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

The structure of Structure of the Light-Independent Protochlorophyllide Reductase Catalyzing A Key Reduction For Greening in the Dark, PDB code: 3aeq 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)	47.25 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.632, 81.278, 177.103, 90.00, 100.43, 90.00
R / Rfree (%)	23.5 / 29.8

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:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the Structure of the Light-Independent Protochlorophyllide Reductase Catalyzing A Key Reduction For Greening in the Dark (pdb code 3aeq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of the Light-Independent Protochlorophyllide Reductase Catalyzing A Key Reduction For Greening in the Dark, PDB code: 3aeq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 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 Iron with other atoms in the Fe 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 A:Fe425 b:33.5 occ:1.00 FE1 A:SF4425 0.0 33.5 1.0 S4 A:SF4425 2.3 31.7 1.0 S3 A:SF4425 2.3 31.8 1.0 S2 A:SF4425 2.3 33.4 1.0 SG A:CYS26 2.6 46.6 1.0 FE2 A:SF4425 2.7 33.0 1.0 FE4 A:SF4425 2.7 33.2 1.0 FE3 A:SF4425 2.7 32.8 1.0 CB A:CYS26 3.6 49.4 1.0 CD2 A:LEU28 3.6 46.5 1.0 S1 A:SF4425 3.8 34.2 1.0 CD2 A:LEU54 4.4 42.6 1.0 N A:GLY145 4.4 46.5 1.0 CG A:LEU28 4.5 46.6 1.0 CB A:LEU28 4.6 46.7 1.0 OD1 B:ASP36 4.6 42.3 1.0 SG A:CYS51 4.7 41.8 1.0 O A:GLY143 4.7 48.1 1.0 CD1 A:LEU28 4.9 46.2 1.0 CA A:GLY145 5.0 46.4 1.0 CA A:CYS26 5.0 49.6 1.0 O B:GLY35 5.0 45.1 1.0

Iron binding site 2 out of 8 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 Iron with other atoms in the Fe 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 A:Fe425 b:33.0 occ:1.00 FE2 A:SF4425 0.0 33.0 1.0 OD1 B:ASP36 2.1 42.3 1.0 S3 A:SF4425 2.3 31.8 1.0 S1 A:SF4425 2.3 34.2 1.0 S4 A:SF4425 2.3 31.7 1.0 FE1 A:SF4425 2.7 33.5 1.0 FE4 A:SF4425 2.7 33.2 1.0 FE3 A:SF4425 2.8 32.8 1.0 CG B:ASP36 3.0 44.0 1.0 OD2 B:ASP36 3.5 43.4 1.0 S2 A:SF4425 3.9 33.4 1.0 CG2 A:THR50 4.0 43.6 1.0 N B:ASP36 4.1 44.8 1.0 CG B:PRO33 4.1 43.9 1.0 CB B:ASP36 4.2 44.6 1.0 CA B:ASP36 4.2 44.9 1.0 C B:GLY35 4.3 44.7 1.0 O B:GLY35 4.5 45.1 1.0 SG A:CYS26 4.8 46.6 1.0 SG A:CYS112 4.8 45.3 1.0 CB A:THR50 4.9 43.5 1.0 CE1 B:TYR38 5.0 44.8 1.0

Iron binding site 3 out of 8 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 Iron with other atoms in the Fe binding site number 3 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 A:Fe425 b:32.8 occ:1.00 FE3 A:SF4425 0.0 32.8 1.0 S4 A:SF4425 2.3 31.7 1.0 S2 A:SF4425 2.3 33.4 1.0 S1 A:SF4425 2.3 34.2 1.0 SG A:CYS51 2.4 41.8 1.0 FE1 A:SF4425 2.7 33.5 1.0 FE4 A:SF4425 2.7 33.2 1.0 FE2 A:SF4425 2.8 33.0 1.0 CB A:CYS51 3.7 42.9 1.0 CA A:CYS51 3.9 43.0 1.0 S3 A:SF4425 4.0 31.8 1.0 N A:CYS51 4.0 43.3 1.0 CD2 A:LEU28 4.0 46.5 1.0 CD A:PRO113 4.3 44.0 1.0 OD1 B:ASP36 4.4 42.3 1.0 CB A:SER111 4.5 42.1 1.0 CG2 A:THR50 4.6 43.6 1.0 N A:CYS112 4.7 43.2 1.0 OG A:SER48 4.8 43.7 1.0 CB A:CYS112 4.8 44.0 1.0 C A:THR50 4.8 43.4 1.0 CB A:THR50 4.8 43.5 1.0 SG A:CYS112 5.0 45.3 1.0

