Magnesium in PDB 6gm1: [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282A

All present enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282A:
1.12.7.2;

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282A, PDB code: 6gm1 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)	48.09 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.990, 72.960, 102.930, 90.00, 96.32, 90.00
R / Rfree (%)	16.7 / 20.5

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282A 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 E282A (pdb code 6gm1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282A, PDB code: 6gm1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282A


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 E282A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:32.4 occ:1.00 O A:HOH837 2.1 27.2 1.0 O A:HOH729 2.1 24.5 1.0 O A:HOH870 2.1 26.8 1.0 O A:HOH768 2.1 29.6 1.0 O A:HOH727 2.1 22.9 1.0 O A:LEU218 2.1 27.2 1.0 C A:LEU218 3.2 29.0 1.0 CA A:LEU218 3.7 28.6 1.0 OD2 A:ASP263 3.9 26.5 1.0 O A:ALA220 3.9 27.9 1.0 OD1 A:ASP263 4.1 30.7 1.0 O A:LYS223 4.2 21.5 1.0 O A:HOH789 4.2 25.0 1.0 O A:ALA217 4.2 24.3 1.0 N A:ASN219 4.3 27.8 1.0 CG A:ASP263 4.5 26.8 1.0 O A:GLY261 4.6 24.7 1.0 CB A:LEU218 4.6 22.8 1.0 CA A:ASN219 4.7 30.4 1.0 C A:ALA220 4.8 31.5 1.0 O A:HOH956 4.8 53.8 1.0 CG2 A:VAL225 4.8 22.8 1.0 C A:ASN219 4.8 30.4 1.0 N A:LEU218 4.9 21.5 1.0 N A:ALA220 4.9 26.5 1.0 C A:ALA217 5.0 28.2 1.0

Magnesium binding site 2 out of 3 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282A


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 E282A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg608 b:28.1 occ:1.00 O A:HOH898 2.1 29.9 1.0 O A:HOH884 2.1 23.3 1.0 O A:HOH832 2.1 27.9 1.0 O A:HOH798 2.1 29.3 1.0 OD1 A:ASP42 2.1 29.4 1.0 OD1 A:ASN40 2.1 25.9 1.0 CG A:ASN40 3.3 24.9 1.0 CG A:ASP42 3.3 30.7 1.0 O A:HOH708 3.9 32.4 1.0 OD2 A:ASP42 3.9 31.5 1.0 ND2 A:ASN40 3.9 21.3 1.0 O B:HOH728 4.0 34.2 1.0 N A:ASN40 4.1 23.1 1.0 O A:HOH993 4.1 39.6 1.0 OD1 B:ASN452 4.3 31.4 1.0 O A:ASN40 4.3 24.0 1.0 CB A:ASP42 4.4 24.4 1.0 CB A:ASN40 4.5 22.6 1.0 CB A:ASP63 4.5 24.9 1.0 CA A:ASP42 4.6 26.9 1.0 C A:ASN40 4.6 25.8 1.0 CA A:ASN40 4.6 27.0 1.0 CG B:ASN452 4.6 29.4 1.0 OD2 A:ASP63 4.6 28.6 1.0 O B:HOH884 4.7 25.4 1.0 N A:ASP42 4.8 25.5 1.0 CB B:ASN452 4.9 23.0 1.0

Magnesium binding site 3 out of 3 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:28.9 occ:1.00 O B:HOH839 2.1 29.0 1.0 O B:HOH877 2.1 28.1 1.0 O B:HOH797 2.1 25.1 1.0 O B:HOH762 2.1 23.7 1.0 O B:HOH774 2.1 24.1 1.0 O B:LEU218 2.1 31.2 1.0 C B:LEU218 3.2 26.6 1.0 CA B:LEU218 3.7 26.8 1.0 OD2 B:ASP263 4.0 24.0 1.0 O B:ALA220 4.0 28.9 1.0 OD1 B:ASP263 4.1 26.5 1.0 O B:HOH792 4.2 26.4 1.0 N B:ASN219 4.3 26.2 1.0 O B:LYS223 4.3 23.4 1.0 O B:ALA217 4.3 26.3 1.0 O B:HOH954 4.5 45.0 1.0 CG B:ASP263 4.5 28.1 1.0 O B:GLY261 4.6 23.5 1.0 CB B:LEU218 4.6 24.2 1.0 CA B:ASN219 4.7 33.2 1.0 O B:HOH948 4.8 36.4 1.0 C B:ALA220 4.8 29.3 1.0 C B:ASN219 4.8 28.4 1.0 CG2 B:VAL225 4.9 22.0 1.0 N B:LEU218 4.9 22.8 1.0 N B:ALA220 4.9 24.8 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