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Magnesium in PDB 5byq: Semisynthetic [Fefe]-Hydrogenase Cpi with Oxodithiolato-Bridged [2FE] Cofactor

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

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

Protein crystallography data

The structure of Semisynthetic [Fefe]-Hydrogenase Cpi with Oxodithiolato-Bridged [2FE] Cofactor, PDB code: 5byq 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) 47.77 / 1.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.660, 72.450, 102.940, 90.00, 96.76, 90.00
R / Rfree (%) 14.6 / 17.6

Other elements in 5byq:

The structure of Semisynthetic [Fefe]-Hydrogenase Cpi with Oxodithiolato-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 Oxodithiolato-Bridged [2FE] Cofactor (pdb code 5byq). 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 Oxodithiolato-Bridged [2FE] Cofactor, PDB code: 5byq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5byq

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

b:29.8
occ:1.00
 O A:HOH886 2.0 32.5 1.0
O A:HOH795 2.1 24.8 1.0
O A:HOH771 2.1 26.8 1.0
O A:LEU218 2.1 28.4 1.0
O A:HOH910 2.1 27.5 1.0
O A:HOH734 2.2 28.5 1.0
C A:LEU218 3.2 26.9 1.0
HA A:LEU218 3.3 31.1 1.0
CA A:LEU218 3.8 25.9 1.0
OD2 A:ASP263 3.9 26.6 1.0
O A:ALA220 4.1 25.2 1.0
HA A:ASN219 4.2 34.2 1.0
OD1 A:ASP263 4.2 27.9 1.0
O A:HOH806 4.3 26.1 1.0
HB3 A:LEU218 4.3 29.5 1.0
O A:LYS223 4.3 24.9 1.0
O A:ALA217 4.3 25.3 1.0
HG23 A:VAL225 4.3 30.6 1.0
N A:ASN219 4.3 28.9 1.0
O A:HOH1114 4.4 47.7 1.0
O A:GLY261 4.5 27.0 1.0
CG A:ASP263 4.5 32.5 1.0
HD23 A:LEU218 4.5 38.2 1.0
CB A:LEU218 4.6 24.6 1.0
CA A:ASN219 4.6 28.5 1.0
O A:HOH755 4.7 43.4 1.0
HG21 A:VAL225 4.7 30.6 1.0
HD22 A:LEU218 4.8 38.2 1.0
C A:ASN219 4.9 32.7 1.0
H A:ALA220 4.9 30.0 1.0
HA A:PRO221 4.9 37.5 1.0
N A:LEU218 4.9 25.8 1.0
N A:ALA220 4.9 25.0 1.0
CG2 A:VAL225 5.0 25.5 1.0
C A:ALA220 5.0 27.6 1.0

Magnesium binding site 2 out of 4 in 5byq

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

b:25.3
occ:1.00
 OD1 A:ASN40 2.0 24.4 1.0
OD1 A:ASP42 2.0 28.8 1.0
O A:HOH748 2.1 27.2 1.0
O A:HOH932 2.1 25.9 1.0
O A:HOH906 2.1 24.6 1.0
O A:HOH891 2.1 27.9 1.0
CG A:ASN40 3.1 25.5 1.0
CG A:ASP42 3.2 31.0 1.0
H A:ASN40 3.2 28.4 1.0
HD21 A:ASN40 3.5 31.7 1.0
OD2 A:ASP42 3.8 37.7 1.0
ND2 A:ASN40 3.8 26.4 1.0
HA A:ASP42 3.9 31.4 1.0
HB3 A:ASP63 3.9 27.1 1.0
O A:HOH727 4.0 38.9 1.0
HB2 A:ASP63 4.0 27.1 1.0
N A:ASN40 4.0 23.6 1.0
O B:HOH712 4.2 44.9 1.0
O A:HOH1074 4.2 36.8 1.0
O A:ASN40 4.2 24.1 1.0
HB3 B:ASN452 4.3 25.2 1.0
OD2 A:ASP63 4.3 25.6 1.0
O B:HOH762 4.3 32.6 1.0
CB A:ASP42 4.3 28.3 1.0
CB A:ASN40 4.4 23.4 1.0
OD1 B:ASN452 4.4 31.8 1.0
CB A:ASP63 4.4 22.6 1.0
O A:HOH863 4.4 39.4 1.0
C A:ASN40 4.5 25.3 1.0
CA A:ASN40 4.5 23.5 1.0
CA A:ASP42 4.5 26.1 1.0
HA A:CYS39 4.5 30.1 1.0
HB3 A:ASP42 4.6 34.0 1.0
CG B:ASN452 4.6 32.9 1.0
HD22 A:ASN40 4.6 31.7 1.0
HB2 A:CYS39 4.7 45.8 1.0
HE2 A:LYS45 4.7 52.8 1.0
HB3 A:ASN40 4.7 28.1 1.0
N A:ASP42 4.8 26.8 1.0
H A:ASP42 4.8 32.2 1.0
O B:HOH1002 4.8 26.7 1.0
CG A:ASP63 4.9 27.7 1.0
CB B:ASN452 4.9 21.0 1.0
H B:GLY453 5.0 25.9 1.0

