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Magnesium in PDB 6gix: Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum (Mutation L91P) with Chlorophyll-B

Protein crystallography data

The structure of Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum (Mutation L91P) with Chlorophyll-B, PDB code: 6gix was solved by D.M.Palm, A.Agostini, V.Averesch, P.Girr, M.Werwie, S.Takahashi, H.Satoh, E.Jaenicke, H.Paulsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.73 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.860, 82.130, 122.460, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum (Mutation L91P) with Chlorophyll-B (pdb code 6gix). 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 (Mutation L91P) with Chlorophyll-B, PDB code: 6gix:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6gix

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Magnesium binding site 1 out of 4 in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum (Mutation L91P) 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 (Mutation L91P) with Chlorophyll-B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:28.2
occ:1.00
 MG A:CHL1001 0.0 28.2 1.0
NA A:CHL1001 2.0 28.8 1.0
ND A:CHL1001 2.0 28.5 1.0
NB A:CHL1001 2.0 26.8 1.0
NC A:CHL1001 2.1 27.1 1.0
O A:PRO36 2.4 24.6 1.0
C4D A:CHL1001 3.0 29.4 1.0
C4A A:CHL1001 3.0 27.8 1.0
C4B A:CHL1001 3.0 26.5 1.0
C1A A:CHL1001 3.0 29.0 1.0
C1B A:CHL1001 3.1 26.9 1.0
C1C A:CHL1001 3.1 27.0 1.0
C4C A:CHL1001 3.1 28.5 1.0
C1D A:CHL1001 3.1 28.2 1.0
CHB A:CHL1001 3.4 27.1 1.0
CHC A:CHL1001 3.4 27.6 1.0
CHA A:CHL1001 3.5 29.5 1.0
CHD A:CHL1001 3.5 28.0 1.0
C A:PRO36 3.6 23.6 1.0
C3D A:CHL1001 4.2 28.8 1.0
C14 B:CHL1001 4.2 74.4 1.0
C3B A:CHL1001 4.3 25.7 1.0
C2D A:CHL1001 4.3 28.4 1.0
C2B A:CHL1001 4.3 26.9 1.0
C2C A:CHL1001 4.3 28.6 1.0
C3C A:CHL1001 4.3 28.7 1.0
C3A A:CHL1001 4.3 27.2 1.0
C2A A:CHL1001 4.4 28.9 1.0
CED B:CHL1001 4.4 30.0 1.0
N A:ALA37 4.4 24.0 1.0
CA A:ALA37 4.5 25.2 1.0
CA A:PRO36 4.6 22.8 1.0
C4 B:CHL1001 4.6 46.2 1.0
N A:PRO36 4.7 21.8 1.0
CB A:PRO36 4.7 22.7 1.0
CB A:ALA37 4.7 25.0 1.0
CD A:PRO36 4.8 22.3 1.0
CBD A:CHL1001 5.0 29.8 1.0

Magnesium binding site 2 out of 4 in 6gix

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Magnesium binding site 2 out of 4 in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum (Mutation L91P) 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 (Mutation L91P) with Chlorophyll-B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:29.9
occ:1.00
 MG B:CHL1001 0.0 29.9 1.0
ND B:CHL1001 2.0 29.3 1.0
NA B:CHL1001 2.0 29.2 1.0
NC B:CHL1001 2.1 28.5 1.0
NB B:CHL1001 2.1 29.0 1.0
O B:PRO36 2.4 28.3 1.0
C4D B:CHL1001 3.0 30.3 1.0
C1A B:CHL1001 3.0 27.9 1.0
C4A B:CHL1001 3.1 27.9 1.0
C4B B:CHL1001 3.1 28.7 1.0
C1C B:CHL1001 3.1 27.6 1.0
C1B B:CHL1001 3.1 28.8 1.0
C4C B:CHL1001 3.1 28.9 1.0
C1D B:CHL1001 3.1 29.7 1.0
CHC B:CHL1001 3.4 27.9 1.0
CHA B:CHL1001 3.4 29.6 1.0
CHB B:CHL1001 3.5 26.9 1.0
CHD B:CHL1001 3.6 27.9 1.0
C B:PRO36 3.6 28.6 1.0
C3D B:CHL1001 4.2 30.6 1.0
C3B B:CHL1001 4.3 29.7 1.0
C2C B:CHL1001 4.3 27.7 1.0
C2D B:CHL1001 4.3 30.4 1.0
C2B B:CHL1001 4.3 30.2 1.0
C3C B:CHL1001 4.3 28.4 1.0
C2A B:CHL1001 4.4 27.5 1.0
C3A B:CHL1001 4.4 27.3 1.0
N B:ALA37 4.5 28.1 1.0
CA B:ALA37 4.5 27.7 1.0
CA B:PRO36 4.5 27.7 1.0
CED A:CHL1001 4.6 34.0 1.0
N B:PRO36 4.6 28.5 1.0
C20 B:CHL1001 4.7 77.0 1.0
CB B:PRO36 4.7 28.1 1.0
CD B:PRO36 4.7 28.4 1.0
C4 A:CHL1001 4.8 44.0 1.0
CB B:ALA37 4.8 25.7 1.0
CBD B:CHL1001 4.9 30.4 1.0

