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

The structure of Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward), PDB code: 3vyt 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)	34.79 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.333, 99.412, 103.923, 90.00, 97.79, 90.00
R / Rfree (%)	20.7 / 25.3

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

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	1 atom

The binding sites of Iron atom in the Crystal Structure of the Hypc-Hypd-Hype Complex (Form I Inward) (pdb code 3vyt). 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 Inward), PDB code: 3vyt:
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 Inward)


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 Inward) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:36.0 occ:1.00 FE1 B:SF4501 0.0 36.0 1.0 S2 B:SF4501 2.0 35.5 1.0 SG B:CYS323 2.3 34.5 1.0 S4 B:SF4501 2.3 33.4 1.0 S3 B:SF4501 2.3 36.7 1.0 FE2 B:SF4501 2.7 36.5 1.0 FE3 B:SF4501 2.9 38.1 1.0 FE4 B:SF4501 2.9 34.4 1.0 CB B:CYS323 3.5 38.9 1.0 CB B:CYS325 3.7 30.8 1.0 S1 B:SF4501 3.7 32.5 1.0 N B:CYS325 3.8 32.8 1.0 CA B:GLY352 3.8 32.5 1.0 CA B:CYS323 3.8 37.7 1.0 N B:ARG324 3.9 33.2 1.0 N B:GLY352 4.2 33.4 1.0 CA B:CYS325 4.2 32.2 1.0 C B:CYS323 4.3 43.7 1.0 C B:GLY352 4.7 25.2 1.0 C B:ARG324 4.7 38.8 1.0 SG B:CYS338 4.8 35.0 1.0 SG B:CYS345 4.9 39.1 1.0 SG B:CYS362 4.9 34.2 1.0 CA B:ARG324 4.9 40.3 1.0

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


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 Inward) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:36.5 occ:1.00 FE2 B:SF4501 0.0 36.5 1.0 S4 B:SF4501 2.0 33.4 1.0 S3 B:SF4501 2.0 36.7 1.0 S1 B:SF4501 2.1 32.5 1.0 SG B:CYS345 2.3 39.1 1.0 FE1 B:SF4501 2.7 36.0 1.0 FE3 B:SF4501 2.8 38.1 1.0 FE4 B:SF4501 2.9 34.4 1.0 CB B:CYS345 3.3 41.3 1.0 S2 B:SF4501 3.8 35.5 1.0 N B:GLY352 3.9 33.4 1.0 CB B:MET355 4.0 28.8 1.0 CA B:GLY352 4.3 32.5 1.0 CB B:VAL351 4.5 35.6 1.0 CE B:MET355 4.6 19.9 1.0 N B:VAL351 4.7 37.7 1.0 SG B:CYS323 4.7 34.5 1.0 CA B:CYS345 4.7 36.5 1.0 CG B:MET355 4.8 26.6 1.0 C B:VAL351 4.8 33.3 1.0 SG B:CYS362 4.8 34.2 1.0 SG B:CYS338 4.9 35.0 1.0 CA B:VAL351 4.9 37.4 1.0 CB B:LEU340 4.9 35.9 1.0 O B:GLY352 5.0 36.0 1.0 CB B:CYS362 5.0 31.3 1.0

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


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 Inward) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:38.1 occ:1.00 FE3 B:SF4501 0.0 38.1 1.0 SG B:CYS338 2.3 35.0 1.0 S1 B:SF4501 2.3 32.5 1.0 S2 B:SF4501 2.3 35.5 1.0 S4 B:SF4501 2.4 33.4 1.0 FE4 B:SF4501 2.8 34.4 1.0 FE2 B:SF4501 2.8 36.5 1.0 FE1 B:SF4501 2.9 36.0 1.0 CB B:CYS338 3.1 27.4 1.0 S3 B:SF4501 3.9 36.7 1.0 N B:ARG324 4.2 33.2 1.0 N B:PHE341 4.3 37.5 1.0 CB B:LEU340 4.4 35.9 1.0 CA B:CYS323 4.5 37.7 1.0 CA B:CYS338 4.5 36.3 1.0 SG B:CYS323 4.7 34.5 1.0 SG B:CYS362 4.7 34.2 1.0 CA B:PHE341 4.7 40.2 1.0 C B:LEU340 4.8 38.8 1.0 O B:PRO335 4.8 39.8 1.0 CB B:PHE341 4.9 36.9 1.0 SG B:CYS345 4.9 39.1 1.0 N B:LEU340 4.9 44.7 1.0 C B:CYS323 4.9 43.7 1.0 CA B:LEU340 4.9 36.8 1.0

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


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 Inward) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:34.4 occ:1.00 FE4 B:SF4501 0.0 34.4 1.0 SG B:CYS362 2.2 34.2 1.0 S1 B:SF4501 2.2 32.5 1.0 S2 B:SF4501 2.3 35.5 1.0 S3 B:SF4501 2.5 36.7 1.0 FE3 B:SF4501 2.8 38.1 1.0 FE1 B:SF4501 2.9 36.0 1.0 FE2 B:SF4501 2.9 36.5 1.0 CB B:CYS362 3.2 31.3 1.0 S4 B:SF4501 3.9 33.4 1.0 CB B:CYS354 4.1 42.7 1.0 CA B:CYS362 4.6 39.6 1.0 CB B:PRO335 4.7 36.6 1.0 N B:MET355 4.8 39.1 1.0 CB B:CYS325 4.8 30.8 1.0 CG2 B:VAL328 4.8 31.4 1.0 SG B:CYS338 4.9 35.0 1.0 CB B:MET355 4.9 28.8 1.0 CA B:CYS325 4.9 32.2 1.0 CB B:CYS338 4.9 27.4 1.0 N B:CYS325 4.9 32.8 1.0 CA B:PRO335 5.0 30.0 1.0 SG B:CYS345 5.0 39.1 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