Iron in PDB 5xfa: Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State

The structure of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State, PDB code: 5xfa was solved by Y.Shomura, M.Taketa, H.Nakashima, H.Tai, H.Nakagawa, Y.Ikeda, M.Ishii, Y.Igarashi, H.Nishihara, K.S.Yoon, S.Ogo, S.Hirota, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	96.24 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.750, 192.470, 130.820, 90.00, 105.08, 90.00
R / Rfree (%)	19.5 / 24.5

The structure of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Magnesium	(Mg)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State (pdb code 5xfa). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 38 binding sites of Iron where determined in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State, PDB code: 5xfa:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 38 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State


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 Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:38.9 occ:1.00 FE1 A:SF4601 0.0 38.9 1.0 S2 A:SF4601 2.2 43.7 1.0 S3 A:SF4601 2.2 34.5 1.0 SG A:CYS485 2.3 46.1 1.0 S4 A:SF4601 2.3 41.4 1.0 FE4 A:SF4601 2.6 41.9 1.0 FE3 A:SF4601 2.6 41.0 1.0 FE2 A:SF4601 2.8 41.5 1.0 CB A:CYS485 3.0 45.0 1.0 OG A:SER478 3.8 58.4 1.0 S1 A:SF4601 3.8 37.3 1.0 CD1 A:PHE527 3.9 62.6 1.0 N A:GLY528 4.2 65.9 1.0 CA A:GLY528 4.4 68.0 1.0 CA A:CYS485 4.4 46.0 1.0 SG A:CYS482 4.5 52.0 1.0 N A:CYS479 4.5 61.4 1.0 CE1 A:PHE527 4.5 68.9 1.0 SG A:CYS525 4.5 59.3 1.0 CG A:PHE527 4.6 61.0 1.0 CB A:SER478 4.7 60.3 1.0 CB A:PHE527 4.7 62.2 1.0 C A:CYS485 4.8 42.1 1.0 SG A:CYS479 4.9 49.9 1.0 CA A:SER478 4.9 62.1 1.0

Iron binding site 2 out of 38 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State


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 Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:41.5 occ:1.00 FE2 A:SF4601 0.0 41.5 1.0 S1 A:SF4601 2.2 37.3 1.0 S3 A:SF4601 2.3 34.5 1.0 S4 A:SF4601 2.3 41.4 1.0 SG A:CYS479 2.3 49.9 1.0 FE3 A:SF4601 2.6 41.0 1.0 FE4 A:SF4601 2.7 41.9 1.0 FE1 A:SF4601 2.8 38.9 1.0 CB A:CYS479 3.5 54.2 1.0 CB A:PHE481 3.8 33.7 1.0 N A:PHE481 3.8 48.5 1.0 S2 A:SF4601 3.8 43.7 1.0 N A:CYS479 4.0 61.4 1.0 CA A:CYS479 4.1 59.1 1.0 N A:GLY480 4.1 57.2 1.0 C A:CYS479 4.2 55.2 1.0 CD A:PRO333 4.2 83.8 1.0 CA A:PHE481 4.3 40.4 1.0 N A:CYS482 4.5 40.6 1.0 CG A:PRO333 4.6 85.2 1.0 SG A:CYS482 4.7 52.0 1.0 SG A:CYS525 4.7 59.3 1.0 SG A:CYS485 4.8 46.1 1.0 OG A:SER478 4.8 58.4 1.0 CG A:PHE481 4.9 29.5 1.0 C A:GLY480 4.9 56.7 1.0 C A:PHE481 4.9 38.3 1.0 CD2 A:PHE481 4.9 28.5 1.0 O A:CYS479 5.0 56.9 1.0

Iron binding site 3 out of 38 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State


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 Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:41.0 occ:1.00 FE3 A:SF4601 0.0 41.0 1.0 SG A:CYS482 2.2 52.0 1.0 S2 A:SF4601 2.2 43.7 1.0 S4 A:SF4601 2.3 41.4 1.0 S1 A:SF4601 2.3 37.3 1.0 FE1 A:SF4601 2.6 38.9 1.0 FE2 A:SF4601 2.6 41.5 1.0 FE4 A:SF4601 2.8 41.9 1.0 CB A:CYS482 3.3 49.8 1.0 CB A:CYS485 3.6 45.0 1.0 N A:CYS482 3.7 40.6 1.0 S3 A:SF4601 3.8 34.5 1.0 CA A:CYS482 3.9 44.5 1.0 SG A:CYS485 4.1 46.1 1.0 N A:ASN524 4.2 55.4 1.0 CB A:ASN524 4.3 68.2 1.0 O A:CYS482 4.3 40.2 1.0 C A:CYS482 4.5 41.7 1.0 C A:PHE481 4.7 38.3 1.0 CB A:PHE481 4.7 33.7 1.0 N A:PHE481 4.8 48.5 1.0 N A:CYS525 4.8 59.0 1.0 CA A:ASN524 4.8 60.2 1.0 SG A:CYS479 4.8 49.9 1.0 CD2 A:PHE481 4.9 28.5 1.0 CA A:CYS485 4.9 46.0 1.0 CA A:PHE481 4.9 40.4 1.0 SG A:CYS525 5.0 59.3 1.0

