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Magnesium in PDB 5bys: Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-Dithiolato-Bridged [2FE] Cofactor

Enzymatic activity of Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-Dithiolato-Bridged [2FE] Cofactor

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

Protein crystallography data

The structure of Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-Dithiolato-Bridged [2FE] Cofactor, PDB code: 5bys was solved by J.Esselborn, N.Muraki, V.Engelbrecht, 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) 48.05 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.830, 73.130, 103.040, 90.00, 96.60, 90.00
R / Rfree (%) 15.8 / 18.8

Other elements in 5bys:

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

Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-Dithiolato-Bridged [2FE] Cofactor (pdb code 5bys). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-Dithiolato-Bridged [2FE] Cofactor, PDB code: 5bys:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5bys

Go back to Magnesium Binding Sites List in 5bys
Magnesium binding site 1 out of 4 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-Dithiolato-Bridged [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 Sulfur-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:27.5
occ:1.00
 O A:HOH795 2.0 21.6 1.0
O A:LEU218 2.1 25.0 1.0
O A:HOH922 2.1 26.6 1.0
O A:HOH743 2.2 24.1 1.0
O A:HOH842 2.2 26.5 1.0
O A:HOH841 2.2 25.4 1.0
C A:LEU218 3.2 25.0 1.0
HA A:LEU218 3.2 26.4 1.0
CA A:LEU218 3.7 22.0 1.0
OD2 A:ASP263 3.9 25.7 1.0
O A:HOH1138 3.9 41.8 1.0
O A:ALA220 4.0 23.7 1.0
O A:LYS223 4.1 22.5 1.0
O A:ALA217 4.2 24.1 1.0
OD1 A:ASP263 4.2 25.5 1.0
O A:HOH852 4.3 25.5 1.0
HG23 A:VAL225 4.3 25.2 1.0
N A:ASN219 4.3 26.9 1.0
HB3 A:LEU218 4.3 27.4 1.0
HA A:ASN219 4.4 35.5 1.0
HD23 A:LEU218 4.4 24.5 1.0
CG A:ASP263 4.5 24.5 1.0
O A:GLY261 4.5 24.3 1.0
CB A:LEU218 4.7 22.9 1.0
O A:HOH853 4.7 36.9 1.0
HG21 A:VAL225 4.7 25.2 1.0
CA A:ASN219 4.8 29.6 1.0
HD22 A:LEU218 4.8 24.5 1.0
N A:LEU218 4.8 21.4 1.0
C A:ALA220 4.9 26.7 1.0
C A:ASN219 4.9 29.9 1.0
C A:ALA217 4.9 23.9 1.0
CG2 A:VAL225 5.0 21.0 1.0
H A:ALA220 5.0 31.4 1.0
N A:ALA220 5.0 26.2 1.0

Magnesium binding site 2 out of 4 in 5bys

Go back to Magnesium Binding Sites List in 5bys
Magnesium binding site 2 out of 4 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-Dithiolato-Bridged [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 Sulfur-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:24.5
occ:1.00
 OD1 A:ASN40 1.9 21.5 1.0
OD1 A:ASP42 2.0 27.3 1.0
O A:HOH908 2.1 27.3 1.0
O A:HOH916 2.1 24.8 1.0
O A:HOH949 2.1 25.2 1.0
O A:HOH791 2.2 24.2 1.0
CG A:ASN40 3.1 23.6 1.0
H A:ASN40 3.2 27.6 1.0
CG A:ASP42 3.2 27.6 1.0
HD21 A:ASN40 3.5 29.6 1.0
ND2 A:ASN40 3.7 24.7 1.0
OD2 A:ASP42 3.8 30.0 1.0
HB3 A:ASP63 3.9 26.4 1.0
HA A:ASP42 4.0 29.9 1.0
O B:HOH775 4.0 36.9 1.0
N A:ASN40 4.0 23.0 1.0
O A:HOH751 4.1 28.2 1.0
HB2 A:ASP63 4.1 26.4 1.0
O A:HOH1051 4.1 36.3 1.0
O A:ASN40 4.2 22.1 1.0
CB A:ASN40 4.3 26.3 1.0
O B:HOH729 4.3 31.9 1.0
HB3 B:ASN452 4.4 23.6 1.0
OD2 A:ASP63 4.4 25.0 1.0
CB A:ASP42 4.4 23.1 1.0
C A:ASN40 4.4 22.1 1.0
OD1 B:ASN452 4.4 26.1 1.0
CB A:ASP63 4.4 22.0 1.0
CA A:ASN40 4.4 22.6 1.0
CA A:ASP42 4.6 25.0 1.0
HD22 A:ASN40 4.6 29.6 1.0
HA A:CYS39 4.6 29.6 1.0
HB3 A:ASN40 4.6 31.6 1.0
CG B:ASN452 4.7 26.9 1.0
HB3 A:ASP42 4.7 27.7 1.0
O A:HOH871 4.7 31.3 1.0
HE2 A:LYS45 4.8 37.5 1.0
O B:HOH979 4.8 25.4 1.0
N A:ASP42 4.8 21.3 1.0
H A:ASP42 4.9 25.5 1.0
CG A:ASP63 5.0 24.8 1.0

