Iron in PDB 3vys: Crystal Structure of the Hypc-Hypd-Hype Complex (Form I)

The structure of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I), PDB code: 3vys was solved by S.Watanabe, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.93 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.567, 99.201, 104.025, 90.00, 97.69, 90.00
R / Rfree (%)	21.8 / 26.1

The structure of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I) also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Iron atom in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I) (pdb code 3vys). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I), PDB code: 3vys:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:48.8 occ:1.00 FE1 B:SF4501 0.0 48.8 1.0 SG B:CYS362 2.2 45.2 1.0 S3 B:SF4501 2.2 49.2 1.0 S4 B:SF4501 2.3 50.6 1.0 S2 B:SF4501 2.5 53.6 1.0 FE2 B:SF4501 2.7 49.7 1.0 FE4 B:SF4501 2.9 52.7 1.0 FE3 B:SF4501 2.9 50.7 1.0 CB B:CYS362 3.2 42.1 1.0 S1 B:SF4501 3.9 48.0 1.0 CB B:CYS354 4.1 52.8 1.0 CA B:CYS362 4.6 47.1 1.0 N B:MET355 4.8 48.4 1.0 SG B:CYS338 4.8 43.3 1.0 CB B:CYS325 4.8 48.4 1.0 SG B:CYS345 4.9 54.4 1.0 CB B:CYS338 4.9 40.0 1.0 CB B:MET355 4.9 41.4 1.0 CA B:CYS325 4.9 51.6 1.0 CG2 B:VAL328 5.0 35.6 1.0 N B:CYS325 5.0 47.7 1.0 C B:CYS354 5.0 47.6 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:49.7 occ:1.00 FE2 B:SF4501 0.0 49.7 1.0 SG B:CYS338 2.3 43.3 1.0 S3 B:SF4501 2.3 49.2 1.0 S4 B:SF4501 2.3 50.6 1.0 S1 B:SF4501 2.4 48.0 1.0 FE1 B:SF4501 2.7 48.8 1.0 FE4 B:SF4501 2.8 52.7 1.0 FE3 B:SF4501 2.9 50.7 1.0 CB B:CYS338 3.1 40.0 1.0 S2 B:SF4501 3.8 53.6 1.0 N B:PHE341 4.2 52.2 1.0 N B:ARG324 4.2 50.6 1.0 CB B:LEU340 4.5 47.7 1.0 CA B:CYS338 4.6 50.4 1.0 CA B:CYS323 4.6 55.7 1.0 CA B:PHE341 4.7 54.2 1.0 CB B:PHE341 4.7 54.8 1.0 SG B:CYS362 4.7 45.2 1.0 SG B:CYS323 4.7 48.9 1.0 SG B:CYS345 4.8 54.4 1.0 C B:LEU340 4.9 55.3 1.0 O B:PRO335 4.9 57.6 1.0 N B:LEU340 5.0 59.0 1.0 C B:CYS323 5.0 56.6 1.0 O B:GLY322 5.0 56.8 1.0 CG B:LEU340 5.0 50.0 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:50.7 occ:1.00 FE3 B:SF4501 0.0 50.7 1.0 S4 B:SF4501 2.0 50.6 1.0 S1 B:SF4501 2.3 48.0 1.0 SG B:CYS323 2.3 48.9 1.0 S2 B:SF4501 2.3 53.6 1.0 FE4 B:SF4501 2.7 52.7 1.0 FE2 B:SF4501 2.9 49.7 1.0 FE1 B:SF4501 2.9 48.8 1.0 CB B:CYS323 3.5 50.8 1.0 CB B:CYS325 3.7 48.4 1.0 S3 B:SF4501 3.7 49.2 1.0 CA B:CYS323 3.8 55.7 1.0 N B:ARG324 3.9 50.6 1.0 CA B:GLY352 3.9 46.8 1.0 N B:CYS325 3.9 47.7 1.0 N B:GLY352 4.2 49.0 1.0 C B:CYS323 4.2 56.6 1.0 CA B:CYS325 4.3 51.6 1.0 C B:ARG324 4.7 51.8 1.0 C B:GLY352 4.7 45.3 1.0 SG B:CYS338 4.8 43.3 1.0 SG B:CYS345 4.8 54.4 1.0 SG B:CYS362 4.9 45.2 1.0 CA B:ARG324 4.9 50.5 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:52.7 occ:1.00 FE4 B:SF4501 0.0 52.7 1.0 S1 B:SF4501 1.9 48.0 1.0 S2 B:SF4501 2.0 53.6 1.0 S3 B:SF4501 2.0 49.2 1.0 SG B:CYS345 2.3 54.4 1.0 FE3 B:SF4501 2.7 50.7 1.0 FE2 B:SF4501 2.8 49.7 1.0 FE1 B:SF4501 2.9 48.8 1.0 CB B:CYS345 3.3 54.8 1.0 S4 B:SF4501 3.7 50.6 1.0 N B:GLY352 3.8 49.0 1.0 CB B:MET355 4.2 41.4 1.0 CA B:GLY352 4.3 46.8 1.0 CB B:VAL351 4.5 52.0 1.0 N B:VAL351 4.7 50.6 1.0 CE B:MET355 4.7 32.3 1.0 SG B:CYS323 4.7 48.9 1.0 CA B:CYS345 4.8 50.4 1.0 C B:VAL351 4.8 46.8 1.0 SG B:CYS362 4.8 45.2 1.0 SG B:CYS338 4.8 43.3 1.0 CA B:VAL351 4.9 50.9 1.0 O B:GLY352 4.9 45.6 1.0 CG B:MET355 4.9 32.9 1.0 C B:GLY352 5.0 45.3 1.0 CB B:LEU340 5.0 47.7 1.0

S.Watanabe, R.Matsumi, H.Atomi, T.Imanaka, K.Miki. Crystal Structures of the Hypcd Complex and the Hypcde Ternary Complex: Transient Intermediate Complexes During [Nife] Hydrogenase Maturation Structure V. 20 2124 2012.
ISSN: ISSN 0969-2126
PubMed: 23123111
DOI: 10.1016/J.STR.2012.09.018