Magnesium in PDB 8ow6: Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K

The structure of Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K, PDB code: 8ow6 was solved by E.Hofmann, T.Schulte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.50 / 1.20
Space group	P 3 1 2
Cell size a, b, c (Å), α, β, γ (°)	90.61, 90.61, 155.61, 90, 90, 120
R / Rfree (%)	14.9 / 17.1

The structure of Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Potassium	(K)	2 atoms

The binding sites of Magnesium atom in the Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K (pdb code 8ow6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K, PDB code: 8ow6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:6.4 occ:1.00 MG A:CLA601 0.0 6.4 1.0 ND A:CLA601 2.0 6.7 1.0 O A:HOH701 2.1 5.7 1.0 NB A:CLA601 2.1 6.3 1.0 NC A:CLA601 2.1 6.2 1.0 NA A:CLA601 2.2 6.3 1.0 C4D A:CLA601 3.0 7.1 1.0 C1B A:CLA601 3.1 6.4 1.0 C1C A:CLA601 3.1 6.7 1.0 C4B A:CLA601 3.1 6.6 1.0 C4A A:CLA601 3.1 6.8 1.0 C1D A:CLA601 3.2 7.1 1.0 C4C A:CLA601 3.2 6.3 1.0 C1A A:CLA601 3.2 6.5 1.0 HAG3 A:W4O615 3.4 11.2 1.0 CHB A:CLA601 3.4 6.5 1.0 CHC A:CLA601 3.5 6.2 1.0 CHA A:CLA601 3.5 6.4 1.0 H22 A:PID612 3.5 8.1 1.0 CHD A:CLA601 3.6 6.5 1.0 NE2 A:HIS65 4.0 6.0 1.0 HAG2 A:W4O615 4.0 11.2 1.0 HM53 A:PID614 4.1 8.3 1.0 H19 A:PID614 4.2 7.9 1.0 CIA A:W4O615 4.2 9.3 1.0 C3D A:CLA601 4.2 6.6 1.0 HD11 A:ILE90 4.3 8.9 1.0 C2B A:CLA601 4.3 6.1 1.0 C3B A:CLA601 4.3 6.5 1.0 C2C A:CLA601 4.3 6.2 1.0 C2D A:CLA601 4.4 6.8 1.0 C3C A:CLA601 4.4 6.2 1.0 HM51 A:PID614 4.4 8.3 1.0 C22 A:PID612 4.4 6.7 1.0 HD13 A:ILE90 4.4 8.9 1.0 C3A A:CLA601 4.5 6.8 1.0 C2A A:CLA601 4.5 7.0 1.0 HD2 A:HIS65 4.5 8.0 1.0 HHB A:CLA601 4.5 7.7 1.0 HHC A:CLA601 4.6 7.5 1.0 CD2 A:HIS65 4.6 6.7 1.0 HAG1 A:W4O615 4.6 11.2 1.0 HHD A:CLA601 4.7 7.8 1.0 C19 A:PID614 4.7 6.6 1.0 CM5 A:PID614 4.7 6.9 1.0 H17 A:PID614 4.7 8.0 1.0 CE1 A:HIS65 4.8 6.0 1.0 C23 A:PID612 4.8 7.0 1.0 CD1 A:ILE90 4.8 7.4 1.0 H20 A:PID612 4.8 9.3 1.0 CBD A:CLA601 4.9 6.7 1.0 HE1 A:HIS65 5.0 7.2 1.0

