0 CB A:SER71 3.6 28.7 1.0 CA A:SER71 3.7 26.6 1.0 N A:LYS72 4.2 26.4 1.0 N A:ASP75 4.3 32.6 1.0 O A:HOH2077 4.3 64.2 1.0 CB A:ASP223 4.4 26.1 1.0 CB A:ASP75 4.4 34.3 1.0 CA A:LYS72 4.6 28.8 1.0 CA A:ASP75 4.7 34.3 1.0 CB A:LEU74 4.8 24.8 1.0 O A:ASP223 4.9 26.8 1.0

T.Schulte, F.P.Sharples, R.G.Hiller, E.Hofmann. X-Ray Structure of the High-Salt Form of the Peridinin-Chlorophyll A-Protein From the Dinoflagellate Amphidinium Carterae: Modulation of the Spectral Properties of Pigments By the Protein Environment. Biochemistry V. 48 4466 2009.
ISSN: ISSN 0006-2960
PubMed: 19371099
DOI: 10.1021/BI802320Q