Magnesium in PDB 4xdd: Apo [Fefe]-Hydrogenase Cpi

All present enzymatic activity of Apo [Fefe]-Hydrogenase Cpi:
1.12.7.2;

The structure of Apo [Fefe]-Hydrogenase Cpi, PDB code: 4xdd was solved by J.Esselborn, E.Hofmann, G.Kurisu, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.96 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.057, 71.807, 103.308, 90.00, 97.93, 90.00
R / Rfree (%)	14.4 / 16.6

The structure of Apo [Fefe]-Hydrogenase Cpi also contains other interesting chemical elements:

Iron	(Fe)	36 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Magnesium atom in the Apo [Fefe]-Hydrogenase Cpi (pdb code 4xdd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Apo [Fefe]-Hydrogenase Cpi, PDB code: 4xdd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Apo [Fefe]-Hydrogenase Cpi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Apo [Fefe]-Hydrogenase Cpi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:26.4 occ:1.00 O A:HOH1071 2.0 33.1 1.0 O A:HOH749 2.1 27.9 1.0 O A:HOH905 2.1 25.9 1.0 O A:HOH758 2.1 26.5 1.0 O A:LEU218 2.1 25.7 1.0 O A:HOH887 2.1 25.5 1.0 C A:LEU218 3.2 26.2 1.0 HA A:LEU218 3.2 26.4 1.0 CA A:LEU218 3.7 22.0 1.0 OD2 A:ASP263 4.0 24.0 1.0 O A:ALA220 4.1 25.8 1.0 O A:HOH737 4.2 27.7 1.0 HB3 A:LEU218 4.2 28.1 1.0 O A:ALA217 4.3 23.4 1.0 HG23 A:VAL225 4.3 26.1 1.0 OD1 A:ASP263 4.3 25.9 1.0 O A:LYS223 4.3 23.0 1.0 N A:ASN219 4.3 25.6 1.0 HA A:ASN219 4.3 33.2 1.0 HD23 A:LEU218 4.4 28.9 1.0 O A:GLY261 4.5 23.1 1.0 O A:HOH945 4.6 44.4 1.0 CG A:ASP263 4.6 25.0 1.0 CB A:LEU218 4.6 23.4 1.0 HG21 A:VAL225 4.7 26.1 1.0 CA A:ASN219 4.7 27.7 1.0 HD22 A:LEU218 4.8 28.9 1.0 C A:ASN219 4.9 27.7 1.0 N A:LEU218 4.9 22.3 1.0 H A:ALA220 4.9 28.3 1.0 CG2 A:VAL225 4.9 21.7 1.0 C A:ALA220 5.0 27.9 1.0 N A:ALA220 5.0 23.6 1.0 HA A:PRO221 5.0 33.4 1.0

Magnesium binding site 2 out of 4 in the Apo [Fefe]-Hydrogenase Cpi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Apo [Fefe]-Hydrogenase Cpi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:46.0 occ:1.00 O A:HOH1095 2.0 41.8 1.0 O A:HOH1085 2.0 41.6 1.0 O A:HOH871 2.1 42.5 1.0 OD1 A:ASP42 2.1 41.4 1.0 OD1 A:ASN40 2.1 34.1 1.0 O A:HOH1111 2.3 42.3 1.0 CG A:ASP42 3.2 39.9 1.0 CG A:ASN40 3.2 33.1 1.0 H A:ASN40 3.2 35.1 1.0 HD21 A:ASN40 3.6 47.5 1.0 OD2 A:ASP42 3.6 40.6 1.0 O A:HOH842 3.6 41.2 1.0 ND2 A:ASN40 3.8 39.5 1.0 HB3 A:ASP63 4.0 45.4 1.0 HB3 B:ASN452 4.0 32.1 1.0 N A:ASN40 4.1 29.3 1.0 O B:HOH910 4.1 36.0 1.0 HA A:ASP42 4.2 47.9 1.0 O A:HOH1238 4.2 51.7 1.0 OD2 A:ASP63 4.3 43.5 1.0 HB2 A:ASP63 4.3 45.4 1.0 CG B:ASN452 4.4 33.1 1.0 O A:ASN40 4.4 32.9 1.0 HE2 A:LYS45 4.4 58.5 1.0 CB A:ASN40 4.4 30.6 1.0 CB A:ASP42 4.4 42.1 1.0 HA A:CYS39 4.5 38.2 1.0 OD1 B:ASN452 4.5 38.3 1.0 CB A:ASP63 4.6 37.9 1.0 ND2 B:ASN452 4.6 43.4 1.0 CA A:ASN40 4.6 27.2 1.0 HD22 A:ASN40 4.7 47.5 1.0 C A:ASN40 4.7 27.1 1.0 CB B:ASN452 4.7 26.7 1.0 CA A:ASP42 4.7 39.9 1.0 HB3 A:ASP42 4.7 50.5 1.0 HD22 B:ASN452 4.8 52.1 1.0 HB3 A:ASN40 4.8 36.8 1.0 HD21 B:ASN452 4.8 52.1 1.0 CG A:ASP63 5.0 41.4 1.0 H B:GLY453 5.0 29.2 1.0 O B:HOH1159 5.0 38.0 1.0