Magnesium binding site 3 out of 4 in 5byq

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

b:29.1
occ:1.00
 O B:HOH873 2.0 30.4 1.0
O B:HOH774 2.0 21.6 1.0
O B:HOH768 2.1 24.9 1.0
O B:LEU218 2.1 26.9 1.0
O B:HOH967 2.2 27.9 1.0
O B:HOH813 2.2 26.7 1.0
C B:LEU218 3.2 27.7 1.0
HA B:LEU218 3.2 27.9 1.0
CA B:LEU218 3.7 23.3 1.0
OD2 B:ASP263 3.9 24.9 1.0
O B:ALA220 4.0 27.9 1.0
O B:HOH807 4.1 25.1 1.0
O B:LYS223 4.2 24.5 1.0
O B:ALA217 4.2 25.0 1.0
HG23 B:VAL225 4.2 27.0 1.0
HB3 B:LEU218 4.2 27.1 1.0
N B:ASN219 4.3 28.8 1.0
OD1 B:ASP263 4.3 23.9 1.0
HA B:ASN219 4.3 35.8 1.0
HD23 B:LEU218 4.4 32.4 1.0
O B:HOH715 4.5 37.2 1.0
CG B:ASP263 4.5 28.3 1.0
O B:GLY261 4.5 22.1 1.0
CB B:LEU218 4.6 22.6 1.0
O B:HOH1034 4.6 47.1 1.0
CA B:ASN219 4.7 29.8 1.0
HG21 B:VAL225 4.7 27.0 1.0
HD22 B:LEU218 4.8 32.4 1.0
H B:ALA220 4.8 30.8 1.0
HA B:PRO221 4.8 36.2 1.0
C B:ASN219 4.8 30.6 1.0
N B:LEU218 4.9 22.1 1.0
N B:ALA220 4.9 25.6 1.0
CG2 B:VAL225 4.9 22.5 1.0
C B:ALA220 4.9 29.1 1.0
C B:ALA217 5.0 24.2 1.0
CD2 B:LEU218 5.0 27.0 1.0

Magnesium binding site 4 out of 4 in 5byq

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

b:33.5
occ:1.00
 O B:HOH921 1.9 37.9 1.0
OD1 B:ASP42 2.1 33.8 1.0
O B:HOH758 2.1 36.0 1.0
OD1 B:ASN40 2.1 27.7 1.0
O B:HOH961 2.2 35.7 1.0
O B:HOH919 2.2 32.1 1.0
CG B:ASP42 3.2 34.1 1.0
CG B:ASN40 3.2 27.1 1.0
H B:ASN40 3.3 33.4 1.0
HD21 B:ASN40 3.6 39.7 1.0
OD2 B:ASP42 3.8 46.3 1.0
ND2 B:ASN40 3.8 33.0 1.0
O B:HOH707 3.9 38.9 1.0
HB3 B:ASP63 4.0 38.3 1.0
N B:ASN40 4.1 27.8 1.0
HA B:ASP42 4.1 40.6 1.0
O A:HOH788 4.2 35.5 1.0
HB3 A:ASN452 4.2 35.5 1.0
OD2 B:ASP63 4.2 35.0 1.0
HB2 B:ASP63 4.3 38.3 1.0
O B:ASN40 4.3 25.5 1.0
OD1 A:ASN452 4.4 37.9 1.0
CB B:ASP42 4.4 35.4 1.0
CB B:ASN40 4.4 25.3 1.0
HA B:CYS39 4.5 35.2 1.0
CG A:ASN452 4.5 30.6 1.0
CB B:ASP63 4.6 31.9 1.0
C B:ASN40 4.6 22.7 1.0
CA B:ASN40 4.6 25.5 1.0
HB2 B:CYS39 4.6 46.3 1.0
CA B:ASP42 4.7 33.9 1.0
HB3 B:ASP42 4.7 42.5 1.0
HD22 B:ASN40 4.7 39.7 1.0
HB3 B:ASN40 4.8 30.4 1.0
O A:HOH1002 4.9 29.2 1.0
CB A:ASN452 4.9 29.6 1.0
ND2 A:ASN452 4.9 40.0 1.0
CG B:ASP63 4.9 34.8 1.0
H A:GLY453 4.9 28.3 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: Mon Dec 14 20:04:37 2020

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