Magnesium binding site 2 out of 4 in the Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:6.8 occ:1.00 MG B:CLA601 0.0 6.8 1.0 NB B:CLA601 2.0 6.5 1.0 O B:HOH701 2.0 6.6 1.0 ND B:CLA601 2.1 6.9 1.0 NC B:CLA601 2.1 6.7 1.0 NA B:CLA601 2.1 6.6 1.0 C4D B:CLA601 3.0 6.8 1.0 C1B B:CLA601 3.0 7.0 1.0 C4B B:CLA601 3.0 6.6 1.0 C1C B:CLA601 3.1 6.6 1.0 C4A B:CLA601 3.1 6.6 1.0 C4C B:CLA601 3.1 6.6 1.0 C1D B:CLA601 3.2 6.6 1.0 C1A B:CLA601 3.2 6.5 1.0 HAG2 B:W4O615 3.3 10.4 1.0 CHC B:CLA601 3.4 6.4 1.0 CHB B:CLA601 3.4 6.9 1.0 H22 B:PID612 3.5 7.7 1.0 CHD B:CLA601 3.5 7.4 1.0 CHA B:CLA601 3.5 6.4 1.0 NE2 B:HIS65 3.9 6.5 1.0 H19 B:PID614 4.0 8.4 1.0 HM52 B:PID614 4.1 9.3 1.0 HD11 B:ILE90 4.1 9.1 1.0 HAG1 B:W4O615 4.2 10.4 1.0 CIA B:W4O615 4.2 8.7 1.0 C2B B:CLA601 4.3 6.9 1.0 C3B B:CLA601 4.3 6.7 1.0 C3D B:CLA601 4.3 6.5 1.0 C2C B:CLA601 4.3 6.6 1.0 C3C B:CLA601 4.4 6.6 1.0 C2D B:CLA601 4.4 6.8 1.0 HM51 B:PID614 4.4 9.3 1.0 C22 B:PID612 4.4 6.4 1.0 HD13 B:ILE90 4.4 9.1 1.0 C3A B:CLA601 4.5 6.7 1.0 HHC B:CLA601 4.5 7.6 1.0 HHB B:CLA601 4.5 8.3 1.0 C2A B:CLA601 4.5 7.3 1.0 C19 B:PID614 4.6 7.0 1.0 HAG3 B:W4O615 4.6 10.4 1.0 H17 B:PID614 4.6 9.1 1.0 HHD B:CLA601 4.6 8.9 1.0 CM5 B:PID614 4.7 7.8 1.0 HD2 B:HIS65 4.7 8.4 1.0 CD2 B:HIS65 4.7 7.0 1.0 CD1 B:ILE90 4.7 7.6 1.0 CE1 B:HIS65 4.8 6.5 1.0 C23 B:PID612 4.8 6.7 1.0 HE1 B:HIS65 4.9 7.8 1.0 H20 B:PID612 4.9 7.7 1.0 CBD B:CLA601 5.0 6.8 1.0

Magnesium binding site 3 out of 4 in the Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:9.0 occ:1.00 MG C:CLA601 0.0 9.0 1.0 NB C:CLA601 2.0 9.3 1.0 O C:HOH701 2.0 8.3 1.0 ND C:CLA601 2.1 8.5 1.0 NC C:CLA601 2.1 8.3 1.0 NA C:CLA601 2.2 8.7 1.0 C4D C:CLA601 3.0 8.7 1.0 C1B C:CLA601 3.0 8.5 1.0 C4B C:CLA601 3.1 8.5 1.0 C1C C:CLA601 3.1 8.1 1.0 C4A C:CLA601 3.1 9.0 1.0 C4C C:CLA601 3.2 8.2 1.0 C1D C:CLA601 3.2 8.3 1.0 C1A C:CLA601 3.2 8.7 1.0 CHB C:CLA601 3.4 8.7 1.0 CHC C:CLA601 3.4 8.1 1.0 CHD C:CLA601 3.5 8.3 1.0 CHA C:CLA601 3.5 8.5 1.0 H22 C:PID612 3.6 9.9 1.0 HAG2 C:W4O615 3.6 12.4 1.0 HAG3 C:W4O615 3.8 12.4 1.0 NE2 C:HIS65 4.0 9.0 1.0 HM53 C:PID614 4.0 11.5 1.0 H19 C:PID614 4.1 10.2 1.0 CIA C:W4O615 4.2 10.3 1.0 C3D C:CLA601 4.3 8.6 1.0 C2B C:CLA601 4.3 8.3 1.0 C3B C:CLA601 4.3 8.8 1.0 C2C C:CLA601 4.3 8.2 1.0 C3C C:CLA601 4.4 8.5 1.0 C2D C:CLA601 4.4 9.0 1.0 HD11 C:ILE90 4.4 12.5 1.0 HM52 C:PID614 4.4 11.5 1.0 HD13 C:ILE90 4.4 12.5 1.0 C3A C:CLA601 4.5 9.0 1.0 C22 C:PID612 4.5 8.3 1.0 HHB C:CLA601 4.5 10.4 1.0 C2A C:CLA601 4.5 9.0 1.0 HHC C:CLA601 4.5 9.7 1.0 HD2 C:HIS65 4.5 10.8 1.0 CD2 C:HIS65 4.6 9.0 1.0 HHD C:CLA601 4.6 9.9 1.0 H17 C:PID614 4.7 10.4 1.0 CM5 C:PID614 4.7 9.6 1.0 C19 C:PID614 4.7 8.5 1.0 CE1 C:HIS65 4.8 8.8 1.0 H20 C:PID612 4.9 9.6 1.0 CD1 C:ILE90 4.9 10.4 1.0 HAG1 C:W4O615 4.9 12.4 1.0 C23 C:PID612 4.9 8.2 1.0 HE1 C:HIS65 4.9 10.5 1.0 HAV1 C:W4O615 5.0 12.4 1.0 CBD C:CLA601 5.0 8.5 1.0

