Magnesium in PDB 6s2y: Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B

The structure of Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B, PDB code: 6s2y was solved by A.Agostini, E.Meneghin, L.Gewehr, D.Pedron, D.M.Palm, D.Carbonera, H.Paulsen, E.Jaenicke, E.Collini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.63 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.310, 82.900, 122.220, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 27.7

The binding sites of Magnesium atom in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B (pdb code 6s2y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B, PDB code: 6s2y:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:23.8 occ:1.00 MG A:CHL1001 0.0 23.8 1.0 NA A:CHL1001 2.0 23.9 1.0 ND A:CHL1001 2.0 22.5 1.0 NB A:CHL1001 2.0 24.7 1.0 NC A:CHL1001 2.1 24.1 1.0 O A:PRO36 2.3 22.1 1.0 C4D A:CHL1001 2.9 23.4 1.0 C1A A:CHL1001 3.0 24.0 1.0 C4A A:CHL1001 3.0 22.7 1.0 C4B A:CHL1001 3.0 24.0 1.0 C1B A:CHL1001 3.1 22.6 1.0 C1C A:CHL1001 3.1 23.2 1.0 C4C A:CHL1001 3.1 24.2 1.0 C1D A:CHL1001 3.1 23.3 1.0 CHB A:CHL1001 3.3 22.1 1.0 CHC A:CHL1001 3.4 22.1 1.0 CHA A:CHL1001 3.4 24.0 1.0 C A:PRO36 3.5 20.7 1.0 CHD A:CHL1001 3.5 23.8 1.0 C9 B:CHL1001 3.9 39.2 1.0 C3D A:CHL1001 4.1 22.7 1.0 C8 B:CHL1001 4.2 38.8 1.0 C3B A:CHL1001 4.3 25.0 1.0 CA A:ALA37 4.3 21.5 1.0 N A:ALA37 4.3 19.9 1.0 C3A A:CHL1001 4.3 23.2 1.0 C2A A:CHL1001 4.3 23.5 1.0 C2D A:CHL1001 4.3 22.1 1.0 C2B A:CHL1001 4.4 24.7 1.0 C2C A:CHL1001 4.4 24.0 1.0 C7 B:CHL1001 4.4 37.3 1.0 C3C A:CHL1001 4.4 23.7 1.0 CA A:PRO36 4.5 21.2 1.0 CD A:PRO36 4.5 20.1 1.0 CB A:ALA37 4.6 20.6 1.0 CB A:PRO36 4.6 19.2 1.0 N A:PRO36 4.6 20.5 1.0 CBD A:CHL1001 4.8 24.3 1.0 CG2 A:VAL35 4.9 17.1 1.0 CG A:PRO36 4.9 21.3 1.0

Magnesium binding site 2 out of 4 in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:25.5 occ:1.00 MG B:CHL1001 0.0 25.5 1.0 NA B:CHL1001 2.0 24.6 1.0 ND B:CHL1001 2.0 24.4 1.0 NB B:CHL1001 2.1 25.0 1.0 NC B:CHL1001 2.1 25.0 1.0 O B:PRO36 2.3 26.0 1.0 C4D B:CHL1001 2.9 24.3 1.0 C1A B:CHL1001 3.0 26.2 1.0 C4A B:CHL1001 3.0 24.6 1.0 C4B B:CHL1001 3.0 24.5 1.0 C1B B:CHL1001 3.1 25.4 1.0 C1C B:CHL1001 3.1 25.9 1.0 C4C B:CHL1001 3.1 25.2 1.0 C1D B:CHL1001 3.1 24.1 1.0 CHB B:CHL1001 3.3 24.0 1.0 CHC B:CHL1001 3.4 26.4 1.0 CHA B:CHL1001 3.4 24.8 1.0 C B:PRO36 3.5 26.8 1.0 CHD B:CHL1001 3.5 23.4 1.0 C9 A:CHL1001 3.9 41.7 1.0 C3D B:CHL1001 4.1 25.5 1.0 C8 A:CHL1001 4.1 44.2 1.0 C2A B:CHL1001 4.3 25.1 1.0 C6 A:CHL1001 4.3 40.7 1.0 C3A B:CHL1001 4.3 24.8 1.0 C3B B:CHL1001 4.3 26.4 1.0 N B:ALA37 4.3 30.1 1.0 C2D B:CHL1001 4.3 24.8 1.0 CA B:ALA37 4.3 33.1 1.0 C2C B:CHL1001 4.4 27.1 1.0 C2B B:CHL1001 4.4 25.7 1.0 CD B:PRO36 4.4 26.5 1.0 C3C B:CHL1001 4.4 24.3 1.0 CA B:PRO36 4.4 27.4 1.0 N B:PRO36 4.5 29.1 1.0 CB B:ALA37 4.6 29.0 1.0 CB B:PRO36 4.6 27.9 1.0 C7 A:CHL1001 4.8 43.4 1.0 CG2 B:VAL35 4.8 29.1 1.0 CBD B:CHL1001 4.9 26.2 1.0 CG B:PRO36 4.9 27.7 1.0