Iron binding site 4 out of 38 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State


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 Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:41.9 occ:1.00 FE4 A:SF4601 0.0 41.9 1.0 S1 A:SF4601 2.3 37.3 1.0 S2 A:SF4601 2.3 43.7 1.0 S3 A:SF4601 2.3 34.5 1.0 SG A:CYS525 2.3 59.3 1.0 FE1 A:SF4601 2.6 38.9 1.0 FE2 A:SF4601 2.7 41.5 1.0 FE3 A:SF4601 2.8 41.0 1.0 CB A:CYS525 3.4 58.7 1.0 S4 A:SF4601 3.8 41.4 1.0 N A:CYS525 3.8 59.0 1.0 CA A:CYS525 4.1 59.2 1.0 CG A:PRO333 4.1 85.2 1.0 CB A:PHE527 4.4 62.2 1.0 N A:GLY528 4.4 65.9 1.0 C A:CYS525 4.5 61.3 1.0 O A:CYS525 4.6 75.4 1.0 SG A:CYS479 4.6 49.9 1.0 CD A:PRO333 4.6 83.8 1.0 SG A:CYS485 4.7 46.1 1.0 SG A:CYS482 4.7 52.0 1.0 C A:ASN524 4.8 54.6 1.0 ND2 A:ASN524 4.8 73.9 1.0 CB A:PRO333 4.9 82.1 1.0 CD1 A:PHE527 5.0 62.6 1.0

Iron binding site 5 out of 38 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:26.6 occ:1.00 FE1 B:SF4301 0.0 26.6 1.0 S3 B:SF4301 2.2 24.2 1.0 S4 B:SF4301 2.2 26.5 1.0 S2 B:SF4301 2.3 30.5 1.0 SG B:CYS105 2.3 39.8 1.0 FE2 B:SF4301 2.6 27.2 1.0 FE3 B:SF4301 2.7 29.3 1.0 FE4 B:SF4301 2.8 30.6 1.0 CB B:CYS105 3.3 37.4 1.0 CA B:CYS105 3.6 38.2 1.0 NE2 B:GLN117 3.8 45.5 1.0 S1 B:SF4301 3.8 26.4 1.0 N B:CYS105 3.9 34.5 1.0 CB B:HIS103 4.1 37.9 1.0 ND1 B:HIS103 4.3 33.3 1.0 CA B:HIS103 4.6 37.8 1.0 CB B:GLN117 4.6 45.6 1.0 CE2 B:PHE98 4.7 45.9 1.0 SG B:CYS114 4.7 44.5 1.0 CB B:CYS108 4.7 34.0 1.0 CG B:HIS103 4.7 36.6 1.0 C B:HIS103 4.7 38.3 1.0 SG B:CYS108 4.7 30.8 1.0 CD B:GLN117 4.8 44.2 1.0 O B:HIS103 4.8 35.2 1.0 C B:PHE104 4.8 33.6 1.0

Iron binding site 6 out of 38 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:27.2 occ:1.00 FE2 B:SF4301 0.0 27.2 1.0 S3 B:SF4301 2.2 24.2 1.0 S4 B:SF4301 2.2 26.5 1.0 S1 B:SF4301 2.3 26.4 1.0 SG B:CYS108 2.3 30.8 1.0 FE1 B:SF4301 2.6 26.6 1.0 FE4 B:SF4301 2.7 30.6 1.0 FE3 B:SF4301 2.8 29.3 1.0 CB B:CYS108 2.9 34.0 1.0 S2 B:SF4301 3.8 30.5 1.0 CA B:CYS105 4.3 38.2 1.0 NE B:ARG152 4.4 48.4 1.0 CA B:CYS108 4.4 35.9 1.0 CD B:ARG152 4.4 44.6 1.0 SG B:CYS105 4.6 39.8 1.0 ND1 B:HIS103 4.7 33.3 1.0 N B:CYS105 4.7 34.5 1.0 CG B:ARG152 4.8 43.0 1.0 CB B:CYS105 4.8 37.4 1.0 N B:GLY209 4.8 47.9 1.0 CZ B:ARG152 4.8 47.8 1.0 SG B:CYS114 4.9 44.5 1.0 CA B:GLY209 4.9 46.5 1.0 N B:SER111 5.0 45.2 1.0

Iron binding site 7 out of 38 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:29.3 occ:1.00 FE3 B:SF4301 0.0 29.3 1.0 S1 B:SF4301 2.2 26.4 1.0 SG B:CYS114 2.3 44.5 1.0 S2 B:SF4301 2.3 30.5 1.0 S4 B:SF4301 2.4 26.5 1.0 FE4 B:SF4301 2.6 30.6 1.0 FE1 B:SF4301 2.7 26.6 1.0 FE2 B:SF4301 2.8 27.2 1.0 CB B:CYS114 3.4 38.9 1.0 S3 B:SF4301 3.8 24.2 1.0 CB B:GLN117 4.3 45.6 1.0 CB B:VAL208 4.4 41.9 1.0 N B:GLY209 4.5 47.9 1.0 N B:GLN117 4.5 48.3 1.0 SG B:CYS108 4.6 30.8 1.0 ND1 B:HIS103 4.6 33.3 1.0 CA B:VAL208 4.7 42.8 1.0 CA B:CYS114 4.8 40.1 1.0 CB B:LEU116 4.8 42.6 1.0 CG1 B:VAL208 4.8 44.7 1.0 SG B:CYS105 4.9 39.8 1.0 NE2 B:GLN117 4.9 45.5 1.0 CD2 B:LEU116 4.9 43.4 1.0 CA B:GLN117 5.0 45.0 1.0

