Magnesium in PDB 2dre: Crystal Structure of Water-Soluble Chlorophyll Protein From Lepidium Virginicum at 2.00 Angstrom Resolution

The structure of Crystal Structure of Water-Soluble Chlorophyll Protein From Lepidium Virginicum at 2.00 Angstrom Resolution, PDB code: 2dre was solved by D.Horigome, H.Satoh, N.Itoh, K.Mitsunaga, I.Oonishi, A.Nakagawa, A.Uchida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.99 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.060, 82.730, 121.880, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 28

The binding sites of Magnesium atom in the Crystal Structure of Water-Soluble Chlorophyll Protein From Lepidium Virginicum at 2.00 Angstrom Resolution (pdb code 2dre). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Water-Soluble Chlorophyll Protein From Lepidium Virginicum at 2.00 Angstrom Resolution, PDB code: 2dre:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Water-Soluble Chlorophyll Protein From Lepidium Virginicum at 2.00 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 Water-Soluble Chlorophyll Protein From Lepidium Virginicum at 2.00 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:22.8 occ:1.00 MG A:CLA1001 0.0 22.8 1.0 ND A:CLA1001 2.0 22.6 1.0 O A:PRO36 2.1 23.6 1.0 NC A:CLA1001 2.2 24.6 1.0 NA A:CLA1001 2.2 24.8 1.0 NB A:CLA1001 2.2 25.7 1.0 C4D A:CLA1001 3.0 23.8 1.0 C1D A:CLA1001 3.1 23.3 1.0 C4C A:CLA1001 3.2 26.3 1.0 C1B A:CLA1001 3.2 23.0 1.0 C1C A:CLA1001 3.2 26.2 1.0 C4A A:CLA1001 3.2 23.8 1.0 C1A A:CLA1001 3.2 25.2 1.0 C4B A:CLA1001 3.2 25.4 1.0 C A:PRO36 3.3 22.0 1.0 CHA A:CLA1001 3.5 24.3 1.0 CHB A:CLA1001 3.5 23.5 1.0 CHD A:CLA1001 3.5 21.7 1.0 CHC A:CLA1001 3.6 24.6 1.0 C9 B:CLA1001 4.0 53.8 1.0 C7 B:CLA1001 4.1 50.0 1.0 N A:ALA37 4.1 21.4 1.0 CA A:ALA37 4.1 22.8 1.0 CD A:PRO36 4.2 17.6 1.0 CA A:PRO36 4.2 20.1 1.0 C3D A:CLA1001 4.2 21.9 1.0 N A:PRO36 4.2 19.7 1.0 CB A:PRO36 4.3 22.0 1.0 C2D A:CLA1001 4.3 20.0 1.0 CB A:ALA37 4.4 20.6 1.0 C3C A:CLA1001 4.4 25.1 1.0 C2C A:CLA1001 4.4 25.9 1.0 C2B A:CLA1001 4.4 25.2 1.0 C3B A:CLA1001 4.5 26.6 1.0 C3A A:CLA1001 4.5 26.4 1.0 C2A A:CLA1001 4.5 26.8 1.0 C8 B:CLA1001 4.6 52.1 1.0 CG2 A:VAL35 4.6 15.4 1.0 CG A:PRO36 4.8 23.1 1.0 CB A:VAL35 4.9 20.0 1.0 CBD A:CLA1001 5.0 23.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Water-Soluble Chlorophyll Protein From Lepidium Virginicum at 2.00 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 Water-Soluble Chlorophyll Protein From Lepidium Virginicum at 2.00 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:28.6 occ:1.00 MG B:CLA1001 0.0 28.6 1.0 NB B:CLA1001 2.1 26.9 1.0 O B:PRO36 2.1 27.4 1.0 ND B:CLA1001 2.1 25.2 1.0 NA B:CLA1001 2.1 27.5 1.0 NC B:CLA1001 2.2 26.3 1.0 C1B B:CLA1001 3.0 27.4 1.0 C4D B:CLA1001 3.1 24.9 1.0 C4A B:CLA1001 3.1 27.7 1.0 C4B B:CLA1001 3.1 25.1 1.0 C1A B:CLA1001 3.2 28.9 1.0 C1C B:CLA1001 3.2 27.9 1.0 C4C B:CLA1001 3.3 26.8 1.0 C1D B:CLA1001 3.3 23.9 1.0 C B:PRO36 3.3 28.6 1.0 CHB B:CLA1001 3.4 26.0 1.0 CHC B:CLA1001 3.5 27.6 1.0 CHA B:CLA1001 3.5 27.4 1.0 CHD B:CLA1001 3.6 24.8 1.0 C9 A:CLA1001 4.0 52.9 1.0 CA B:ALA37 4.1 29.9 1.0 N B:ALA37 4.1 31.2 1.0 CA B:PRO36 4.3 29.0 1.0 C2B B:CLA1001 4.3 28.3 1.0 C3D B:CLA1001 4.3 25.8 1.0 C3B B:CLA1001 4.3 29.2 1.0 CB B:ALA37 4.4 30.3 1.0 N B:PRO36 4.4 28.2 1.0 C3A B:CLA1001 4.4 27.5 1.0 C2C B:CLA1001 4.4 25.3 1.0 CB B:PRO36 4.4 29.0 1.0 C3C B:CLA1001 4.5 24.8 1.0 C2D B:CLA1001 4.5 24.7 1.0 C2A B:CLA1001 4.5 29.4 1.0 CD B:PRO36 4.5 29.1 1.0 CG2 B:VAL35 4.8 24.8 1.0 C6 A:CLA1001 4.8 48.3 1.0 C7 A:CLA1001 4.9 51.