Magnesium binding site 3 out of 4 in 6gix

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Magnesium binding site 3 out of 4 in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum (Mutation L91P) 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 (Mutation L91P) with Chlorophyll-B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:25.9
occ:1.00
 MG C:CHL1001 0.0 25.9 1.0
ND C:CHL1001 2.0 25.2 1.0
NA C:CHL1001 2.0 26.1 1.0
NB C:CHL1001 2.0 25.6 1.0
NC C:CHL1001 2.1 26.0 1.0
O C:PRO36 2.4 25.3 1.0
C4D C:CHL1001 3.0 25.8 1.0
C4A C:CHL1001 3.0 25.8 1.0
C1A C:CHL1001 3.1 25.6 1.0
C4B C:CHL1001 3.1 26.0 1.0
C1B C:CHL1001 3.1 25.6 1.0
C1C C:CHL1001 3.1 25.8 1.0
C1D C:CHL1001 3.1 25.4 1.0
C4C C:CHL1001 3.1 25.8 1.0
CHC C:CHL1001 3.4 25.4 1.0
CHB C:CHL1001 3.4 25.7 1.0
CHA C:CHL1001 3.5 25.9 1.0
CHD C:CHL1001 3.5 24.9 1.0
C C:PRO36 3.6 25.5 1.0
C3D C:CHL1001 4.1 25.1 1.0
C3B C:CHL1001 4.3 25.5 1.0
C2D C:CHL1001 4.3 25.7 1.0
C2B C:CHL1001 4.3 25.9 1.0
C2C C:CHL1001 4.3 26.5 1.0
C3C C:CHL1001 4.4 25.9 1.0
C3A C:CHL1001 4.4 25.8 1.0
C2A C:CHL1001 4.4 25.3 1.0
N C:ALA37 4.5 23.8 1.0
CA C:ALA37 4.5 24.6 1.0
CA C:PRO36 4.6 25.4 1.0
N C:PRO36 4.7 25.8 1.0
CB C:ALA37 4.7 24.8 1.0
CB C:PRO36 4.7 24.9 1.0
CD C:PRO36 4.8 25.2 1.0
CED D:CHL1001 4.8 26.2 1.0
CBD C:CHL1001 4.9 26.0 1.0

Magnesium binding site 4 out of 4 in 6gix

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Magnesium binding site 4 out of 4 in the Water-Soluble Chlorophyll Protein (Wscp) From Lepidium Virginicum (Mutation L91P) 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 (Mutation L91P) with Chlorophyll-B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1001

b:23.7
occ:1.00
 MG D:CHL1001 0.0 23.7 1.0
NA D:CHL1001 2.0 24.0 1.0
ND D:CHL1001 2.0 24.0 1.0
NB D:CHL1001 2.0 23.7 1.0
NC D:CHL1001 2.1 23.7 1.0
O D:PRO36 2.3 24.4 1.0
C4D D:CHL1001 3.0 24.8 1.0
C4A D:CHL1001 3.0 23.4 1.0
C4B D:CHL1001 3.0 23.5 1.0
C1A D:CHL1001 3.0 24.2 1.0
C1C D:CHL1001 3.1 23.4 1.0
C1B D:CHL1001 3.1 23.9 1.0
C1D D:CHL1001 3.1 24.1 1.0
C4C D:CHL1001 3.1 23.5 1.0
CHC D:CHL1001 3.4 23.6 1.0
CHB D:CHL1001 3.4 23.6 1.0
CHA D:CHL1001 3.5 24.9 1.0
CHD D:CHL1001 3.5 23.8 1.0
C D:PRO36 3.6 24.7 1.0
C14 C:CHL1001 4.0 61.5 1.0
C3D D:CHL1001 4.1 24.7 1.0
C3B D:CHL1001 4.3 23.7 1.0
C2C D:CHL1001 4.3 24.4 1.0
C2D D:CHL1001 4.3 24.6 1.0
C2B D:CHL1001 4.3 23.6 1.0
C3A D:CHL1001 4.4 23.3 1.0
C3C D:CHL1001 4.4 23.7 1.0
C2A D:CHL1001 4.4 23.5 1.0
N D:ALA37 4.4 23.3 1.0
CA D:ALA37 4.5 23.8 1.0
CED C:CHL1001 4.5 23.9 1.0
CA D:PRO36 4.5 24.7 1.0
N D:PRO36 4.6 24.7 1.0
CB D:PRO36 4.7 24.7 1.0
CB D:ALA37 4.7 22.9 1.0
CD D:PRO36 4.7 25.3 1.0
CBD D:CHL1001 4.9 25.0 1.0
CG2 D:VAL35 5.0 21.1 1.0
CB D:VAL35 5.0 22.1 1.0

Reference:

D.M.Palm, A.Agostini, V.Averesch, P.Girr, M.Werwie, S.Takahashi, H.Satoh, E.Jaenicke, H.Paulsen. Chlorophyll A/B Binding-Specificity in Water-Soluble Chlorophyll Protein. Nat Plants V. 4 920 2018.
ISSN: ESSN 2055-0278
PubMed: 30297830
DOI: 10.1038/S41477-018-0273-Z
Page generated: Tue Oct 1 01:11:29 2024

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