Iron in PDB 3aet: 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: 3aet 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)	40.05 / 2.91
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	80.442, 81.440, 95.864, 102.53, 110.89, 94.44
R / Rfree (%)	21.1 / 27.5

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 3aet). 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: 3aet:
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:51.1 occ:1.00 FE1 A:SF4425 0.0 51.1 1.0 S3 A:SF4425 2.3 50.3 1.0 S2 A:SF4425 2.3 51.2 1.0 S4 A:SF4425 2.3 51.2 1.0 SG A:CYS26 2.5 53.5 1.0 FE4 A:SF4425 2.7 49.8 1.0 FE3 A:SF4425 2.7 52.1 1.0 FE2 A:SF4425 2.8 49.9 1.0 CB A:CYS26 3.5 55.3 1.0 CD2 A:LEU28 3.6 52.6 1.0 S1 A:SF4425 3.9 51.8 1.0 N A:GLY145 4.3 54.5 1.0 CD1 A:LEU54 4.3 45.9 1.0 SG A:CYS51 4.5 45.8 1.0 CG A:LEU28 4.7 51.6 1.0 CB A:LEU28 4.8 51.3 1.0 CA A:GLY145 4.8 54.7 1.0 O B:GLY35 4.9 55.7 1.0 SG A:CYS112 4.9 48.2 1.0 CA A:CYS26 5.0 55.1 1.0 O A:GLY143 5.0 55.3 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:49.9 occ:1.00 FE2 A:SF4425 0.0 49.9 1.0 S3 A:SF4425 2.3 50.3 1.0 S4 A:SF4425 2.3 51.2 1.0 S1 A:SF4425 2.3 51.8 1.0 SG B:CYS36 2.5 54.2 1.0 FE4 A:SF4425 2.8 49.8 1.0 FE1 A:SF4425 2.8 51.1 1.0 FE3 A:SF4425 2.8 52.1 1.0 CB B:CYS36 3.0 54.3 1.0 CA B:CYS36 3.6 54.4 1.0 CG B:PRO33 3.9 55.1 1.0 S2 A:SF4425 4.0 51.2 1.0 CG2 A:THR50 4.2 42.0 1.0 N B:CYS36 4.3 54.7 1.0 C B:GLY35 4.7 55.5 1.0 O B:GLY35 4.8 55.7 1.0 CB B:PRO33 4.9 55.3 1.0 CD B:PRO33 4.9 55.2 1.0 SG A:CYS26 4.9 53.5 1.0 C B:CYS36 4.9 54.4 1.0 CB A:THR50 5.0 42.4 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:52.1 occ:1.00 FE3 A:SF4425 0.0 52.1 1.0 S2 A:SF4425 2.3 51.2 1.0 S4 A:SF4425 2.3 51.2 1.0 S1 A:SF4425 2.3 51.8 1.0 SG A:CYS51 2.6 45.8 1.0 FE4 A:SF4425 2.6 49.8 1.0 FE1 A:SF4425 2.7 51.1 1.0 FE2 A:SF4425 2.8 49.9 1.0 S3 A:SF4425 3.9 50.3 1.0 CD A:PRO113 3.9 48.9 1.0 CB A:CYS51 4.0 44.1 1.0 CA A:CYS51 4.2 43.7 1.0 N A:CYS51 4.2 43.3 1.0 CD2 A:LEU28 4.3 52.6 1.0 CB A:SER111 4.4 46.6 1.0 N A:CYS112 4.5 47.6 1.0 CG A:PRO113 4.5 48.8 1.0 SG A:CYS112 4.8 48.2 1.0 CB A:CYS112 4.8 47.9 1.0 SG B:CYS36 5.0 54.2 1.0 C A:THR50 5.0 42.9 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:49.8 occ:1.00 FE4 A:SF4425 0.0 49.8 1.0 S2 A:SF4425 2.3 51.2 1.0 S1 A:SF4425 2.3 51.8 1.0 S3 A:SF4425 2.3 50.3 1.0 SG A:CYS112 2.5 48.2 1.0 FE3 A:SF4425 2.6 52.1 1.0 FE1 A:SF4425 2.7 51.1 1.0 FE2 A:SF4425 2.8 49.9 1.0 CB A:CYS112 3.2 47.9 1.0 N A:GLY145 3.6 54.5 1.0 N A:CYS112 3.8 47.6 1.0 S4 A:SF4425 3.8 51.2 1.0 CG B:PRO33 3.8 55.1 1.0 CA A:CYS112 4.1 48.0 1.0 CA A:GLY145 4.2 54.7 1.0 CB B:PRO33 4.2 55.3 1.0 CD A:PRO113 4.4 48.9 1.0 C A:SER144 4.6 54.6 