Magnesium in PDB 6h63: Semisynthetic [Fefe]-Hydrogenase Cpi with Ethanedithiolate [2FE] Cofactor

All present enzymatic activity of Semisynthetic [Fefe]-Hydrogenase Cpi with Ethanedithiolate [2FE] Cofactor:
1.12.7.2;

The structure of Semisynthetic [Fefe]-Hydrogenase Cpi with Ethanedithiolate [2FE] Cofactor, PDB code: 6h63 was solved by J.Duan, M.Winkler, E.Hofmann, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.61 / 2.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.020, 73.530, 104.140, 90.00, 97.66, 90.00
R / Rfree (%)	20.1 / 24.5

The structure of Semisynthetic [Fefe]-Hydrogenase Cpi with Ethanedithiolate [2FE] Cofactor also contains other interesting chemical elements:

Iron

(Fe)

40 atoms

The binding sites of Magnesium atom in the Semisynthetic [Fefe]-Hydrogenase Cpi with Ethanedithiolate [2FE] Cofactor (pdb code 6h63). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Semisynthetic [Fefe]-Hydrogenase Cpi with Ethanedithiolate [2FE] Cofactor, PDB code: 6h63:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Ethanedithiolate [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Semisynthetic [Fefe]-Hydrogenase Cpi with Ethanedithiolate [2FE] Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:28.7 occ:0.86 O A:HOH855 2.1 34.4 1.0 O A:HOH888 2.1 35.2 1.0 O A:HOH863 2.1 28.5 1.0 OD1 A:ASP42 2.1 38.5 1.0 O A:HOH950 2.1 29.5 1.0 OD1 A:ASN40 2.1 32.7 1.0 CG A:ASP42 3.2 40.2 1.0 H A:ASN40 3.3 32.6 1.0 CG A:ASN40 3.3 34.6 1.0 O A:HOH771 3.5 31.4 1.0 HD21 A:ASN40 3.7 35.6 1.0 OD2 A:ASP42 3.7 43.7 1.0 O B:HOH874 3.7 41.1 1.0 ND2 A:ASN40 3.9 29.7 1.0 N A:ASN40 4.1 27.2 1.0 HB3 A:ASP63 4.1 43.6 1.0 O A:ASN40 4.3 32.5 1.0 HA A:ASP42 4.3 47.8 1.0 HB3 B:ASN452 4.4 37.6 1.0 HA A:CYS39 4.4 43.4 1.0 HB2 A:ASP63 4.4 43.6 1.0 CB A:ASP42 4.5 42.9 1.0 O B:HOH854 4.5 39.3 1.0 CB A:ASN40 4.5 24.7 1.0 OD1 B:ASN452 4.5 38.6 1.0 C A:ASN40 4.6 33.0 1.0 CA A:ASN40 4.6 30.8 1.0 CB A:ASP63 4.7 36.3 1.0 HB3 A:ASP42 4.7 51.5 1.0 OD2 A:ASP63 4.7 35.8 1.0 CG B:ASN452 4.7 38.0 1.0 HD22 A:ASN40 4.7 35.6 1.0 CA A:ASP42 4.8 39.8 1.0 HB3 A:ASN40 4.8 29.6 1.0 HE2 A:LYS45 4.9 51.7 1.0 O B:HOH959 4.9 33.9 1.0 H A:ASP42 4.9 45.4 1.0 N A:ASP42 4.9 37.9 1.0

Magnesium binding site 2 out of 3 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Ethanedithiolate [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Semisynthetic [Fefe]-Hydrogenase Cpi with Ethanedithiolate [2FE] Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg608 b:46.0 occ:1.00 O A:HOH850 2.1 31.6 1.0 O A:HOH836 2.1 33.4 1.0 O A:HOH741 2.1 30.8 1.0 O A:HOH813 2.1 35.4 1.0 O A:LEU218 2.1 39.8 1.0 C A:LEU218 3.1 38.0 1.0 HA A:LEU218 3.1 41.7 1.0 CA A:LEU218 3.6 34.7 1.0 OD2 A:ASP263 4.0 33.8 1.0 HB3 A:LEU218 4.0 44.6 1.0 O A:ALA220 4.2 40.5 1.0 HD23 A:LEU218 4.2 43.0 1.0 N A:ASN219 4.3 36.6 1.0 OD1 A:ASP263 4.3 42.3 1.0 O A:HOH915 4.3 39.0 1.0 HA A:ASN219 4.3 49.7 1.0 O A:ALA217 4.3 35.0 1.0 HD22 A:LEU218 4.4 43.0 1.0 HG23 A:VAL225 4.4 37.6 1.0 CB A:LEU218 4.4 37.2 1.0 O A:LYS223 4.4 31.8 1.0 O A:GLY261 4.5 28.9 1.0 CG A:ASP263 4.6 37.8 1.0 HG21 A:VAL225 4.7 37.6 1.0 CA A:ASN219 4.7 41.4 1.0 CD2 A:LEU218 4.7 35.9 1.0 N A:LEU218 4.8 35.2 1.0 C A:ASN219 5.0 39.6 1.0 H A:ALA220 5.0 41.7 1.0 CG2 A:VAL225 5.0 31.3 1.0

Magnesium binding site 3 out of 3 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Ethanedithiolate [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Semisynthetic [Fefe]-Hydrogenase Cpi with Ethanedithiolate [2FE] Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:40.3 occ:1.00 O B:HOH868 2.1 34.2 1.0 O B:HOH737 2.1 32.2 1.0 O B:HOH731 2.1 38.1 1.0 O B:HOH761 2.1 32.2 1.0 O B:HOH924 2.1 36.0 1.0 O B:LEU218 2.1 37.3 1.0 C B:LEU218 3.2 34.9 1.0 HA B:LEU218 3.2 37.6 1.0 CA B:LEU218 3.7 31.4 1.0 O B:ALA220 4.0 35.4 1.0 OD2 B:ASP263 4.0 32.6 1.0 HB3 B:LEU218 4.1 39.1 1.0 O B:HOH950 4.1 34.8 1.0 O B:HOH796 4.2 26.4 1.0 O B:HOH715 4.2 39.6 1.0 O B:LYS223 4.2 32.8 1.0 HG23 B:VAL225 4.3 43.5 1.0 N B:ASN219 4.3 38.6 1.0 O B:ALA217 4.3 33.7 1.0 OD1 B:ASP263 4.4 32.1 1.0 HA B:ASN219 4.4 43.8 1.0 HD23 B:LEU218 4.4 44.9 1.0 CB B:LEU218 4.5 32.5 1.0 O B:GLY261 4.6 27.6 1.0 CG B:ASP263 4.6 37.7 1.0 HG21 B:VAL225 4.6 43.5 1.0 HD22 B:LEU218 4.7 44.9 1.0 CA B:ASN219 4.7 36.5 1.0 H B:ALA220 4.8 42.1 1.0 N B:LEU218 4.8 35.1 1.0 HA B:PRO221 4.9 41.3 1.0 C B:ALA220 4.9 34.4 1.0 C B:ASN219 4.9 36.1 1.0 N B:ALA220 4.9 35.1 1.0 CG2 B:VAL225 4.9 36.3 1.0 CD2 B:LEU218 5.0 37.4 1.0

J.Duan, S.Mebs, K.Laun, F.Wittkamp, J.Heberle, T.Happe, E.Hofmann, U.-P.Apfel, M.Winkler, M.Senger, M.Haumann, S.Stripp. Geometry of the Catalytic Active Site in [Fefe]-Hydrogenase Is Determined By Hydrogen Bonding and Proton Transfer Acs Catalysis 2019.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.9B02203