Magnesium 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
Iron	(Fe)	38 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Nad+-Reducing [Nife]-Hydrogenase in the H2- Reduced State, PDB code: 5xfa:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg503 b:31.5 occ:1.00 O D:LEU416 2.1 34.2 1.0 O D:HOH623 2.1 36.9 1.0 O D:HOH628 2.1 32.8 1.0 O D:HOH629 2.1 33.2 1.0 OE2 D:GLU61 2.2 38.0 1.0 NE2 D:HIS468 2.4 37.9 1.0 CD D:GLU61 3.1 41.0 1.0 CE1 D:HIS468 3.3 40.9 1.0 C D:LEU416 3.3 37.1 1.0 OE1 D:GLU61 3.4 37.2 1.0 CD2 D:HIS468 3.5 44.6 1.0 OE2 D:GLU285 4.0 63.5 1.0 O D:HOH639 4.0 37.2 1.0 N D:LEU416 4.1 40.3 1.0 OD1 D:ASN415 4.2 51.6 1.0 CA D:LEU416 4.2 41.6 1.0 N D:ILE417 4.3 40.0 1.0 CB D:LEU416 4.4 42.0 1.0 NZ D:LYS294 4.4 48.5 1.0 CA D:ILE417 4.4 42.2 1.0 OE1 D:GLU285 4.4 77.3 1.0 ND1 D:HIS468 4.4 39.7 1.0 CG D:GLU61 4.5 47.7 1.0 CE D:LYS294 4.6 47.0 1.0 CD D:GLU285 4.6 68.3 1.0 CG D:HIS468 4.6 41.0 1.0 CD D:LYS294 4.6 43.6 1.0 O D:HOH626 4.9 37.9 1.0 CG D:ASN415 4.9 47.5 1.0 CG1 D:ILE417 5.0 49.8 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg503 b:52.7 occ:1.00 O H:HOH602 2.1 52.2 1.0 O H:HOH607 2.1 72.0 1.0 O H:HOH628 2.1 54.3 1.0 O H:LEU416 2.1 51.5 1.0 OE2 H:GLU61 2.2 53.7 1.0 NE2 H:HIS468 2.6 53.0 1.0 CD H:GLU61 3.1 59.1 1.0 C H:LEU416 3.3 52.3 1.0 OE1 H:GLU61 3.3 65.7 1.0 CE1 H:HIS468 3.5 55.2 1.0 CD2 H:HIS468 3.6 55.3 1.0 OE2 H:GLU285 3.8 72.9 1.0 OD1 H:ASN415 4.0 65.7 1.0 N H:LEU416 4.0 50.4 1.0 OE1 H:GLU285 4.1 77.1 1.0 CA H:LEU416 4.2 52.6 1.0 NZ H:LYS294 4.2 49.9 1.0 N H:ILE417 4.3 55.5 1.0 CD H:GLU285 4.4 77.3 1.0 CB H:LEU416 4.4 53.1 1.0 CA H:ILE417 4.5 56.6 1.0 CG H:GLU61 4.5 56.2 1.0 CE H:LYS294 4.5 50.8 1.0 CD H:LYS294 4.5 53.8 1.0 ND1 H:HIS468 4.6 56.6 1.0 CG H:HIS468 4.7 54.9 1.0 CG H:ASN415 4.7 70.6 1.0 CG1 H:ILE417 4.9 59.3 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