Magnesium in PDB 6glz: [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D

All present enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D:
1.12.7.2;

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D, PDB code: 6glz 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)	46.92 / 2.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.800, 72.600, 102.990, 90.00, 97.16, 90.00
R / Rfree (%)	20.2 / 24.9

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D 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 C299D (pdb code 6glz). 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 C299D, PDB code: 6glz:
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 C299D


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 C299D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:40.6 occ:1.00 O A:HOH748 2.1 21.0 1.0 O A:HOH756 2.1 23.1 1.0 O A:HOH703 2.1 38.6 1.0 O A:HOH702 2.1 34.0 1.0 O A:HOH1012 2.1 36.9 1.0 O A:LEU218 2.1 26.4 1.0 CA A:LEU218 2.1 27.4 1.0 C A:LEU218 2.4 27.2 1.0 CB A:LEU218 3.0 27.2 1.0 O A:ALA217 3.2 23.7 1.0 N A:LEU218 3.3 23.7 1.0 N A:ASN219 3.7 29.3 1.0 C A:ALA217 3.7 24.7 1.0 CD2 A:LEU218 3.9 20.2 1.0 OD2 A:ASP263 3.9 20.7 1.0 CG2 A:VAL225 4.0 14.4 1.0 CG A:LEU218 4.0 22.3 1.0 O A:ALA220 4.1 23.0 1.0 O A:LYS223 4.4 17.2 1.0 O A:GLY261 4.5 22.4 1.0 CA A:ASN219 4.6 24.7 1.0 OD1 A:ASP263 4.7 25.6 1.0 N A:ALA220 4.7 23.0 1.0 CG A:ASP263 4.7 28.2 1.0 C A:ASN219 4.9 27.4 1.0 CB A:VAL225 4.9 19.1 1.0

Magnesium binding site 2 out of 3 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


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 C299D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg608 b:24.4 occ:1.00 O A:HOH754 2.1 23.6 1.0 O A:HOH701 2.1 26.1 1.0 O A:HOH854 2.1 20.1 1.0 OD2 A:ASP42 2.1 28.5 1.0 OD1 A:ASP42 2.1 28.7 1.0 OD1 A:ASN40 2.1 20.2 1.0 CG A:ASP42 2.3 24.2 1.0 CG A:ASN40 3.3 19.6 1.0 O A:HOH797 3.4 24.8 1.0 N A:ASN40 3.8 19.4 1.0 CB A:ASP42 3.8 26.1 1.0 O A:ASN40 3.9 24.4 1.0 ND2 A:ASN40 4.1 20.8 1.0 C A:ASN40 4.3 19.0 1.0 CA A:ASN40 4.4 19.6 1.0 O B:HOH868 4.4 28.8 1.0 CB A:ASN40 4.4 21.0 1.0 CA A:ASP42 4.5 22.1 1.0 N A:ASP42 4.7 23.0 1.0 OD1 B:ASN452 4.8 22.4 1.0 C A:CYS39 4.8 20.6 1.0 O B:HOH907 4.9 22.5 1.0 CA A:CYS39 4.9 22.4 1.0 SG A:CYS39 4.9 62.4 1.0

Magnesium binding site 3 out of 3 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


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 C299D within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:25.0 occ:1.00 O B:HOH833 2.1 26.0 1.0 O B:HOH856 2.1 24.7 1.0 O B:HOH847 2.1 21.2 1.0 O B:HOH857 2.1 19.1 1.0 O B:HOH740 2.1 15.0 1.0 O B:LEU218 2.1 25.9 1.0 C B:LEU218 3.1 21.7 1.0 CA B:LEU218 3.7 21.8 1.0 O B:ALA220 3.9 23.2 1.0 O B:LYS223 4.1 23.2 1.0 O B:ALA217 4.2 22.6 1.0 OD2 B:ASP263 4.2 17.7 1.0 N B:ASN219 4.2 22.7 1.0 OD1 B:ASP263 4.3 21.8 1.0 O B:HOH942 4.3 19.0 1.0 CB B:LEU218 4.5 19.0 1.0 O B:HOH959 4.6 29.3 1.0 CA B:ASN219 4.6 26.4 1.0 O B:GLY261 4.7 13.9 1.0 CG B:ASP263 4.7 20.2 1.0 C B:ALA220 4.8 24.8 1.0 N B:LEU218 4.8 18.2 1.0 C B:ASN219 4.8 24.9 1.0 N B:ALA220 4.8 21.0 1.0 C B:ALA217 4.9 18.6 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