Iron binding site 8 out of 38 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:30.6 occ:1.00 FE4 B:SF4301 0.0 30.6 1.0 ND1 B:HIS103 2.2 33.3 1.0 S2 B:SF4301 2.2 30.5 1.0 S1 B:SF4301 2.2 26.4 1.0 S3 B:SF4301 2.3 24.2 1.0 FE3 B:SF4301 2.6 29.3 1.0 FE2 B:SF4301 2.7 27.2 1.0 FE1 B:SF4301 2.8 26.6 1.0 CE1 B:HIS103 3.1 37.1 1.0 CG B:HIS103 3.2 36.6 1.0 CB B:HIS103 3.6 37.9 1.0 S4 B:SF4301 3.8 26.5 1.0 CA B:HIS103 4.1 37.8 1.0 NE2 B:HIS103 4.2 39.9 1.0 CD2 B:HIS103 4.3 37.3 1.0 CG B:ARG152 4.4 43.0 1.0 CD2 B:LEU116 4.4 43.4 1.0 CB B:ARG152 4.5 39.9 1.0 SG B:CYS114 4.6 44.5 1.0 SG B:CYS108 4.8 30.8 1.0 O B:ARG152 4.9 34.6 1.0 CD B:ARG152 4.9 44.6 1.0 SG B:CYS105 4.9 39.8 1.0 CB B:VAL208 5.0 41.9 1.0

Iron binding site 9 out of 38 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:25.8 occ:1.00 FE1 B:SF4302 0.0 25.8 1.0 S4 B:SF4302 2.2 27.9 1.0 S2 B:SF4302 2.3 29.7 1.0 SG B:CYS153 2.3 27.5 1.0 S3 B:SF4302 2.4 24.0 1.0 FE3 B:SF4302 2.7 27.6 1.0 FE4 B:SF4302 2.8 30.9 1.0 FE2 B:SF4302 2.8 31.6 1.0 CB B:CYS153 3.2 40.0 1.0 CA B:CYS153 3.6 37.5 1.0 CB B:ALA210 3.8 44.3 1.0 N B:ILE154 3.8 42.0 1.0 S1 B:SF4302 3.9 30.5 1.0 C B:CYS153 4.1 42.0 1.0 N B:LEU155 4.1 48.3 1.0 SG B:CYS206 4.6 48.0 1.0 CA B:LEU155 4.7 47.3 1.0 N B:CYS153 4.8 36.9 1.0 SG B:CYS159 4.9 39.6 1.0 CD2 B:LEU182 4.9 52.8 1.0 N B:CYS156 5.0 49.3 1.0 SG B:CYS156 5.0 42.0 1.0

Iron binding site 10 out of 38 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:31.6 occ:1.00 FE2 B:SF4302 0.0 31.6 1.0 S1 B:SF4302 2.2 30.5 1.0 S3 B:SF4302 2.3 24.0 1.0 S4 B:SF4302 2.3 27.9 1.0 SG B:CYS159 2.3 39.6 1.0 FE4 B:SF4302 2.5 30.9 1.0 FE3 B:SF4302 2.7 27.6 1.0 FE1 B:SF4302 2.8 25.8 1.0 CB B:CYS159 3.2 39.5 1.0 S2 B:SF4302 3.8 29.7 1.0 N B:CYS159 3.9 46.2 1.0 CA B:CYS159 4.2 42.0 1.0 CD2 B:LEU182 4.4 52.8 1.0 CD1 B:LEU182 4.4 52.4 1.0 SG B:CYS156 4.4 42.0 1.0 SG B:CYS153 4.7 27.5 1.0 N B:GLY157 4.7 50.6 1.0 N B:LEU158 4.7 44.6 1.0 SG B:CYS206 4.9 48.0 1.0 CG B:LEU182 4.9 52.1 1.0 CB B:CYS206 4.9 41.7 1.0 CA B:GLY157 4.9 51.1 1.0

Y.Shomura, M.Taketa, H.Nakashima, H.Tai, H.Nakagawa, Y.Ikeda, M.Ishii, Y.Igarashi, H.Nishihara, K.S.Yoon, S.Ogo, S.Hirota, Y.Higuchi. Structural Basis of the Redox Switches in the Nad(+)-Reducing Soluble [Nife]-Hydrogenase Science V. 357 928 2017.
ISSN: ESSN 1095-9203
PubMed: 28860386
DOI: 10.1126/SCIENCE.AAN4497