Magnesium in PDB 6gly: [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299A

All present enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299A:
1.12.7.2;

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299A, PDB code: 6gly 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)	47.55 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.740, 72.170, 103.050, 90.00, 97.40, 90.00
R / Rfree (%)	16.7 / 20.9

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299A 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 C299A (pdb code 6gly). 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 C299A, PDB code: 6gly:
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 C299A


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 C299A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:39.6 occ:1.00 O A:HOH824 2.0 32.1 1.0 O A:HOH839 2.0 32.1 1.0 O A:HOH777 2.1 31.0 1.0 O A:LEU218 2.1 39.1 1.0 O A:HOH780 2.1 34.4 1.0 O A:HOH716 2.3 32.6 1.0 C A:LEU218 3.1 33.0 1.0 CA A:LEU218 3.7 32.1 1.0 O A:ALA220 4.0 34.6 1.0 OD2 A:ASP263 4.0 31.5 1.0 OD1 A:ASP263 4.2 33.3 1.0 O A:ALA217 4.2 31.5 1.0 O A:HOH760 4.2 33.9 1.0 O A:LYS223 4.2 23.9 1.0 N A:ASN219 4.3 35.7 1.0 CG A:ASP263 4.6 36.3 1.0 CB A:LEU218 4.6 28.7 1.0 O A:GLY261 4.6 32.6 1.0 CA A:ASN219 4.7 36.1 1.0 C A:ALA220 4.8 34.8 1.0 N A:LEU218 4.8 32.2 1.0 N A:ALA220 4.8 29.2 1.0 C A:ASN219 4.8 32.1 1.0 CG2 A:VAL225 4.9 30.1 1.0 CD2 A:LEU218 4.9 30.4 1.0 C A:ALA217 5.0 29.4 1.0

Magnesium binding site 2 out of 3 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299A


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 C299A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg608 b:35.6 occ:1.00 OD1 A:ASN40 1.9 30.8 1.0 O A:HOH776 2.1 32.9 1.0 O A:HOH889 2.1 34.8 1.0 O A:HOH755 2.2 33.5 1.0 OD1 A:ASP42 2.2 35.5 1.0 O A:HOH855 2.2 35.7 1.0 CG A:ASN40 3.1 33.1 1.0 CG A:ASP42 3.3 35.6 1.0 ND2 A:ASN40 3.7 25.7 1.0 O A:HOH702 3.9 42.7 1.0 OD2 A:ASP42 3.9 40.7 1.0 N A:ASN40 4.1 27.9 1.0 O A:HOH875 4.1 36.4 1.0 O A:HOH948 4.2 43.7 1.0 OD2 A:ASP63 4.2 31.7 1.0 O B:HOH765 4.2 34.9 1.0 O A:ASN40 4.3 30.5 1.0 CB A:ASN40 4.3 28.1 1.0 CB A:ASP63 4.4 28.0 1.0 OD1 B:ASN452 4.4 38.3 1.0 CB A:ASP42 4.5 32.6 1.0 C A:ASN40 4.5 31.0 1.0 CA A:ASN40 4.5 30.8 1.0 CG B:ASN452 4.6 32.3 1.0 CA A:ASP42 4.7 30.8 1.0 O B:HOH922 4.7 31.4 1.0 CG A:ASP63 4.8 34.5 1.0 N A:ASP42 4.9 35.3 1.0 CB B:ASN452 5.0 28.9 1.0

Magnesium binding site 3 out of 3 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299A


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 C299A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:37.1 occ:1.00 O B:HOH904 2.0 34.1 1.0 O B:HOH886 2.1 37.8 1.0 O B:HOH782 2.1 30.4 1.0 O B:HOH778 2.1 31.2 1.0 O B:HOH780 2.2 30.8 1.0 O B:LEU218 2.2 37.3 1.0 C B:LEU218 3.3 31.9 1.0 CA B:LEU218 3.9 31.0 1.0 O B:ALA220 4.0 32.5 1.0 O B:HOH740 4.0 31.5 1.0 OD2 B:ASP263 4.0 31.1 1.0 OD1 B:ASP263 4.2 32.5 1.0 O B:LYS223 4.2 31.6 1.0 O B:ALA217 4.3 34.3 1.0 N B:ASN219 4.4 35.5 1.0 CG B:ASP263 4.5 34.2 1.0 O B:GLY261 4.7 30.5 1.0 CA B:ASN219 4.7 35.9 1.0 CB B:LEU218 4.7 27.7 1.0 C B:ALA220 4.8 35.4 1.0 C B:ASN219 4.8 36.2 1.0 N B:ALA220 4.9 33.8 1.0 CD2 B:LEU218 5.0 21.9 1.0 N B:LEU218 5.0 27.9 1.0 CG2 B:VAL225 5.0 25.9 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