Iron in PDB 3aek: 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: 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

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 3aek). 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: 3aek:
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:26.0 occ:1.00 FE1 A:SF4425 0.0 26.0 1.0 S4 A:SF4425 2.3 25.1 1.0 S2 A:SF4425 2.3 26.1 1.0 S3 A:SF4425 2.3 25.5 1.0 SG A:CYS26 2.4 35.1 1.0 FE2 A:SF4425 2.7 26.0 1.0 FE4 A:SF4425 2.7 27.6 1.0 FE3 A:SF4425 2.8 26.1 1.0 CB A:CYS26 3.2 35.0 1.0 S1 A:SF4425 3.9 25.5 1.0 CD2 A:LEU28 4.0 34.6 1.0 N A:GLY145 4.2 35.6 1.0 CD2 A:LEU54 4.3 37.6 1.0 OD1 B:ASP36 4.4 29.3 1.0 O B:HOH568 4.5 19.9 1.0 CA A:CYS26 4.6 35.2 1.0 CA A:GLY145 4.7 35.7 1.0 CB A:LEU28 4.8 35.0 1.0 SG A:CYS112 4.8 34.6 1.0 SG A:CYS51 4.9 31.2 1.0 O A:GLY143 4.9 36.3 1.0 CG A:LEU28 4.9 35.9 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:26.0 occ:1.00 FE2 A:SF4425 0.0 26.0 1.0 S3 A:SF4425 2.3 25.5 1.0 S4 A:SF4425 2.3 25.1 1.0 S1 A:SF4425 2.3 25.5 1.0 SG A:CYS112 2.4 34.6 1.0 FE4 A:SF4425 2.7 27.6 1.0 FE1 A:SF4425 2.7 26.0 1.0 FE3 A:SF4425 2.8 26.1 1.0 CB A:CYS112 3.3 33.3 1.0 N A:GLY145 3.7 35.6 1.0 N A:CYS112 3.8 33.3 1.0 S2 A:SF4425 3.9 26.1 1.0 CG B:PRO33 4.0 31.7 1.0 CA A:CYS112 4.1 33.5 1.0 OD1 B:ASP36 4.3 29.3 1.0 CA A:GLY145 4.4 35.7 1.0 CD A:PRO113 4.5 33.3 1.0 CB B:PRO33 4.6 32.1 1.0 OG1 B:THR96 4.7 37.3 1.0 C A:SER144 4.8 35.7 1.0 CA A:SER144 4.8 35.9 1.0 SG A:CYS51 4.8 31.2 1.0 SG A:CYS26 4.9 35.1 1.0 CB A:CYS26 4.9 35.0 1.0 C A:SER111 4.9 33.4 1.0 O B:HOH569 5.0 37.4 1.0 O B:GLN34 5.0 33.8 1.0 CB A:SER144 5.0 35.6 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:26.1 occ:1.00 FE3 A:SF4425 0.0 26.1 1.0 SG A:CYS51 2.3 31.2 1.0 S2 A:SF4425 2.3 26.1 1.0 S1 A:SF4425 2.3 25.5 1.0 S4 A:SF4425 2.3 25.1 1.0 FE2 A:SF4425 2.8 26.0 1.0 FE1 A:SF4425 2.8 26.0 1.0 FE4 A:SF4425 2.8 27.6 1.0 CB A:CYS51 3.4 32.8 1.0 CA A:CYS51 3.8 32.7 1.0 N A:CYS51 4.0 32.8 1.0 CD2 A:LEU28 4.0 34.6 1.0 S3 A:SF4425 4.0 25.5 1.0 CB A:SER111 4.3 33.3 1.0 CD A:PRO113 4.4 33.3 1.0 CG2 A:THR50 4.6 32.7 1.0 OD1 B:ASP36 4.6 29.3 1.0 C A:THR50 4.7 32.9 1.0 N A:CYS112 4.8 33.3 1.0 CB A:THR50 4.9 33.2 1.0 SG A:CYS26 4.9 35.1 1.0 SG A:CYS112 5.0 34.6 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:27.6 occ:1.00 FE4 A:SF4425 0.0 27.6 1.0 OD1 B:ASP36 2.0 29.3 1.0 S1 A:SF4425 2.3 25.5 1.0 S3 A:SF4425 2.3 25.5 1.0 S2 A:SF4425 2.3 26.1 1.0 FE2 A:SF4425 2.7 26.0 1.0 FE1 A:SF4425 2.7 26.0 1.0 FE3 A:SF4425 2.8 26.1 1.0 CG B:ASP36 3.1 32.0 1.0 OD2 B:ASP36 3.6 31.2 1.0 CG2 A:THR50 3.8 32.7 1.0 S4 A:SF4425 3.9 25.1 1.0 CB B:ASP36 4.3 31.8 1.0 CA B:ASP36 4.4 32.0 1.0 CG B:PRO33 4.4 31.7 1.0 N B:ASP36 4.4 32.0 1.0 O B:HOH569 4.4 37.4 1.0 C B:GLY35 4.6 32.1 1.0 O B:GLY35 4.8 32.1 1.0 CE1 