Nickel 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:

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 H2- Reduced State (pdb code 5xfa). 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 H2- Reduced State, PDB code: 5xfa:
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 H2- Reduced 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 H2- Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni502 b:50.8 occ:1.00 SG D:CYS465 2.3 53.1 1.0 SG D:CYS83 2.3 47.1 1.0 SG D:CYS462 2.3 56.3 1.0 SG D:CYS80 2.3 39.3 1.0 FE D:FCO501 2.5 51.1 1.0 CB D:CYS80 3.0 40.2 1.0 C1 D:FCO501 3.3 55.4 1.0 CB D:CYS462 3.4 57.1 1.0 C2 D:FCO501 3.4 46.3 1.0 CB D:CYS465 3.4 51.3 1.0 CB D:CYS83 3.8 37.9 1.0 N D:CYS83 4.1 36.3 1.0 C3 D:FCO501 4.2 51.5 1.0 N1 D:FCO501 4.2 59.6 1.0 N2 D:FCO501 4.3 44.5 1.0 CA D:CYS83 4.5 39.0 1.0 CA D:CYS80 4.5 38.2 1.0 CA D:CYS465 4.6 50.4 1.0 CD D:ARG396 4.7 41.0 1.0 CA D:CYS462 4.8 52.3 1.0 NE D:ARG396 4.8 38.3 1.0 N D:CYS465 4.8 49.9 1.0 NE2 D:HIS87 4.8 52.8 1.0 CB D:ILE82 4.8 40.8 1.0 NH2 D:ARG396 4.9 35.8 1.0 CZ D:ARG396 4.9 37.3 1.0 C D:ILE82 5.0 37.6 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced 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 H2- Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni502 b:63.3 occ:1.00 SG H:CYS462 2.3 67.9 1.0 SG H:CYS83 2.3 51.5 1.0 SG H:CYS465 2.4 54.9 1.0 SG H:CYS80 2.4 63.9 1.0 FE H:FCO501 2.4 51.5 1.0 CB H:CYS80 3.1 57.8 1.0 C2 H:FCO501 3.2 45.9 1.0 C1 H:FCO501 3.3 54.6 1.0 CB H:CYS462 3.3 71.5 1.0 CB H:CYS465 3.5 56.1 1.0 CB H:CYS83 3.8 49.1 1.0 O H:HOH613 4.1 0.3 1.0 N H:CYS83 4.1 43.5 1.0 C3 H:FCO501 4.1 50.5 1.0 N2 H:FCO501 4.1 46.1 1.0 N1 H:FCO501 4.2 65.1 1.0 CA H:CYS83 4.5 45.9 1.0 CA H:CYS80 4.6 57.6 1.0 CA H:CYS465 4.6 55.4 1.0 CD H:ARG396 4.7 49.3 1.0 CA H:CYS462 4.7 68.9 1.0 CE1 H:HIS87 4.7 53.4 1.0 NE H:ARG396 4.8 51.4 1.0 NH2 H:ARG396 4.8 50.7 1.0 N H:CYS465 4.8 55.6 1.0 CZ H:ARG396 4.8 52.9 1.0 CB H:ILE82 4.9 45.7 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