Magnesium in PDB 6gm3: [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant R286A

All present enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant R286A:
1.12.7.2;

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant R286A, PDB code: 6gm3 was solved by J.Duan, J.Esselborn, E.Hofmann, M.Winkler, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.67 / 2.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.810, 72.890, 103.140, 90.00, 96.11, 90.00
R / Rfree (%)	18.5 / 23

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant R286A also contains other interesting chemical elements:

Iron

(Fe)

40 atoms

The binding sites of Magnesium atom in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant R286A (pdb code 6gm3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant R286A, PDB code: 6gm3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant R286A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant R286A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:36.4 occ:1.00 O A:HOH752 2.1 31.2 1.0 O A:HOH739 2.1 32.2 1.0 O A:HOH880 2.1 36.1 1.0 OD1 A:ASP42 2.1 36.4 1.0 O A:HOH783 2.1 31.1 1.0 OD1 A:ASN40 2.1 33.0 1.0 CG A:ASN40 3.2 22.1 1.0 CG A:ASP42 3.2 37.6 1.0 ND2 A:ASN40 3.7 26.1 1.0 OD2 A:ASP42 3.8 49.7 1.0 OD2 A:ASP63 4.2 36.3 1.0 OD1 B:ASN452 4.2 36.2 1.0 N A:ASN40 4.3 27.3 1.0 CB A:ASP63 4.3 21.7 1.0 CB A:ASP42 4.4 27.4 1.0 O A:ASN40 4.4 32.4 1.0 CB A:ASN40 4.5 31.1 1.0 CG B:ASN452 4.5 40.3 1.0 CA A:ASP42 4.6 35.6 1.0 CA A:ASN40 4.7 34.0 1.0 C A:ASN40 4.7 34.0 1.0 CG A:ASP63 4.8 27.8 1.0 CB B:ASN452 4.9 27.9 1.0 N A:ASP42 4.9 33.0 1.0

Magnesium binding site 2 out of 2 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant R286A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant R286A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:33.7 occ:1.00 O B:HOH785 2.1 27.9 1.0 O B:HOH731 2.1 23.6 1.0 O B:HOH759 2.1 24.2 1.0 O B:HOH766 2.1 22.3 1.0 O B:LEU218 2.1 38.2 1.0 C B:LEU218 3.2 31.3 1.0 CA B:LEU218 3.8 30.4 1.0 O B:ALA220 4.1 33.2 1.0 OD2 B:ASP263 4.1 26.7 1.0 OD1 B:ASP263 4.2 34.9 1.0 O B:HOH763 4.3 26.8 1.0 N B:ASN219 4.3 30.8 1.0 O B:GLY261 4.5 28.6 1.0 O B:ALA217 4.5 29.3 1.0 O B:LYS223 4.5 27.2 1.0 CG B:ASP263 4.6 32.5 1.0 O B:HOH924 4.6 43.5 1.0 CB B:LEU218 4.6 28.7 1.0 CA B:ASN219 4.7 34.9 1.0 C B:ASN219 4.8 33.1 1.0 C B:ALA220 4.9 34.5 1.0 O B:HOH953 4.9 50.6 1.0 N B:ALA220 4.9 29.3 1.0

J.Duan, M.Senger, J.Esselborn, V.Engelbrecht, F.Wittkamp, U.P.Apfel, E.Hofmann, S.T.Stripp, T.Happe, M.Winkler. Crystallographic and Spectroscopic Assignment of the Proton Transfer Pathway in [Fefe]-Hydrogenases. Nat Commun V. 9 4726 2018.
ISSN: ESSN 2041-1723
PubMed: 30413719
DOI: 10.1038/S41467-018-07140-X