Magnesium binding site 3 out of 4 in 5bys

Go back to Magnesium Binding Sites List in 5bys
Magnesium binding site 3 out of 4 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-Dithiolato-Bridged [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 Sulfur-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:26.4
occ:1.00
 O B:HOH809 2.0 19.9 1.0
O B:HOH918 2.1 21.3 1.0
O B:HOH770 2.1 22.5 1.0
O B:HOH815 2.1 20.5 1.0
O B:HOH928 2.2 24.3 1.0
O B:LEU218 2.2 25.5 1.0
C B:LEU218 3.3 25.2 1.0
HA B:LEU218 3.3 25.5 1.0
CA B:LEU218 3.8 21.2 1.0
OD2 B:ASP263 3.9 21.1 1.0
O B:HOH852 4.0 22.0 1.0
O B:ALA220 4.1 24.8 1.0
O B:LYS223 4.2 20.8 1.0
OD1 B:ASP263 4.2 21.8 1.0
HB3 B:LEU218 4.3 27.8 1.0
O B:ALA217 4.3 22.0 1.0
HG23 B:VAL225 4.3 22.3 1.0
N B:ASN219 4.3 25.4 1.0
HA B:ASN219 4.4 32.1 1.0
HD23 B:LEU218 4.5 23.5 1.0
CG B:ASP263 4.5 22.7 1.0
O B:GLY261 4.5 19.3 1.0
CB B:LEU218 4.6 23.2 1.0
CA B:ASN219 4.8 26.8 1.0
HG21 B:VAL225 4.8 22.3 1.0
O B:HOH1051 4.8 38.2 1.0
HD22 B:LEU218 4.8 23.5 1.0
H B:ALA220 4.9 25.1 1.0
C B:ASN219 4.9 24.5 1.0
N B:LEU218 4.9 21.6 1.0

Magnesium binding site 4 out of 4 in 5bys

Go back to Magnesium Binding Sites List in 5bys
Magnesium binding site 4 out of 4 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-Dithiolato-Bridged [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:31.1
occ:1.00
 O B:HOH984 2.0 28.3 1.0
OD1 B:ASP42 2.1 28.6 1.0
O B:HOH752 2.1 32.1 1.0
O B:HOH961 2.2 32.1 1.0
OD1 B:ASN40 2.2 27.1 1.0
O B:HOH966 2.3 29.3 1.0
CG B:ASP42 3.2 28.3 1.0
H B:ASN40 3.2 33.7 1.0
CG B:ASN40 3.3 27.2 1.0
OD2 B:ASP42 3.6 36.8 1.0
HD21 B:ASN40 3.8 35.9 1.0
ND2 B:ASN40 4.0 29.9 1.0
N B:ASN40 4.1 28.1 1.0
HA B:ASP42 4.1 34.0 1.0
HB3 B:ASP63 4.1 37.6 1.0
HB3 A:ASN452 4.2 34.0 1.0
HB2 B:ASP63 4.3 37.6 1.0
O B:ASN40 4.3 23.7 1.0
O A:HOH715 4.4 36.4 1.0
OD2 B:ASP63 4.4 30.0 1.0
OD1 A:ASN452 4.4 34.9 1.0
CB B:ASP42 4.4 28.1 1.0
CG A:ASN452 4.5 28.6 1.0
CB B:ASN40 4.5 25.5 1.0
HA B:CYS39 4.5 34.6 1.0
C B:ASN40 4.5 24.8 1.0
CA B:ASN40 4.6 25.8 1.0
CB B:ASP63 4.6 31.3 1.0
CA B:ASP42 4.7 28.3 1.0
HB3 B:ASP42 4.7 33.8 1.0
H A:GLY453 4.8 24.1 1.0
O A:HOH995 4.8 31.9 1.0
CB A:ASN452 4.8 28.3 1.0
ND2 A:ASN452 4.8 37.5 1.0
HD22 B:ASN40 4.8 35.9 1.0
HB3 B:ASN40 4.9 30.6 1.0
H A:ILE454 5.0 23.4 1.0
HD21 A:ASN452 5.0 45.0 1.0

Reference:

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
Page generated: Tue Aug 12 06:10:02 2025

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