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Magnesium in PDB 3aek: Structure of the Light-Independent Protochlorophyllide Reductase Catalyzing A Key Reduction For Greening in the Dark

Protein crystallography data

The structure of Structure of the Light-Independent Protochlorophyllide Reductase Catalyzing A Key Reduction For Greening in the Dark, PDB code: 3aek was solved by N.Muraki, J.Nomata, T.Shiba, Y.Fujita, G.Kurisu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.06 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.596, 81.219, 175.928, 90.00, 100.86, 90.00
R / Rfree (%) 19.1 / 23.2

Other elements in 3aek:

The structure of Structure of the Light-Independent Protochlorophyllide Reductase Catalyzing A Key Reduction For Greening in the Dark also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Light-Independent Protochlorophyllide Reductase Catalyzing A Key Reduction For Greening in the Dark (pdb code 3aek). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Light-Independent Protochlorophyllide Reductase Catalyzing A Key Reduction For Greening in the Dark, PDB code: 3aek:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3aek

Go back to Magnesium Binding Sites List in 3aek
Magnesium binding site 1 out of 2 in the Structure of the Light-Independent Protochlorophyllide Reductase Catalyzing A Key Reduction For Greening in the Dark


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Light-Independent Protochlorophyllide Reductase Catalyzing A Key Reduction For Greening in the Dark within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg526

b:36.5
occ:1.00
MG B:PMR526 0.0 36.5 1.0
ND B:PMR526 1.9 36.6 1.0
NB B:PMR526 1.9 36.9 1.0
NC B:PMR526 2.0 36.9 1.0
NA B:PMR526 2.0 36.0 1.0
O B:HOH762 2.1 28.4 1.0
C4D B:PMR526 2.9 36.8 1.0
C4A B:PMR526 2.9 36.3 1.0
C1B B:PMR526 2.9 37.0 1.0
C1C B:PMR526 3.0 37.2 1.0
C4B B:PMR526 3.0 36.8 1.0
C4C B:PMR526 3.0 37.2 1.0
C1D B:PMR526 3.0 36.3 1.0
C1A B:PMR526 3.0 36.0 1.0
CHB B:PMR526 3.3 36.8 1.0
CHC B:PMR526 3.3 36.9 1.0
CHD B:PMR526 3.4 37.0 1.0
CHA B:PMR526 3.4 36.4 1.0
O B:HOH728 4.1 40.1 1.0
C2B B:PMR526 4.1 36.5 1.0
C3A B:PMR526 4.1 35.4 1.0
C3D B:PMR526 4.1 36.5 1.0
C3B B:PMR526 4.2 37.0 1.0
C2C B:PMR526 4.2 38.0 1.0
C2D B:PMR526 4.2 36.3 1.0
C2A B:PMR526 4.2 35.5 1.0
C3C B:PMR526 4.2 37.6 1.0
CD2 C:LEU372 4.2 37.6 1.0
O C:ALA57 4.5 54.3 1.0
O C:ALA58 4.8 57.6 1.0
CD1 C:ILE389 4.8 42.5 1.0
CBD B:PMR526 4.9 36.7 1.0
CG B:LEU410 5.0 59.6 1.0

Magnesium binding site 2 out of 2 in 3aek

Go back to Magnesium Binding Sites List in 3aek
Magnesium binding site 2 out of 2 in the Structure of the Light-Independent Protochlorophyllide Reductase Catalyzing A Key Reduction For Greening in the Dark


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Light-Independent Protochlorophyllide Reductase Catalyzing A Key Reduction For Greening in the Dark within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg526

b:35.7
occ:1.00
MG D:PMR526 0.0 35.7 1.0
NB D:PMR526 1.9 35.4 1.0
ND D:PMR526 1.9 35.6 1.0
NC D:PMR526 2.0 35.4 1.0
NA D:PMR526 2.0 34.3 1.0
O D:HOH597 2.1 41.7 1.0
C4D D:PMR526 2.9 35.0 1.0
C4A D:PMR526 2.9 34.4 1.0
C1B D:PMR526 3.0 35.2 1.0
C4B D:PMR526 3.0 35.3 1.0
C1C D:PMR526 3.0 35.1 1.0
C1A D:PMR526 3.0 34.3 1.0
C1D D:PMR526 3.0 35.3 1.0
C4C D:PMR526 3.0 35.7 1.0
CHC D:PMR526 3.3 35.0 1.0
CHB D:PMR526 3.3 34.6 1.0
CHA D:PMR526 3.4 34.9 1.0
CHD D:PMR526 3.4 35.2 1.0
CD2 A:LEU372 3.8 35.6 1.0
C2B D:PMR526 4.1 35.5 1.0
C3A D:PMR526 4.1 34.0 1.0
C3B D:PMR526 4.1 35.7 1.0
C3D D:PMR526 4.2 34.7 1.0
C2C D:PMR526 4.2 35.4 1.0
C2D D:PMR526 4.2 35.1 1.0
C2A D:PMR526 4.2 33.8 1.0
O D:HOH767 4.2 39.7 1.0
C3C D:PMR526 4.2 35.4 1.0
O A:ALA57 4.7 48.4 1.0
O A:ALA58 4.7 52.2 1.0
CD1 A:ILE389 4.8 41.2 1.0
CBD D:PMR526 4.9 35.2 1.0
CG D:LEU410 4.9 55.4 1.0

Reference:

N.Muraki, J.Nomata, K.Ebata, T.Mizoguchi, T.Shiba, H.Tamiaki, G.Kurisu, Y.Fujita. X-Ray Crystal Structure of the Light-Independent Protochlorophyllide Reductase Nature V. 465 110 2010.
ISSN: ISSN 0028-0836
PubMed: 20400946
DOI: 10.1038/NATURE08950
Page generated: Mon Dec 14 07:53:03 2020

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