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Water-Soluble Chlorophyll Protein From Lepidium Virginicum at 2.00 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 Water-Soluble Chlorophyll Protein From Lepidium Virginicum at 2.00 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:20.8 occ:1.00 MG C:CLA1001 0.0 20.8 1.0 ND C:CLA1001 2.0 17.9 1.0 O C:PRO36 2.1 16.4 1.0 NC C:CLA1001 2.2 19.4 1.0 NB C:CLA1001 2.2 20.5 1.0 NA C:CLA1001 2.2 20.9 1.0 C4D C:CLA1001 3.0 18.2 1.0 C1D C:CLA1001 3.1 18.7 1.0 C1B C:CLA1001 3.2 22.4 1.0 C4A C:CLA1001 3.2 19.7 1.0 C4C C:CLA1001 3.2 20.0 1.0 C1A C:CLA1001 3.2 19.9 1.0 C1C C:CLA1001 3.2 22.0 1.0 C4B C:CLA1001 3.2 23.0 1.0 C C:PRO36 3.3 18.3 1.0 CHA C:CLA1001 3.5 17.7 1.0 CHB C:CLA1001 3.5 20.3 1.0 CHD C:CLA1001 3.5 18.7 1.0 CHC C:CLA1001 3.6 18.7 1.0 C9 D:CLA1001 4.1 38.5 1.0 C7 D:CLA1001 4.1 41.3 1.0 CD C:PRO36 4.2 16.3 1.0 C3D C:CLA1001 4.2 15.3 1.0 CA C:PRO36 4.2 19.2 1.0 N C:ALA37 4.2 18.9 1.0 N C:PRO36 4.2 18.5 1.0 CA C:ALA37 4.3 20.1 1.0 C2D C:CLA1001 4.3 17.7 1.0 CB C:PRO36 4.3 20.0 1.0 C3C C:CLA1001 4.4 18.6 1.0 C2B C:CLA1001 4.4 22.6 1.0 C2C C:CLA1001 4.4 18.4 1.0 C3B C:CLA1001 4.5 22.5 1.0 C3A C:CLA1001 4.5 21.4 1.0 C2A C:CLA1001 4.5 20.3 1.0 CB C:ALA37 4.6 20.4 1.0 C8 D:CLA1001 4.6 41.4 1.0 CG2 C:VAL35 4.7 14.6 1.0 CG C:PRO36 4.8 18.2 1.0 CB C:VAL35 4.8 17.6 1.0 CBD C:CLA1001 4.9 18.8 1.0 C C:VAL35 5.0 18.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Water-Soluble Chlorophyll Protein From Lepidium Virginicum at 2.00 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 Water-Soluble Chlorophyll Protein From Lepidium Virginicum at 2.00 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:22.5 occ:1.00 MG D:CLA1001 0.0 22.5 1.0 NB D:CLA1001 2.1 21.8 1.0 O D:PRO36 2.1 22.5 1.0 ND D:CLA1001 2.1 19.3 1.0 NC D:CLA1001 2.2 19.5 1.0 NA D:CLA1001 2.2 20.8 1.0 C1B D:CLA1001 3.1 22.9 1.0 C4D D:CLA1001 3.1 17.1 1.0 C4B D:CLA1001 3.1 21.4 1.0 C1C D:CLA1001 3.2 20.3 1.0 C4A D:CLA1001 3.2 24.4 1.0 C4C D:CLA1001 3.2 19.1 1.0 C1D D:CLA1001 3.2 15.5 1.0 C D:PRO36 3.2 22.9 1.0 C1A D:CLA1001 3.3 23.1 1.0 CHB D:CLA1001 3.4 22.6 1.0 CHC D:CLA1001 3.5 23.4 1.0 CHA D:CLA1001 3.6 22.2 1.0 CHD D:CLA1001 3.6 19.9 1.0 C9 C:CLA1001 3.6 48.8 1.0 N D:ALA37 4.1 22.7 1.0 CA D:ALA37 4.2 22.6 1.0 CA D:PRO36 4.2 21.7 1.0 N D:PRO36 4.2 21.5 1.0 CD D:PRO36 4.3 19.5 1.0 C2B D:CLA1001 4.3 21.6 1.0 C3D D:CLA1001 4.3 17.8 1.0 C3B D:CLA1001 4.4 25.1 1.0 CB D:PRO36 4.4 23.5 1.0 C2C D:CLA1001 4.4 20.6 1.0 C3C D:CLA1001 4.4 20.5 1.0 CB D:ALA37 4.4 21.4 1.0 C2D D:CLA1001 4.4 17.3 1.0 C3A D:CLA1001 4.5 26.1 1.0 C2A D:CLA1001 4.5 25.2 1.0 CG2 D:VAL35 4.8 17.6 1.0 C8 C:CLA1001 4.8 50.6 1.0 CB D:VAL35 4.9 18.4 1.0 CG D:PRO36 4.9 22.2 1.0 C7 C:CLA1001 5.0 47.7 1.0

D.Horigome, H.Satoh, N.Itoh, K.Mitsunaga, I.Oonishi, A.Nakagawa, A.Uchida. Structural Mechanism and Photoprotective Function of Water-Soluble Chlorophyll-Binding Protein. J.Biol.Chem. V. 282 6525 2007.
ISSN: ISSN 0021-9258
PubMed: 17170107
DOI: 10.1074/JBC.M609458200