Iron in PDB 3vyr: Crystal Structure of the Hypc-Hypd Complex

The structure of Crystal Structure of the Hypc-Hypd Complex, PDB code: 3vyr 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)	45.30 / 2.55
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	181.179, 181.179, 49.433, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 21.2

The binding sites of Iron atom in the Crystal Structure of the Hypc-Hypd Complex (pdb code 3vyr). 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 Complex, PDB code: 3vyr:
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 Complex


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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:48.6 occ:1.00 FE1 B:SF4501 0.0 48.6 1.0 SG B:CYS362 2.3 51.3 1.0 S4 B:SF4501 2.3 46.5 1.0 S3 B:SF4501 2.3 50.0 1.0 S2 B:SF4501 2.4 48.4 1.0 FE2 B:SF4501 2.7 49.3 1.0 FE4 B:SF4501 2.8 55.4 1.0 FE3 B:SF4501 2.9 49.5 1.0 CB B:CYS362 3.3 46.5 1.0 S1 B:SF4501 3.8 51.5 1.0 CB B:CYS354 4.2 42.0 1.0 CA B:CYS362 4.7 42.5 1.0 SG B:CYS338 4.8 56.0 1.0 SG B:CYS345 4.8 53.0 1.0 CG2 B:VAL328 4.8 35.0 1.0 CB B:PRO335 4.9 36.3 1.0 N B:CYS325 4.9 41.7 1.0 CB B:CYS325 4.9 32.0 1.0 CA B:CYS325 4.9 53.6 1.0 CE B:MET355 4.9 29.0 1.0 CB B:CYS338 4.9 54.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Hypc-Hypd Complex


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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:49.3 occ:1.00 FE2 B:SF4501 0.0 49.3 1.0 SG B:CYS338 2.3 56.0 1.0 S3 B:SF4501 2.3 50.0 1.0 S4 B:SF4501 2.3 46.5 1.0 S1 B:SF4501 2.4 51.5 1.0 FE1 B:SF4501 2.7 48.6 1.0 FE4 B:SF4501 2.8 55.4 1.0 FE3 B:SF4501 2.9 49.5 1.0 CB B:CYS338 3.2 54.0 1.0 S2 B:SF4501 3.8 48.4 1.0 N B:ARG324 4.1 42.6 1.0 N B:PHE341 4.3 57.7 1.0 CB B:LEU340 4.4 37.3 1.0 CA B:CYS323 4.6 52.5 1.0 CA B:CYS338 4.6 52.5 1.0 CB B:PHE341 4.7 51.1 1.0 CA B:PHE341 4.7 53.0 1.0 SG B:CYS323 4.8 48.7 1.0 SG B:CYS362 4.8 51.3 1.0 C B:LEU340 4.8 54.0 1.0 SG B:CYS345 4.9 53.0 1.0 C B:CYS323 4.9 51.5 1.0 CB B:ARG324 4.9 44.3 1.0 CB B:CYS345 5.0 61.6 1.0 CA B:LEU340 5.0 54.4 1.0 N B:LEU340 5.0 48.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Hypc-Hypd Complex


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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:49.5 occ:1.00 FE3 B:SF4501 0.0 49.5 1.0 S4 B:SF4501 2.1 46.5 1.0 SG B:CYS323 2.3 48.7 1.0 S1 B:SF4501 2.3 51.5 1.0 S2 B:SF4501 2.3 48.4 1.0 FE4 B:SF4501 2.7 55.4 1.0 FE2 B:SF4501 2.9 49.3 1.0 FE1 B:SF4501 2.9 48.6 1.0 CB B:CYS323 3.4 57.4 1.0 CA B:CYS323 3.7 52.5 1.0 N B:CYS325 3.7 41.7 1.0 CB B:CYS325 3.7 32.0 1.0 N B:ARG324 3.8 42.6 1.0 S3 B:SF4501 3.8 50.0 1.0 C B:CYS323 4.1 51.5 1.0 CA B:GLY352 4.1 38.1 1.0 CA B:CYS325 4.2 53.6 1.0 N B:GLY352 4.2 43.6 1.0 C B:ARG324 4.6 59.2 1.0 CA B:ARG324 4.8 50.0 1.0 SG B:CYS338 4.8 56.0 1.0 SG B:CYS345 4.8 53.0 1.0 SG B:CYS362 4.9 51.3 1.0 C B:GLY352 4.9 43.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Hypc-Hypd Complex


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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:55.4 occ:1.00 FE4 B:SF4501 0.0 55.4 1.0 S1 B:SF4501 1.9 51.5 1.0 S2 B:SF4501 1.9 48.4 1.0 S3 B:SF4501 2.0 50.0 1.0 SG B:CYS345 2.3 53.0 1.0 FE3 B:SF4501 2.7 49.5 1.0 FE2 B:SF4501 2.8 49.3 1.0 FE1 B:SF4501 2.8 48.6 1.0 CB B:CYS345 3.2 61.6 1.0 S4 B:SF4501 3.7 46.5 1.0 N B:GLY352 4.0 43.6 1.0 CB B:MET355 4.3 41.2 1.0 CB B:VAL351 4.4 46.0 1.0 CE B:MET355 4.5 29.0 1.0 CA B:GLY352 4.7 38.1 1.0 SG B:CYS323 4.7 48.7 1.0 CA B:CYS345 4.7 59.8 1.0 N B:VAL351 4.7 48.8 1.0 SG B:CYS362 4.7 51.3 1.0 SG B:CYS338 4.9 56.0 1.0 CA B:VAL351 4.9 39.4 1.0 C B:VAL351 4.9 48.3 1.0 CG B:MET355 5.0 36.5 1.0 CB B:CYS362 5.0 46.5 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