Magnesium in PDB 1yqw: Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase

All present enzymatic activity of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase:
1.12.2.1;

The structure of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase, PDB code: 1yqw was solved by A.Volbeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.410, 99.700, 182.830, 90.00, 91.42, 90.00
R / Rfree (%)	14.6 / 18.5

The structure of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase also contains other interesting chemical elements:

Nickel	(Ni)	3 atoms
Iron	(Fe)	39 atoms

The binding sites of Magnesium atom in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase (pdb code 1yqw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase, PDB code: 1yqw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg555 b:29.6 occ:1.00 O Q:HOH1031 2.1 17.3 1.0 O Q:HOH1026 2.3 17.7 1.0 OD1 Q:ASN181 2.4 5.0 1.0 O C:HOH269 2.4 31.8 1.0 O C:HOH270 2.6 24.5 1.0 O A:HOH360 2.7 12.4 1.0 CG Q:ASN181 3.6 5.0 1.0 O C:HOH274 3.8 17.4 1.0 O C:HOH442 3.9 40.7 1.0 N Q:ASN181 4.0 6.2 1.0 O Q:HOH981 4.0 27.8 1.0 CA Q:ASN181 4.1 6.1 1.0 OE2 C:GLU215 4.1 11.1 1.0 O C:HOH268 4.1 28.8 1.0 O C:SER196 4.3 6.4 1.0 CB Q:ASN181 4.4 4.7 1.0 CD2 C:PHE198 4.5 2.5 1.0 ND2 Q:ASN181 4.5 7.9 1.0 O C:PHE198 4.6 5.8 1.0 O2 Q:GOL558 4.6 10.9 1.0 CB C:PHE198 4.6 6.3 1.0 CD1 Q:LEU185 4.7 8.4 1.0 NE2 A:GLN62 4.9 17.8 1.0 CG2 Q:THR180 4.9 8.7 1.0 OE1 A:GLN62 4.9 10.0 1.0 N C:PHE198 4.9 5.4 1.0

Magnesium binding site 2 out of 3 in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg556 b:35.2 occ:1.00 O Q:HOH1027 2.0 23.0 1.0 O Q:HOH1025 2.7 18.7 1.0 O Q:HOH699 2.9 8.8 1.0 OD2 Q:ASP88 3.0 12.3 1.0 CB Q:ASP88 3.5 7.8 1.0 NH1 Q:ARG103 3.5 7.9 1.0 O Q:HOH652 3.5 9.5 1.0 CG Q:ASP88 3.7 8.8 1.0 CG2 Q:ILE95 3.7 9.7 1.0 O Q:ASP299 3.7 8.0 1.0 CA Q:ARG85 4.0 9.8 1.0 CD1 Q:ILE95 4.0 7.1 1.0 O Q:HOH753 4.0 19.7 1.0 CG Q:ARG85 4.1 7.1 1.0 O Q:HOH782 4.2 30.9 1.0 CG1 Q:ILE95 4.2 6.3 1.0 CB Q:ARG85 4.4 7.8 1.0 O Q:ARG85 4.5 8.8 1.0 O Q:HOH680 4.6 14.1 1.0 CZ Q:ARG103 4.6 9.0 1.0 CB Q:ILE95 4.6 8.2 1.0 C Q:ARG85 4.7 8.3 1.0 N Q:ARG85 4.8 8.1 1.0 O Q:SER84 4.8 7.0 1.0 OD1 Q:ASP88 4.9 11.0 1.0 C Q:ASP299 4.9 8.9 1.0 CA Q:ASP88 5.0 8.1 1.0

Magnesium binding site 3 out of 3 in the Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg1308 b:30.2 occ:1.00 O R:HOH1628 2.2 6.9 1.0 O R:HOH1676 2.2 15.7 1.0 OD1 R:ASN181 2.4 7.5 1.0 O B:HOH1626 2.5 12.9 1.0 CG R:ASN181 3.6 9.2 1.0 O R:HOH1470 3.8 24.1 1.0 N R:ASN181 3.9 4.5 1.0 CA R:ASN181 4.1 6.2 1.0 O B:HOH1692 4.2 35.9 1.0 CB R:ASN181 4.4 4.4 1.0 ND2 R:ASN181 4.6 9.3 1.0 O2 R:GOL1301 4.7 7.6 1.0 CD1 R:LEU185 4.7 9.3 1.0 NE2 B:GLN62 4.8 18.4 1.0 CG2 R:THR180 4.8 5.5 1.0 OE1 B:GLN62 4.9 18.1 1.0

A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, J.C.Fontecilla-Camps. Structural Differences Between the Ready and Unready Oxidized States of [Nife] Hydrogenases. J.Biol.Inorg.Chem. V. 10 239 2005.
ISSN: ISSN 0949-8257
PubMed: 15803334
DOI: 10.1007/S00775-005-0632-X