Iron in PDB 3w5v: Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase

The structure of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase, PDB code: 3w5v was solved by Y.Kimata-Ariga, H.Kubota-Kawai, N.Muraki, T.Hase, G.Kurisu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.67 / 3.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.170, 120.345, 84.577, 90.00, 109.70, 90.00
R / Rfree (%)	27.7 / 30.6

The binding sites of Iron atom in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase (pdb code 3w5v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase, PDB code: 3w5v:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:40.0 occ:1.00 FE1 B:FES101 0.0 40.0 1.0 SG B:CYS47 1.8 40.0 1.0 S2 B:FES101 2.2 40.0 1.0 S1 B:FES101 2.2 40.0 1.0 SG B:CYS77 2.3 40.0 1.0 FE2 B:FES101 3.1 40.0 1.0 CB B:CYS77 3.1 40.0 1.0 CB B:CYS47 3.2 40.0 1.0 N B:CYS77 3.9 40.0 1.0 CA B:CYS77 4.0 40.0 1.0 SG B:CYS39 4.1 40.0 1.0 SG B:CYS44 4.2 40.0 1.0 N B:CYS47 4.2 40.0 1.0 CA B:CYS47 4.3 40.0 1.0 CD2 B:LEU75 4.5 40.0 1.0 CB B:LEU75 4.5 40.0 1.0 N B:ARG40 4.5 40.0 1.0 N B:GLY42 4.6 40.0 1.0 CA B:GLY42 4.7 40.0 1.0 CD1 B:LEU75 4.7 40.0 1.0 CA B:ARG40 4.7 40.0 1.0 CG B:LEU75 4.8 40.0 1.0 C B:CYS77 4.8 40.0 1.0 N B:THR76 4.9 40.0 1.0

Iron binding site 2 out of 4 in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:40.0 occ:1.00 FE2 B:FES101 0.0 40.0 1.0 SG B:CYS44 1.8 40.0 1.0 SG B:CYS39 2.0 40.0 1.0 S1 B:FES101 2.2 40.0 1.0 S2 B:FES101 2.2 40.0 1.0 CB B:CYS44 2.8 40.0 1.0 CB B:CYS39 3.0 40.0 1.0 FE1 B:FES101 3.1 40.0 1.0 N B:CYS39 3.3 40.0 1.0 N B:CYS44 3.5 40.0 1.0 CA B:CYS44 3.5 40.0 1.0 CA B:CYS39 3.7 40.0 1.0 N B:ARG40 3.8 40.0 1.0 C B:CYS44 3.9 40.0 1.0 SG B:CYS77 4.2 40.0 1.0 C B:CYS39 4.3 40.0 1.0 O B:CYS44 4.3 40.0 1.0 SG B:CYS47 4.3 40.0 1.0 N B:SER45 4.4 40.0 1.0 N B:SER43 4.4 40.0 1.0 C B:SER38 4.4 40.0 1.0 N B:GLY42 4.4 40.0 1.0 C B:SER43 4.4 40.0 1.0 N B:SER38 4.5 40.0 1.0 CB B:SER38 4.5 40.0 1.0 CA B:SER38 4.7 40.0 1.0 N B:ALA41 4.7 40.0 1.0 N B:SER46 4.8 40.0 1.0 CA B:ARG40 4.8 40.0 1.0 CA B:GLY42 4.8 40.0 1.0

Iron binding site 3 out of 4 in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe101 b:40.0 occ:1.00 FE1 D:FES101 0.0 40.0 1.0 SG D:CYS47 1.9 40.0 1.0 S2 D:FES101 2.2 40.0 1.0 S1 D:FES101 2.2 40.0 1.0 SG D:CYS77 2.6 40.0 1.0 CB D:CYS77 3.0 40.0 1.0 FE2 D:FES101 3.1 40.0 1.0 CB D:CYS47 3.3 40.0 1.0 N D:CYS77 3.9 40.0 1.0 CA D:CYS77 4.0 40.0 1.0 SG D:CYS39 4.1 40.0 1.0 N D:CYS47 4.2 40.0 1.0 SG D:CYS44 4.3 40.0 1.0 CA D:CYS47 4.4 40.0 1.0 N D:ARG40 4.4 40.0 1.0 CD2 D:LEU75 4.5 40.0 1.0 N D:GLY42 4.5 40.0 1.0 CB D:LEU75 4.6 40.0 1.0 CA D:ARG40 4.6 40.0 1.0 CA D:GLY42 4.7 40.0 1.0 CD1 D:LEU75 4.8 40.0 1.0 CG D:LEU75 4.9 40.0 1.0 C D:CYS77 4.9 40.0 1.0 N D:THR76 4.9 40.0 1.0

Iron binding site 4 out of 4 in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe101 b:40.0 occ:1.00 FE2 D:FES101 0.0 40.0 1.0 SG D:CYS44 1.9 40.0 1.0 SG D:CYS39 2.1 40.0 1.0 S1 D:FES101 2.2 40.0 1.0 S2 D:FES101 2.2 40.0 1.0 CB D:CYS44 2.8 40.0 1.0 CB D:CYS39 3.0 40.0 1.0 FE1 D:FES101 3.1 40.0 1.0 N D:CYS39 3.3 40.0 1.0 N D:CYS44 3.5 40.0 1.0 CA D:CYS44 3.5 40.0 1.0 CA D:CYS39 3.7 40.0 1.0 N D:ARG40 3.8 40.0 1.0 C D:CYS44 3.9 40.0 1.0 C D:CYS39 4.2 40.0 1.0 N D:SER45 4.3 40.0 1.0 C D:SER38 4.4 40.0 1.0 O D:CYS44 4.4 40.0 1.0 CB D:SER38 4.4 40.0 1.0 N D:SER43 4.5 40.0 1.0 N D:GLY42 4.5 40.0 1.0 N D:SER38 4.5 40.0 1.0 SG D:CYS77 4.5 40.0 1.0 SG D:CYS47 4.5 40.0 1.0 C D:SER43 4.5 40.0 1.0 CA D:SER38 4.7 40.0 1.0 N D:SER46 4.7 40.0 1.0 N D:ALA41 4.7 40.0 1.0 CA D:ARG40 4.8 40.0 1.0 CA D:GLY42 4.9 40.0 1.0

Y.Kimata-Ariga, H.Kubota-Kawai, Y.-H.Lee, N.Muraki, T.Ikegami, G.Kurisu, T.Hase. Concentration-Dependent Oligomerization of Cross-Linked Complexes Between Ferredoxin and Ferredoxin-Nadp(+) Reductase Biochem.Biophys.Res.Commun. V. 434 867 2013.
ISSN: ISSN 0006-291X
PubMed: 23618857
DOI: 10.1016/J.BBRC.2013.04.033