Magnesium in PDB 6yf4: [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant E279D

All present enzymatic activity of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant E279D:
1.12.7.2;

The structure of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant E279D, PDB code: 6yf4 was solved by J.Duan, E.Hofmann, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.48 / 1.77
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.810, 72.020, 102.930, 90.00, 97.48, 90.00
R / Rfree (%)	20 / 23.4

The structure of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant E279D also contains other interesting chemical elements:

Iron

(Fe)

40 atoms

The binding sites of Magnesium atom in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant E279D (pdb code 6yf4). 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 I From Clostridium Pasteurianum (Cpi), Variant E279D, PDB code: 6yf4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant E279D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant E279D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:38.9 occ:1.00 O A:HOH810 2.1 38.7 1.0 O A:HOH977 2.1 38.2 1.0 O A:HOH816 2.1 28.1 1.0 O A:HOH919 2.1 34.6 1.0 O A:HOH860 2.1 35.0 1.0 O A:LEU218 2.3 35.4 1.0 C A:LEU218 3.4 34.1 1.0 HA A:LEU218 3.4 45.2 1.0 CA A:LEU218 3.9 37.7 1.0 OD2 A:ASP263 4.0 29.0 1.0 O A:ALA220 4.0 32.7 1.0 O A:HOH883 4.1 29.3 1.0 HG23 A:VAL225 4.2 33.4 1.0 O A:LYS223 4.2 30.1 1.0 OD1 A:ASP263 4.2 29.4 1.0 HB3 A:LEU218 4.3 33.6 1.0 O A:ALA217 4.4 25.2 1.0 HA A:ASN219 4.5 42.3 1.0 N A:ASN219 4.5 32.9 1.0 CG A:ASP263 4.5 34.5 1.0 HD23 A:LEU218 4.6 41.6 1.0 O A:GLY261 4.6 29.2 1.0 HD22 A:LEU218 4.6 41.6 1.0 O A:HOH722 4.6 39.8 1.0 CB A:LEU218 4.7 28.0 1.0 HG21 A:VAL225 4.8 33.4 1.0 HA A:PRO221 4.8 42.2 1.0 CA A:ASN219 4.9 35.3 1.0 CG2 A:VAL225 4.9 27.8 1.0 C A:ALA220 5.0 33.0 1.0 C A:ASN219 5.0 32.3 1.0

Magnesium binding site 2 out of 3 in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant E279D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant E279D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg608 b:27.9 occ:1.00 OD1 A:ASP42 2.1 29.8 1.0 O A:HOH945 2.1 30.4 1.0 O A:HOH906 2.1 28.9 1.0 O A:HOH853 2.1 30.9 1.0 O A:HOH979 2.1 31.9 1.0 OD1 A:ASN40 2.1 25.0 1.0 CG A:ASP42 3.2 33.5 1.0 CG A:ASN40 3.2 25.2 1.0 H A:ASN40 3.4 30.0 1.0 HD21 A:ASN40 3.5 35.3 1.0 OD2 A:ASP42 3.7 36.0 1.0 ND2 A:ASN40 3.8 29.4 1.0 O A:HOH735 3.9 32.0 1.0 HB3 A:ASP63 3.9 29.7 1.0 HB2 A:ASP63 4.1 29.7 1.0 O A:HOH1049 4.1 40.6 1.0 O B:HOH728 4.1 36.2 1.0 HA A:ASP42 4.1 29.0 1.0 HB3 B:ASN452 4.2 35.3 1.0 O A:ASN40 4.2 29.1 1.0 N A:ASN40 4.2 25.0 1.0 O A:HOH934 4.3 39.5 1.0 CB A:ASP63 4.4 24.8 1.0 OD2 A:ASP63 4.4 28.4 1.0 CB A:ASP42 4.4 27.1 1.0 CB A:ASN40 4.4 20.8 1.0 C A:ASN40 4.6 25.6 1.0 HA A:CYS39 4.6 35.9 1.0 CA A:ASN40 4.6 21.8 1.0 OD1 B:ASN452 4.7 35.7 1.0 HD22 A:ASN40 4.7 35.3 1.0 CA A:ASP42 4.7 24.2 1.0 O B:HOH956 4.7 33.6 1.0 CG B:ASN452 4.7 36.4 1.0 HB3 A:ASP42 4.7 32.6 1.0 HB3 A:ASN40 4.8 24.9 1.0 CB B:ASN452 4.9 29.4 1.0 N A:ASP42 4.9 24.8 1.0 CG A:ASP63 4.9 26.8 1.0 H A:ASP42 5.0 29.8 1.0

Magnesium binding site 3 out of 3 in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant E279D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant E279D within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:39.0 occ:1.00 O B:HOH850 2.1 28.9 1.0 O B:HOH720 2.1 26.1 1.0 O B:HOH858 2.1 34.6 1.0 O B:HOH966 2.1 37.3 1.0 O B:HOH848 2.1 32.7 1.0 O B:LEU218 2.3 33.2 1.0 HA B:LEU218 3.2 38.4 1.0 C B:LEU218 3.3 34.0 1.0 CA B:LEU218 3.7 32.0 1.0 O B:HOH886 3.9 28.9 1.0 OD2 B:ASP263 4.0 26.1 1.0 HG23 B:VAL225 4.0 26.9 1.0 O B:ALA220 4.1 30.5 1.0 O B:LYS223 4.1 29.7 1.0 HB3 B:LEU218 4.2 30.3 1.0 O B:HOH722 4.2 34.7 1.0 OD1 B:ASP263 4.2 36.1 1.0 HD23 B:LEU218 4.2 37.5 1.0 O B:ALA217 4.3 27.9 1.0 N B:ASN219 4.5 31.9 1.0 O B:HOH1001 4.5 44.9 1.0 O B:GLY261 4.5 27.3 1.0 CG B:ASP263 4.5 33.1 1.0 CB B:LEU218 4.5 25.2 1.0 HA B:ASN219 4.6 39.2 1.0 HG21 B:VAL225 4.7 26.9 1.0 HD22 B:LEU218 4.7 37.5 1.0 CG2 B:VAL225 4.8 22.4 1.0 HA B:PRO221 4.8 36.2 1.0 CD2 B:LEU218 4.9 31.3 1.0 N B:LEU218 4.9 28.6 1.0 CA B:ASN219 4.9 32.7 1.0 C B:ALA220 5.0 34.8 1.0 H B:ALA220 5.0 32.4 1.0

O.Lampret, J.Duan, E.Hofmann, M.Winkler, F.A.Armstrong, T.Happe. The Roles of Long-Range Proton-Coupled Electron Transfer in the Directionality and Efficiency of [Fefe]-Hydrogenases. Proc.Natl.Acad.Sci.Usa V. 117 20520 2020.
ISSN: ESSN 1091-6490
PubMed: 32796105
DOI: 10.1073/PNAS.2007090117