Magnesium binding site 3 out of 4 in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:21.1 occ:1.00 MG C:CHL1001 0.0 21.1 1.0 NA C:CHL1001 2.0 21.0 1.0 NB C:CHL1001 2.0 22.5 1.0 ND C:CHL1001 2.0 19.7 1.0 NC C:CHL1001 2.1 22.5 1.0 O C:PRO36 2.3 19.4 1.0 C4D C:CHL1001 2.9 18.8 1.0 C1A C:CHL1001 3.0 20.6 1.0 C4A C:CHL1001 3.0 19.3 1.0 C1B C:CHL1001 3.0 21.4 1.0 C4B C:CHL1001 3.0 22.0 1.0 C1C C:CHL1001 3.1 20.8 1.0 C4C C:CHL1001 3.1 20.0 1.0 C1D C:CHL1001 3.1 19.7 1.0 CHB C:CHL1001 3.3 18.8 1.0 CHC C:CHL1001 3.4 20.9 1.0 CHA C:CHL1001 3.4 19.2 1.0 C C:PRO36 3.5 17.2 1.0 CHD C:CHL1001 3.5 19.2 1.0 C7 D:CHL1001 3.6 39.9 1.0 C8 D:CHL1001 3.7 40.1 1.0 C9 D:CHL1001 3.8 36.7 1.0 C3D C:CHL1001 4.1 19.3 1.0 C2A C:CHL1001 4.3 21.8 1.0 C3B C:CHL1001 4.3 21.3 1.0 C3A C:CHL1001 4.3 20.3 1.0 N C:ALA37 4.3 17.4 1.0 C2B C:CHL1001 4.3 21.8 1.0 C2C C:CHL1001 4.3 21.3 1.0 C2D C:CHL1001 4.4 21.2 1.0 CA C:ALA37 4.4 20.3 1.0 C3C C:CHL1001 4.4 20.1 1.0 CD C:PRO36 4.4 18.1 1.0 CA C:PRO36 4.5 18.6 1.0 N C:PRO36 4.6 18.8 1.0 CB C:ALA37 4.6 20.3 1.0 CB C:PRO36 4.6 16.9 1.0 CG2 C:VAL35 4.8 19.2 1.0 CBD C:CHL1001 4.9 20.1 1.0 CG C:PRO36 4.9 17.0 1.0 C6 D:CHL1001 5.0 36.5 1.0

Magnesium binding site 4 out of 4 in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum with Chlorophyll-B within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:23.6 occ:1.00 MG D:CHL1001 0.0 23.6 1.0 NA D:CHL1001 2.0 23.8 1.0 ND D:CHL1001 2.0 21.3 1.0 NB D:CHL1001 2.0 22.5 1.0 NC D:CHL1001 2.1 21.5 1.0 O D:PRO36 2.2 21.5 1.0 C4D D:CHL1001 2.9 20.2 1.0 C4A D:CHL1001 3.0 22.9 1.0 C1A D:CHL1001 3.0 23.7 1.0 C1B D:CHL1001 3.0 22.1 1.0 C4B D:CHL1001 3.0 21.0 1.0 C4C D:CHL1001 3.1 20.5 1.0 C1C D:CHL1001 3.1 19.4 1.0 C1D D:CHL1001 3.1 19.9 1.0 CHB D:CHL1001 3.3 22.7 1.0 C D:PRO36 3.4 21.1 1.0 CHC D:CHL1001 3.4 22.1 1.0 CHA D:CHL1001 3.4 21.8 1.0 CHD D:CHL1001 3.5 19.5 1.0 C8 C:CHL1001 3.7 42.4 1.0 C7 C:CHL1001 3.8 42.8 1.0 C9 C:CHL1001 4.0 40.0 1.0 C3D D:CHL1001 4.1 20.0 1.0 N D:ALA37 4.2 21.8 1.0 CA D:ALA37 4.2 24.6 1.0 C3B D:CHL1001 4.3 20.3 1.0 C3A D:CHL1001 4.3 24.0 1.0 C2A D:CHL1001 4.3 22.1 1.0 C2B D:CHL1001 4.3 19.2 1.0 C2D D:CHL1001 4.4 19.3 1.0 CA D:PRO36 4.4 23.1 1.0 C2C D:CHL1001 4.4 20.1 1.0 C3C D:CHL1001 4.4 19.6 1.0 CD D:PRO36 4.4 23.7 1.0 CB D:ALA37 4.5 21.2 1.0 N D:PRO36 4.5 22.7 1.0 CB D:PRO36 4.5 23.5 1.0 CG2 D:VAL35 4.8 19.9 1.0 C10 C:CHL1001 4.8 40.0 1.0 CBD D:CHL1001 4.9 21.6 1.0 CG D:PRO36 4.9 25.1 1.0

A.Agostini, E.Meneghin, L.Gewehr, D.Pedron, D.M.Palm, D.Carbonera, H.Paulsen, E.Jaenicke, E.Collini. How Water-Mediated Hydrogen Bonds Affect Chlorophyll A/B Selectivity in Water-Soluble Chlorophyll Protein. Sci Rep V. 9 18255 2019.
ISSN: ESSN 2045-2322
PubMed: 31796824
DOI: 10.1038/S41598-019-54520-4