Iron binding site 4 out of 8 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 Iron with other atoms in the Fe binding site number 4 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 A:Fe425 b:33.2 occ:1.00 FE4 A:SF4425 0.0 33.2 1.0 S1 A:SF4425 2.3 34.2 1.0 S2 A:SF4425 2.3 33.4 1.0 S3 A:SF4425 2.3 31.8 1.0 SG A:CYS112 2.5 45.3 1.0 FE1 A:SF4425 2.7 33.5 1.0 FE2 A:SF4425 2.7 33.0 1.0 FE3 A:SF4425 2.7 32.8 1.0 CB A:CYS112 3.2 44.0 1.0 N A:GLY145 3.4 46.5 1.0 N A:CYS112 3.8 43.2 1.0 S4 A:SF4425 3.9 31.7 1.0 CG B:PRO33 4.0 43.9 1.0 CA A:CYS112 4.1 43.9 1.0 CA A:GLY145 4.1 46.4 1.0 C A:SER144 4.5 46.9 1.0 CB B:PRO33 4.5 43.5 1.0 CA A:SER144 4.5 47.1 1.0 CD A:PRO113 4.6 44.0 1.0 OD1 B:ASP36 4.6 42.3 1.0 SG A:CYS26 4.8 46.6 1.0 SG A:CYS51 4.9 41.8 1.0 C A:SER111 4.9 42.7 1.0 CB A:SER144 4.9 47.1 1.0 CB A:CYS26 5.0 49.4 1.0 OG1 B:THR96 5.0 54.9 1.0

Iron binding site 5 out of 8 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 Iron with other atoms in the Fe binding site number 5 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 C:Fe425 b:34.2 occ:1.00 FE1 C:SF4425 0.0 34.2 1.0 S3 C:SF4425 2.3 35.6 1.0 S4 C:SF4425 2.3 35.3 1.0 S2 C:SF4425 2.3 36.3 1.0 SG C:CYS26 2.4 49.8 1.0 FE2 C:SF4425 2.7 33.7 1.0 FE3 C:SF4425 2.7 35.6 1.0 FE4 C:SF4425 2.7 35.0 1.0 CB C:CYS26 3.3 50.2 1.0 CD2 C:LEU28 3.5 45.0 1.0 S1 C:SF4425 3.9 34.9 1.0 N C:GLY145 4.3 48.0 1.0 OD1 D:ASP36 4.4 42.4 1.0 CB C:LEU28 4.6 46.3 1.0 CD1 C:LEU54 4.6 46.8 1.0 CG C:LEU28 4.6 45.2 1.0 CA C:CYS26 4.7 50.4 1.0 CA C:GLY145 4.9 48.1 1.0 SG C:CYS51 4.9 42.7 1.0 O C:GLY143 4.9 48.6 1.0

