Magnesium 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:

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 Air- Oxidized State (pdb code 5xf9). 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 Air- Oxidized State, PDB code: 5xf9:
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 Air- Oxidized 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 Air- Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:29.4 occ:1.00 O D:HOH647 2.0 29.8 1.0 NE2 D:HIS468 2.1 31.5 1.0 O D:LEU416 2.2 28.7 1.0 O D:HOH609 2.2 26.1 1.0 O D:HOH634 2.2 29.5 1.0 OE2 D:GLU61 2.3 33.3 1.0 CE1 D:HIS468 3.0 32.2 1.0 CD2 D:HIS468 3.1 32.6 1.0 CD D:GLU61 3.2 35.3 1.0 C D:LEU416 3.4 28.8 1.0 OE1 D:GLU61 3.5 37.0 1.0 O D:HOH602 3.5 50.0 1.0 O D:HOH699 4.1 22.9 1.0 ND1 D:HIS468 4.1 32.5 1.0 N D:LEU416 4.2 27.1 1.0 CA D:LEU416 4.2 27.9 1.0 CG D:HIS468 4.2 32.0 1.0 CB D:LEU416 4.3 27.5 1.0 OE2 D:GLU285 4.4 47.9 1.0 N D:ILE417 4.4 29.2 1.0 OD1 D:ASN415 4.4 28.8 1.0 CG D:GLU61 4.5 35.3 1.0 CA D:ILE417 4.6 30.2 1.0 NZ D:LYS294 4.8 35.2 1.0 OE1 D:GLU285 4.8 51.1 1.0 O D:HOH713 4.9 43.1 1.0 CE D:LYS294 5.0 33.8 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg503 b:36.4 occ:1.00 O H:HOH641 1.9 37.8 1.0 O H:LEU416 2.0 37.6 1.0 O H:HOH669 2.1 33.9 1.0 OE2 H:GLU61 2.3 33.8 1.0 NE2 H:HIS468 2.4 37.0 1.0 O H:HOH667 2.4 35.4 1.0 CE1 H:HIS468 3.1 37.3 1.0 C H:LEU416 3.3 36.6 1.0 CD H:GLU61 3.3 34.7 1.0 CD2 H:HIS468 3.5 38.2 1.0 OE1 H:GLU61 3.7 34.8 1.0 N H:LEU416 4.1 35.3 1.0 OE2 H:GLU285 4.1 60.2 1.0 CA H:LEU416 4.1 35.2 1.0 OD1 H:ASN415 4.2 31.8 1.0 N H:ILE417 4.2 37.6 1.0 CB H:LEU416 4.3 33.8 1.0 ND1 H:HIS468 4.3 39.1 1.0 CA H:ILE417 4.4 38.7 1.0 O H:HOH645 4.4 32.5 1.0 OE1 H:GLU285 4.5 61.4 1.0 CG H:HIS468 4.6 38.6 1.0 CG H:GLU61 4.6 34.5 1.0 NZ H:LYS294 4.6 44.1 1.0 CD H:GLU285 4.8 62.4 1.0 CE H:LYS294 4.9 44.2 1.0 CD H:LYS294 4.9 45.1 1.0 CG1 H:ILE417 4.9 40.4 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