Magnesium binding site 3 out of 4 in the Apo [Fefe]-Hydrogenase Cpi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Apo [Fefe]-Hydrogenase Cpi within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg608 b:28.2 occ:1.00 O B:HOH994 2.1 29.6 1.0 O B:HOH954 2.1 34.0 1.0 O B:HOH879 2.1 25.6 1.0 O B:LEU218 2.1 26.7 1.0 O B:HOH735 2.1 30.2 1.0 O B:HOH711 2.1 29.1 1.0 C B:LEU218 3.2 27.4 1.0 HA B:LEU218 3.2 31.1 1.0 CA B:LEU218 3.7 25.9 1.0 OD2 B:ASP263 4.0 26.0 1.0 O B:ALA220 4.1 24.5 1.0 O B:HOH717 4.2 29.7 1.0 OD1 B:ASP263 4.2 28.8 1.0 O B:ALA217 4.2 25.9 1.0 HB3 B:LEU218 4.3 32.5 1.0 N B:ASN219 4.3 27.9 1.0 O B:LYS223 4.3 22.9 1.0 HG23 B:VAL225 4.4 30.0 1.0 HA B:ASN219 4.4 37.3 1.0 HD23 B:LEU218 4.4 33.8 1.0 O B:HOH1115 4.5 51.1 1.0 CG B:ASP263 4.6 29.6 1.0 O B:GLY261 4.6 25.8 1.0 CB B:LEU218 4.6 27.1 1.0 HD22 B:LEU218 4.7 33.8 1.0 CA B:ASN219 4.7 31.1 1.0 HG21 B:VAL225 4.8 30.0 1.0 H B:ALA220 4.8 29.4 1.0 O B:HOH1029 4.9 50.6 1.0 C B:ASN219 4.9 31.8 1.0 N B:LEU218 4.9 23.4 1.0 N B:ALA220 4.9 24.5 1.0 C B:ALA220 4.9 27.6 1.0 CD2 B:LEU218 5.0 28.1 1.0

Magnesium binding site 4 out of 4 in the Apo [Fefe]-Hydrogenase Cpi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Apo [Fefe]-Hydrogenase Cpi within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg609 b:26.8 occ:1.00 O B:HOH1097 2.0 27.8 1.0 O B:HOH1052 2.0 27.6 1.0 OD1 B:ASP42 2.1 33.4 1.0 OD1 B:ASN40 2.1 25.7 1.0 O B:HOH899 2.1 26.4 1.0 O B:HOH1081 2.1 31.0 1.0 H B:ASN40 3.1 31.5 1.0 CG B:ASP42 3.2 33.7 1.0 CG B:ASN40 3.3 26.2 1.0 OD2 B:ASP42 3.7 37.2 1.0 HD21 B:ASN40 3.8 30.9 1.0 HB3 B:ASP63 3.9 28.6 1.0 ND2 B:ASN40 4.0 25.8 1.0 N B:ASN40 4.0 26.2 1.0 HB3 A:ASN452 4.0 23.4 1.0 HB2 B:ASP63 4.0 28.6 1.0 O B:HOH809 4.0 32.8 1.0 HA B:ASP42 4.1 35.4 1.0 O B:HOH1156 4.1 41.4 1.0 OD1 A:ASN452 4.2 28.6 1.0 O B:ASN40 4.2 25.4 1.0 OD2 B:ASP63 4.3 25.8 1.0 CG A:ASN452 4.4 25.2 1.0 CB B:ASP42 4.4 27.2 1.0 CB B:ASP63 4.4 23.9 1.0 HA B:CYS39 4.4 30.8 1.0 O A:HOH954 4.4 32.7 1.0 CB B:ASN40 4.4 24.5 1.0 CA B:ASN40 4.5 23.3 1.0 C B:ASN40 4.5 26.3 1.0 CA B:ASP42 4.6 29.5 1.0 HB3 B:ASP42 4.6 32.7 1.0 CB A:ASN452 4.7 19.5 1.0 HG B:CYS39 4.7 53.5 0.5 H B:ASP42 4.8 34.6 1.0 HB3 B:ASN40 4.8 29.4 1.0 O A:HOH1177 4.8 32.1 1.0 HD22 B:ASN40 4.8 30.9 1.0 SG B:CYS39 4.8 44.5 0.5 N B:ASP42 4.8 28.8 1.0 H A:GLY453 4.9 24.2 1.0 CG B:ASP63 4.9 26.0 1.0 ND2 A:ASN452 4.9 25.1 1.0 HB2 B:CYS39 4.9 42.6 0.6 O A:ILE454 5.0 24.7 1.0 O B:HOH1049 5.0 43.5 1.0

J.Esselborn, N.Muraki, K.Klein, V.Engelbrecht, N.Metzler-Nolte, U.P.Apfel, E.Hofmann, G.Kurisu, T.Happe. A Structural View of Synthetic Cofactor Integration Into [Fefe]-Hydrogenases. Chem Sci V. 7 959 2016.
ISSN: ISSN 2041-6520
PubMed: 29896366
DOI: 10.1039/C5SC03397G