Iron binding site 6 out of 8 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 Iron with other atoms in the Fe binding site number 6 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 C:Fe425 b:33.7 occ:1.00 FE2 C:SF4425 0.0 33.7 1.0 OD1 D:ASP36 1.9 42.4 1.0 S1 C:SF4425 2.3 34.9 1.0 S4 C:SF4425 2.3 35.3 1.0 S3 C:SF4425 2.3 35.6 1.0 FE1 C:SF4425 2.7 34.2 1.0 FE4 C:SF4425 2.7 35.0 1.0 FE3 C:SF4425 2.7 35.6 1.0 CG D:ASP36 2.9 43.6 1.0 OD2 D:ASP36 3.4 44.6 1.0 CG2 C:THR50 3.8 42.2 1.0 S2 C:SF4425 3.9 36.3 1.0 CB D:ASP36 4.2 43.6 1.0 CA D:ASP36 4.2 43.9 1.0 N D:ASP36 4.2 43.7 1.0 CG D:PRO33 4.4 43.0 1.0 C D:GLY35 4.6 43.8 1.0 SG C:CYS26 4.6 49.8 1.0 CB C:THR50 4.9 42.4 1.0 SG C:CYS51 4.9 42.7 1.0 O D:GLY35 4.9 44.0 1.0 CE1 D:TYR38 5.0 42.8 1.0 SG C:CYS112 5.0 46.0 1.0

Iron binding site 7 out of 8 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 Iron with other atoms in the Fe binding site number 7 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 C:Fe425 b:35.6 occ:1.00 FE3 C:SF4425 0.0 35.6 1.0 S4 C:SF4425 2.3 35.3 1.0 S2 C:SF4425 2.3 36.3 1.0 S1 C:SF4425 2.3 34.9 1.0 SG C:CYS51 2.5 42.7 1.0 FE1 C:SF4425 2.7 34.2 1.0 FE2 C:SF4425 2.7 33.7 1.0 FE4 C:SF4425 2.8 35.0 1.0 CB C:CYS51 3.5 43.1 1.0 CD2 C:LEU28 3.8 45.0 1.0 S3 C:SF4425 3.9 35.6 1.0 CA C:CYS51 3.9 43.0 1.0 N C:CYS51 4.2 43.0 1.0 CB C:SER111 4.2 42.4 1.0 CD C:PRO113 4.3 43.4 1.0 OD1 D:ASP36 4.4 42.4 1.0 N C:CYS112 4.5 42.9 1.0 CG2 C:THR50 4.7 42.2 1.0 SG C:CYS112 4.9 46.0 1.0 C C:THR50 4.9 42.9 1.0 CB C:CYS112 5.0 43.5 1.0 CB C:THR50 5.0 42.4 1.0 CA C:SER111 5.0 42.3 1.0 OG C:SER111 5.0 42.2 1.0

Iron binding site 8 out of 8 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 Iron with other atoms in the Fe binding site number 8 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 C:Fe425 b:35.0 occ:1.00 FE4 C:SF4425 0.0 35.0 1.0 S3 C:SF4425 2.3 35.6 1.0 S1 C:SF4425 2.3 34.9 1.0 S2 C:SF4425 2.3 36.3 1.0 SG C:CYS112 2.5 46.0 1.0 FE2 C:SF4425 2.7 33.7 1.0 FE1 C:SF4425 2.7 34.2 1.0 FE3 C:SF4425 2.8 35.6 1.0 CB C:CYS112 3.4 43.5 1.0 N C:GLY145 3.4 48.0 1.0 N C:CYS112 3.8 42.9 1.0 S4 C:SF4425 3.9 35.3 1.0 CG D:PRO33 4.0 43.0 1.0 CA C:GLY145 4.0 48.1 1.0 CA C:CYS112 4.2 43.6 1.0 OD1 D:ASP36 4.3 42.4 1.0 C C:SER144 4.5 48.1 1.0 CA C:SER144 4.6 48.3 1.0 CB D:PRO33 4.7 43.2 1.0 O D:GLN34 4.7 44.0 1.0 CD C:PRO113 4.7 43.4 1.0 OG1 D:THR96 4.8 52.9 1.0 CB C:CYS26 4.8 50.2 1.0 SG C:CYS26 4.8 49.8 1.0 CB C:SER144 4.8 48.6 1.0 C C:SER111 4.9 42.4 1.0 CG D:ASP36 4.9 43.6 1.0 OD2 D:ASP36 5.0 44.6 1.0

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