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

The structure of Crystal Structure of the Hypc-Hypd-Hype Complex (Form II), PDB code: 3vyu 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)	36.81 / 2.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.677, 121.461, 67.354, 90.00, 97.20, 90.00
R / Rfree (%)	21.9 / 25.8

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:99.4 occ:1.00 FE1 B:SF4501 0.0 99.4 1.0 S2 B:SF4501 2.0 0.3 1.0 S4 B:SF4501 2.3 0.4 1.0 S3 B:SF4501 2.3 0.8 1.0 SG B:CYS323 2.3 0.8 1.0 FE2 B:SF4501 2.7 0.9 1.0 FE3 B:SF4501 2.9 0.9 1.0 FE4 B:SF4501 2.9 0.1 1.0 CB B:CYS323 3.5 0.5 1.0 CA B:CYS323 3.7 0.8 1.0 S1 B:SF4501 3.7 0.8 1.0 CB B:CYS325 3.7 91.8 1.0 N B:CYS325 3.9 0.2 1.0 N B:ARG324 3.9 0.2 1.0 C B:CYS323 4.1 98.5 1.0 CA B:GLY352 4.1 91.5 1.0 N B:GLY352 4.2 90.0 1.0 CA B:CYS325 4.2 98.7 1.0 C B:ARG324 4.6 0.4 1.0 SG B:CYS345 4.8 0.6 1.0 CB B:CYS354 4.8 93.4 1.0 SG B:CYS338 4.8 0.8 1.0 CA B:ARG324 4.9 0.8 1.0 C B:GLY352 4.9 93.9 1.0 SG B:CYS362 4.9 94.0 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:0.9 occ:1.00 FE2 B:SF4501 0.0 0.9 1.0 S4 B:SF4501 1.9 0.4 1.0 S3 B:SF4501 1.9 0.8 1.0 S1 B:SF4501 2.0 0.8 1.0 SG B:CYS345 2.3 0.6 1.0 FE1 B:SF4501 2.7 99.4 1.0 FE3 B:SF4501 2.8 0.9 1.0 FE4 B:SF4501 2.9 0.1 1.0 CB B:CYS345 3.3 0.0 1.0 S2 B:SF4501 3.7 0.3 1.0 N B:GLY352 4.2 90.0 1.0 CE B:MET355 4.3 78.8 1.0 CB B:MET355 4.3 81.7 1.0 CB B:VAL351 4.5 90.7 1.0 SG B:CYS323 4.7 0.8 1.0 CA B:CYS345 4.7 0.3 1.0 N B:VAL351 4.8 94.0 1.0 SG B:CYS362 4.8 94.0 1.0 SG B:CYS338 4.8 0.8 1.0 CA B:GLY352 4.9 91.5 1.0 CG B:MET355 5.0 72.6 1.0 CB B:CYS362 5.0 90.0 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:0.9 occ:1.00 FE3 B:SF4501 0.0 0.9 1.0 SG B:CYS338 2.3 0.8 1.0 S2 B:SF4501 2.3 0.3 1.0 S1 B:SF4501 2.3 0.8 1.0 S4 B:SF4501 2.4 0.4 1.0 FE4 B:SF4501 2.7 0.1 1.0 FE2 B:SF4501 2.8 0.9 1.0 FE1 B:SF4501 2.9 99.4 1.0 CB B:CYS338 3.2 99.5 1.0 S3 B:SF4501 3.8 0.8 1.0 N B:PHE341 4.3 98.2 1.0 N B:ARG324 4.3 0.2 1.0 CB B:LEU340 4.5 86.4 1.0 CA B:CYS338 4.6 98.6 1.0 CB B:PHE341 4.7 91.8 1.0 CA B:PHE341 4.7 99.5 1.0 CA B:CYS323 4.8 0.8 1.0 SG B:CYS362 4.8 94.0 1.0 C B:LEU340 4.8 97.4 1.0 SG B:CYS345 4.9 0.6 1.0 SG B:CYS323 4.9 0.8 1.0 N B:LEU340 5.0 94.3 1.0 O B:PRO335 5.0 0.5 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:0.1 occ:1.00 FE4 B:SF4501 0.0 0.1 1.0 S1 B:SF4501 2.2 0.8 1.0 SG B:CYS362 2.2 94.0 1.0 S2 B:SF4501 2.3 0.3 1.0 S3 B:SF4501 2.5 0.8 1.0 FE3 B:SF4501 2.7 0.9 1.0 FE2 B:SF4501 2.9 0.9 1.0 FE1 B:SF4501 2.9 99.4 1.0 CB B:CYS362 3.3 90.0 1.0 S4 B:SF4501 3.8 0.4 1.0 CB B:CYS354 3.9 93.4 1.0 CB B:PRO335 4.6 0.5 1.0 CA B:CYS362 4.7 90.6 1.0 SG B:CYS338 4.8 0.8 1.0 CG2 B:VAL328 4.8 88.6 1.0 SG B:CYS354 4.9 97.2 1.0 SG B:CYS345 4.9 0.6 1.0 CB B:CYS325 4.9 91.8 1.0 CA B:CYS325 5.0 98.7 1.0 CE B:MET355 5.0 78.8 1.0 CA B:PRO335 5.0 99.8 1.0 C B:CYS354 5.0 87.5 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