1.0 OG1 B:THR96 4.6 58.3 1.0 CA A:SER144 4.7 54.7 1.0 SG A:CYS26 4.7 53.5 1.0 CB A:CYS26 4.9 55.3 1.0 SG B:CYS36 4.9 54.2 1.0 C A:SER111 5.0 47.1 1.0 CB B:CYS36 5.0 54.3 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:49.9 occ:1.00 FE1 C:SF4425 0.0 49.9 1.0 S2 C:SF4425 2.3 50.4 1.0 S4 C:SF4425 2.3 50.0 1.0 S3 C:SF4425 2.3 49.4 1.0 SG C:CYS26 2.4 53.6 1.0 FE3 C:SF4425 2.7 48.1 1.0 FE4 C:SF4425 2.7 50.8 1.0 FE2 C:SF4425 2.8 47.1 1.0 CB C:CYS26 3.4 55.4 1.0 CD2 C:LEU28 3.5 49.4 1.0 S1 C:SF4425 3.9 50.0 1.0 N C:GLY145 4.3 55.5 1.0 SG C:CYS51 4.7 47.1 1.0 CG C:LEU28 4.7 50.3 1.0 CB C:LEU28 4.7 51.0 1.0 CD1 C:LEU54 4.7 45.6 1.0 O D:GLY35 4.7 55.3 1.0 CA C:GLY145 4.9 55.2 1.0 CA C:CYS26 4.9 55.1 1.0 SG C:CYS112 4.9 49.4 1.0 O C:GLY143 4.9 55.2 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:47.1 occ:1.00 FE2 C:SF4425 0.0 47.1 1.0 S3 C:SF4425 2.3 49.4 1.0 S4 C:SF4425 2.3 50.0 1.0 S1 C:SF4425 2.3 50.0 1.0 SG D:CYS36 2.5 53.2 1.0 FE4 C:SF4425 2.7 50.8 1.0 FE1 C:SF4425 2.8 49.9 1.0 FE3 C:SF4425 2.8 48.1 1.0 CB D:CYS36 3.1 54.3 1.0 CA D:CYS36 3.7 54.3 1.0 CG D:PRO33 4.0 54.7 1.0 S2 C:SF4425 4.0 50.4 1.0 CG2 C:THR50 4.2 41.6 1.0 N D:CYS36 4.4 54.4 1.0 CD D:PRO33 4.7 54.9 1.0 SG C:CYS112 4.8 49.4 1.0 C D:GLY35 4.8 55.1 1.0 O D:GLY35 4.9 55.3 1.0 SG C:CYS26 4.9 53.6 1.0 CB C:THR50 4.9 42.6 1.0 OG1 D:THR96 4.9 56.8 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:48.1 occ:1.00 FE3 C:SF4425 0.0 48.1 1.0 S2 C:SF4425 2.3 50.4 1.0 S4 C:SF4425 2.3 50.0 1.0 S1 C:SF4425 2.3 50.0 1.0 SG C:CYS51 2.4 47.1 1.0 FE1 C:SF4425 2.7 49.9 1.0 FE4 C:SF4425 2.7 50.8 1.0 FE2 C:SF4425 2.8 47.1 1.0 CB C:CYS51 3.7 44.1 1.0 CD2 C:LEU28 3.9 49.4 1.0 S3 C:SF4425 3.9 49.4 1.0 CA C:CYS51 4.0 43.7 1.0 N C:CYS51 4.2 43.1 1.0 CD C:PRO113 4.3 49.5 1.0 CB C:SER111 4.5 47.6 1.0 N C:CYS112 4.6 48.4 1.0 SG C:CYS112 4.9 49.4 1.0 OG C:SER48 4.9 40.1 1.0 C C:THR50 4.9 42.7 1.0 CB C:CYS112 4.9 48.5 1.0 SG C:CYS26 5.0 53.6 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:50.8 occ:1.00 FE4 C:SF4425 0.0 50.8 1.0 S1 C:SF4425 2.3 50.0 1.0 S3 C:SF4425 2.3 49.4 1.0 S2 C:SF4425 2.3 50.4 1.0 SG C:CYS112 2.4 49.4 1.0 FE3 C:SF4425 2.7 48.1 1.0 FE1 C:SF4425 2.7 49.9 1.0 FE2 C:SF4425 2.7 47.1 1.0 CB C:CYS112 3.2 48.5 1.0 N C:GLY145 3.6 55.5 1.0 N C:CYS112 3.7 48.4 1.0 S4 C:SF4425 3.8 50.0 1.0 CG D:PRO33 3.9 54.7 1.0 CA C:CYS112 4.1 48.7 1.0 CA C:GLY145 4.3 55.2 1.0 CB D:PRO33 4.4 54.5 1.0 CD C:PRO113 4.5 49.5 1.0 OG1 D:THR96 4.5 56.8 1.0 CA C:SER144 4.6 55.6 1.0 C C:SER144 4.6 55.8 1.0 SG C:CYS26 4.7 53.6 1.0 SG C:CYS51 4.8 47.1 1.0 C C:SER111 4.9 48.0 1.0 CB C:CYS26 5.0 55.4 1.0 SG D:CYS36 5.0 53.2 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