Magnesium in PDB 6gm8: [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q

All present enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q:
1.12.7.2;

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q, PDB code: 6gm8 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)	46.83 / 1.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.650, 72.340, 103.150, 90.00, 96.73, 90.00
R / Rfree (%)	17.6 / 22.1

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q 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 E282Q (pdb code 6gm8). 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 E282Q, PDB code: 6gm8:
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 E282Q


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 E282Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:25.4 occ:1.00 O A:HOH902 2.1 24.0 1.0 OD1 A:ASP42 2.1 30.1 1.0 O A:HOH775 2.1 23.2 1.0 O A:HOH804 2.1 25.3 1.0 OD1 A:ASN40 2.1 23.7 1.0 O A:HOH835 2.1 25.0 1.0 CG A:ASN40 3.2 24.3 1.0 CG A:ASP42 3.2 26.8 1.0 ND2 A:ASN40 3.8 26.1 1.0 OD2 A:ASP42 3.8 32.2 1.0 O A:HOH706 3.9 29.6 1.0 O A:HOH992 4.2 39.7 1.0 N A:ASN40 4.2 24.6 1.0 OD1 B:ASN452 4.2 32.2 1.0 O A:ASN40 4.3 24.6 1.0 OD2 A:ASP63 4.3 22.8 1.0 CB A:ASP63 4.4 21.1 1.0 CB A:ASP42 4.4 24.8 1.0 CB A:ASN40 4.4 21.5 1.0 O B:HOH713 4.5 38.7 1.0 CG B:ASN452 4.5 30.6 1.0 CA A:ASP42 4.5 25.7 1.0 C A:ASN40 4.6 24.9 1.0 CA A:ASN40 4.6 25.8 1.0 CB B:ASN452 4.8 21.3 1.0 O B:HOH905 4.8 27.4 1.0 N A:ASP42 4.8 24.2 1.0 CG A:ASP63 4.9 26.8 1.0

Magnesium binding site 2 out of 3 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q


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 E282Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg608 b:25.0 occ:0.75 O A:HOH794 2.1 26.8 1.0 O A:HOH910 2.1 24.5 1.0 O A:HOH801 2.1 28.3 1.0 O A:HOH790 2.1 22.9 1.0 O A:HOH850 2.1 25.9 1.0 O A:LEU218 2.1 29.9 1.0 C A:LEU218 3.2 27.4 1.0 CA A:LEU218 3.8 23.5 1.0 OD2 A:ASP263 4.0 26.3 1.0 O A:ALA220 4.0 25.5 1.0 OD1 A:ASP263 4.2 24.4 1.0 O A:HOH783 4.2 26.5 1.0 O A:LYS223 4.3 23.4 1.0 N A:ASN219 4.3 27.9 1.0 O A:ALA217 4.4 24.1 1.0 CG A:ASP263 4.5 30.5 1.0 O A:GLY261 4.6 26.2 1.0 CB A:LEU218 4.6 21.1 1.0 CA A:ASN219 4.7 31.2 1.0 CG2 A:VAL225 4.8 22.0 1.0 C A:ASN219 4.9 33.2 1.0 C A:ALA220 4.9 27.4 1.0 N A:LEU218 5.0 21.4 1.0 CD2 A:LEU218 5.0 18.6 1.0

Magnesium binding site 3 out of 3 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant E282Q


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 E282Q within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:30.7 occ:1.00 O B:HOH759 2.1 25.8 1.0 O B:HOH803 2.1 25.8 1.0 O B:HOH733 2.1 19.4 1.0 O B:HOH878 2.1 28.4 1.0 O B:HOH860 2.1 28.1 1.0 O B:LEU218 2.1 30.2 1.0 C B:LEU218 3.2 24.4 1.0 CA B:LEU218 3.8 24.0 1.0 O B:HOH839 3.9 25.9 1.0 OD2 B:ASP263 4.0 21.1 1.0 O B:ALA220 4.0 28.4 1.0 O B:LYS223 4.0 22.3 1.0 OD1 B:ASP263 4.1 22.2 1.0 O B:ALA217 4.3 24.8 1.0 N B:ASN219 4.3 24.8 1.0 O B:HOH737 4.3 36.3 1.0 CG B:ASP263 4.5 25.5 1.0 O B:GLY261 4.5 17.9 1.0 O B:HOH1096 4.6 43.6 1.0 CB B:LEU218 4.7 28.7 1.0 CA B:ASN219 4.7 34.5 1.0 CG2 B:VAL225 4.8 16.9 1.0 C B:ALA220 4.9 28.5 1.0 C B:ASN219 4.9 33.7 1.0 N B:LEU218 4.9 15.9 1.0 N B:ALA220 5.0 26.8 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