Magnesium binding site 4 out of 4 in the Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Peridinin-Chlorophyll-Protein of Heterocapsa Pygmaea, 100K within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:8.4 occ:1.00 MG D:CLA601 0.0 8.4 1.0 NB D:CLA601 2.0 8.2 1.0 ND D:CLA601 2.1 8.7 1.0 O D:HOH701 2.1 8.3 1.0 NC D:CLA601 2.1 7.8 1.0 NA D:CLA601 2.1 8.5 1.0 C4D D:CLA601 3.0 8.9 1.0 C1B D:CLA601 3.0 8.0 1.0 C4B D:CLA601 3.1 8.6 1.0 C4A D:CLA601 3.1 8.6 1.0 C1C D:CLA601 3.1 7.6 1.0 C4C D:CLA601 3.2 7.8 1.0 C1D D:CLA601 3.2 8.5 1.0 C1A D:CLA601 3.2 9.6 1.0 HAG1 D:W4O615 3.2 13.0 1.0 CHC D:CLA601 3.4 7.8 1.0 CHB D:CLA601 3.4 8.0 1.0 CHA D:CLA601 3.5 9.3 1.0 CHD D:CLA601 3.5 8.0 1.0 H22 D:PID612 3.6 9.4 1.0 HAG3 D:W4O615 3.7 13.0 1.0 H19 D:PID614 4.0 11.6 1.0 NE2 D:HIS65 4.0 7.9 1.0 CIA D:W4O615 4.0 10.9 1.0 HM52 D:PID614 4.1 11.3 1.0 HD11 D:ILE90 4.1 10.8 1.0 C3D D:CLA601 4.3 8.4 1.0 C2B D:CLA601 4.3 7.9 1.0 C3B D:CLA601 4.3 8.5 1.0 C2C D:CLA601 4.3 7.8 1.0 C3C D:CLA601 4.4 8.3 1.0 HAG2 D:W4O615 4.4 13.0 1.0 HM51 D:PID614 4.4 11.3 1.0 C2D D:CLA601 4.4 8.3 1.0 C3A D:CLA601 4.4 9.4 1.0 C22 D:PID612 4.5 7.8 1.0 HHC D:CLA601 4.5 9.3 1.0 C2A D:CLA601 4.5 9.5 1.0 HD13 D:ILE90 4.5 10.8 1.0 HHB D:CLA601 4.5 9.6 1.0 C19 D:PID614 4.6 9.7 1.0 H17 D:PID614 4.6 10.8 1.0 HHD D:CLA601 4.6 9.5 1.0 CM5 D:PID614 4.7 9.4 1.0 CD2 D:HIS65 4.7 7.8 1.0 HD2 D:HIS65 4.7 9.3 1.0 CE1 D:HIS65 4.8 8.4 1.0 CD1 D:ILE90 4.8 9.0 1.0 HE1 D:HIS65 4.9 10.1 1.0 C23 D:PID612 4.9 8.0 1.0 HM72 D:PID612 4.9 9.8 1.0 H20 D:PID612 5.0 9.8 1.0 CBD D:CLA601 5.0 9.2 1.0

T.Schulte, N.C.M.Magdaong, M.Di Valentin, A.Agostini, C.E.Tait, D.M.Niedzwiedzki, D.Carbonera, E.Hofmann. Structural and Spectroscopic Characterization of the Peridinin-Chlorophyll A-Protein (Pcp) Complex From Heterocapsa Pygmaea (Hppcp) To Be Published.