Nickel in PDB 5xf9: Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State

The structure of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State, PDB code: 5xf9 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)	95.04 / 2.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.590, 190.090, 124.580, 90.00, 109.44, 90.00
R / Rfree (%)	19.7 / 24.4

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

Magnesium	(Mg)	2 atoms
Iron	(Fe)	38 atoms

The binding sites of Nickel atom in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State (pdb code 5xf9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State, PDB code: 5xf9:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni502 b:43.9 occ:1.00 OE1 D:GLU32 2.2 44.8 1.0 OE2 D:GLU32 2.2 41.7 1.0 SG D:CYS462 2.3 43.0 1.0 SG D:CYS465 2.3 36.2 1.0 SG D:CYS83 2.3 39.0 1.0 SG D:CYS80 2.4 43.0 1.0 CD D:GLU32 2.5 43.3 1.0 FE D:FCO501 2.9 32.9 1.0 CB D:CYS462 3.1 39.4 1.0 CB D:CYS80 3.5 37.6 1.0 CB D:CYS83 3.5 34.0 1.0 CB D:CYS465 3.7 35.2 1.0 CA D:CYS462 3.8 38.8 1.0 N D:CYS465 3.9 36.5 1.0 CG D:GLU32 4.0 43.1 1.0 C1 D:FCO501 4.0 31.5 1.0 C2 D:FCO501 4.0 31.8 1.0 N D:CYS83 4.3 30.3 1.0 CA D:CYS465 4.4 35.1 1.0 C3 D:FCO501 4.4 31.4 1.0 NH2 D:ARG396 4.5 41.6 1.0 C D:CYS462 4.5 37.3 1.0 CA D:CYS83 4.6 31.5 1.0 CB D:SER464 4.7 42.7 1.0 O D:CYS462 4.9 38.0 1.0 CA D:CYS80 4.9 35.1 1.0 N2 D:FCO501 4.9 31.3 1.0 CZ D:ARG396 4.9 38.2 1.0 CB D:GLU32 4.9 42.1 1.0 CB D:ILE82 4.9 30.4 1.0 N D:ILE82 5.0 29.8 1.0 C D:SER464 5.0 37.7 1.0 N1 D:FCO501 5.0 33.1 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the Air- Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni502 b:44.2 occ:1.00 OE2 H:GLU32 2.2 45.9 1.0 OE1 H:GLU32 2.2 47.7 1.0 SG H:CYS462 2.3 39.8 1.0 SG H:CYS83 2.3 41.0 1.0 SG H:CYS80 2.4 41.5 1.0 SG H:CYS465 2.4 35.4 1.0 CD H:GLU32 2.5 48.3 1.0 FE H:FCO501 2.9 34.0 1.0 CB H:CYS462 3.1 39.7 1.0 CB H:CYS80 3.5 37.8 1.0 CB H:CYS83 3.5 36.9 1.0 CB H:CYS465 3.7 35.9 1.0 CA H:CYS462 3.8 39.3 1.0 CG H:GLU32 4.0 46.6 1.0 N H:CYS465 4.0 35.5 1.0 C2 H:FCO501 4.0 31.8 1.0 C1 H:FCO501 4.1 35.9 1.0 N H:CYS83 4.3 32.3 1.0 C3 H:FCO501 4.3 36.2 1.0 CA H:CYS465 4.4 35.5 1.0 NH1 H:ARG396 4.5 39.8 1.0 C H:CYS462 4.5 38.7 1.0 CA H:CYS83 4.6 34.3 1.0 CB H:SER464 4.7 37.6 1.0 CZ H:ARG396 4.8 38.5 1.0 CA H:CYS80 4.9 35.0 1.0 CB H:ILE82 4.9 33.1 1.0 O H:CYS462 4.9 36.3 1.0 CB H:GLU32 4.9 44.7 1.0 N1 H:FCO501 5.0 36.2 1.0 N2 H:FCO501 5.0 31.0 1.0 C H:SER464 5.0 36.0 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