B:TYR38 4.8 31.1 1.0 SG A:CYS112 4.8 34.6 1.0 CB A:THR50 4.8 33.2 1.0 SG A:CYS26 4.8 35.1 1.0 SG A:CYS51 4.9 31.2 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:25.7 occ:1.00 FE1 C:SF4425 0.0 25.7 1.0 S2 C:SF4425 2.3 26.3 1.0 S3 C:SF4425 2.3 26.5 1.0 S4 C:SF4425 2.3 25.7 1.0 SG C:CYS26 2.3 35.6 1.0 FE4 C:SF4425 2.7 30.1 1.0 FE2 C:SF4425 2.7 27.6 1.0 FE3 C:SF4425 2.8 27.1 1.0 CB C:CYS26 3.2 36.0 1.0 S1 C:SF4425 3.9 27.6 1.0 CD2 C:LEU28 4.1 36.2 1.0 N C:GLY145 4.2 38.9 1.0 CD2 C:LEU54 4.3 39.8 1.0 O D:HOH598 4.4 26.9 1.0 OD1 D:ASP36 4.5 32.0 1.0 CA C:CYS26 4.7 36.0 1.0 CB C:LEU28 4.8 36.4 1.0 CA C:GLY145 4.8 39.6 1.0 SG C:CYS112 4.8 34.0 1.0 O C:GLY143 4.9 36.5 1.0 CG C:LEU28 4.9 37.3 1.0 SG C:CYS51 5.0 31.9 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:27.6 occ:1.00 FE2 C:SF4425 0.0 27.6 1.0 S1 C:SF4425 2.3 27.6 1.0 S4 C:SF4425 2.3 25.7 1.0 S3 C:SF4425 2.3 26.5 1.0 SG C:CYS112 2.4 34.0 1.0 FE4 C:SF4425 2.7 30.1 1.0 FE3 C:SF4425 2.7 27.1 1.0 FE1 C:SF4425 2.7 25.7 1.0 CB C:CYS112 3.2 33.2 1.0 N C:CYS112 3.6 33.2 1.0 N C:GLY145 3.8 38.9 1.0 S2 C:SF4425 3.9 26.3 1.0 CA C:CYS112 4.0 33.4 1.0 CG D:PRO33 4.1 33.3 1.0 OD1 D:ASP36 4.3 32.0 1.0 CA C:GLY145 4.4 39.6 1.0 CD C:PRO113 4.6 33.8 1.0 O D:HOH633 4.6 33.1 1.0 CB D:PRO33 4.7 33.6 1.0 OG1 D:THR96 4.7 34.2 1.0 C C:SER111 4.8 33.2 1.0 CA C:SER144 4.8 38.2 1.0 C C:SER144 4.8 38.5 1.0 SG C:CYS26 4.9 35.6 1.0 O D:GLN34 4.9 36.5 1.0 SG C:CYS51 4.9 31.9 1.0 CB C:CYS26 5.0 36.0 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:27.1 occ:1.00 FE3 C:SF4425 0.0 27.1 1.0 S2 C:SF4425 2.3 26.3 1.0 S1 C:SF4425 2.3 27.6 1.0 S4 C:SF4425 2.3 25.7 1.0 SG C:CYS51 2.5 31.9 1.0 FE2 C:SF4425 2.7 27.6 1.0 FE1 C:SF4425 2.8 25.7 1.0 FE4 C:SF4425 2.8 30.1 1.0 CB C:CYS51 3.5 32.4 1.0 CA C:CYS51 3.8 32.8 1.0 S3 C:SF4425 3.9 26.5 1.0 CD2 C:LEU28 4.0 36.2 1.0 N C:CYS51 4.1 33.0 1.0 CB C:SER111 4.3 33.4 1.0 CD C:PRO113 4.5 33.8 1.0 OD1 D:ASP36 4.6 32.0 1.0 N C:CYS112 4.6 33.2 1.0 C C:THR50 4.8 32.9 1.0 CG2 C:THR50 4.8 31.1 1.0 SG C:CYS26 4.9 35.6 1.0 SG C:CYS112 5.0 34.0 1.0 CB C:THR50 5.0 33.0 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:30.1 occ:1.00 FE4 C:SF4425 0.0 30.1 1.0 OD1 D:ASP36 2.0 32.0 1.0 S3 C:SF4425 2.3 26.5 1.0 S2 C:SF4425 2.3 26.3 1.0 S1 C:SF4425 2.3 27.6 1.0 FE2 C:SF4425 2.7 27.6 1.0 FE1 C:SF4425 2.7 25.7 1.0 FE3 C:SF4425 2.8 27.1 1.0 CG D:ASP36 3.2 33.4 1.0 OD2 D:ASP36 3.8 32.3 1.0 CG2 C:THR50 3.9 31.1 1.0 S4 C:SF4425 3.9 25.7 1.0 O D:HOH633 4.0 33.1 1.0 CA D:ASP36 4.3 33.1 1.0 CB D:ASP36 4.3 33.0 1.0 N D:ASP36 4.3 33.8 1.0 CG D:PRO33 4.5 33.3 1.0 C D:GLY35 4.5 34.4 1.0 O D:GLY35 4.7 34.7 1.0 CE1 D:TYR38 4.8 32.1 1.0 SG C:CYS26 4.8 35.6 1.0 SG C:CYS112 4.8 34.0 1.0 CB C:THR50 4.8 33.0 1.0 CD1 D:TYR38 5.0 32.5 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