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

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

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

Protein crystallography data

The structure of Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor, PDB code: 5byr 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) 47.58 / 1.82
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.470, 72.070, 102.710, 90.00, 100.86, 90.00
R / Rfree (%) 15.6 / 19.2

Other elements in 5byr:

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

Magnesium binding site 1 out of 5 in 5byr

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

b:25.7
occ:1.00
 O A:HOH823 2.0 28.0 1.0
O A:HOH777 2.1 23.9 1.0
O A:LEU218 2.1 24.1 1.0
O A:HOH743 2.1 21.1 1.0
O A:HOH795 2.1 25.8 1.0
O A:HOH923 2.2 26.4 1.0
C A:LEU218 3.1 25.9 1.0
HA A:LEU218 3.3 29.3 1.0
CA A:LEU218 3.7 24.4 1.0
OD2 A:ASP263 4.0 23.0 1.0
O A:ALA220 4.1 23.9 1.0
HB3 A:LEU218 4.1 27.3 1.0
HA A:ASN219 4.1 30.9 1.0
O A:HOH816 4.2 24.2 1.0
N A:ASN219 4.2 26.4 1.0
O A:LYS223 4.3 19.8 1.0
HG23 A:VAL225 4.3 23.8 1.0
OD1 A:ASP263 4.3 24.6 1.0
O A:ALA217 4.3 21.9 1.0
O A:HOH1108 4.4 42.1 1.0
CB A:LEU218 4.5 22.8 1.0
O A:GLY261 4.5 24.9 1.0
O A:HOH825 4.5 40.4 1.0
HD23 A:LEU218 4.6 31.8 1.0
CA A:ASN219 4.6 25.8 1.0
CG A:ASP263 4.6 25.7 1.0
HG21 A:VAL225 4.7 23.8 1.0
C A:ASN219 4.8 25.8 1.0
H A:ALA220 4.9 28.2 1.0
HD22 A:LEU218 4.9 31.8 1.0
N A:ALA220 4.9 23.5 1.0
N A:LEU218 4.9 20.2 1.0
O A:HOH901 4.9 38.5 1.0
HA A:PRO221 4.9 32.2 1.0
C A:ALA220 4.9 26.8 1.0
CG2 A:VAL225 4.9 19.8 1.0
H A:ASN219 5.0 31.6 1.0

Magnesium binding site 2 out of 5 in 5byr

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Magnesium binding site 2 out of 5 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-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 Propane-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:45.4
occ:1.00
 O A:HOH749 2.1 40.4 1.0
HG A:SER320 2.5 34.3 1.0
O A:HOH724 2.7 41.6 1.0
OG A:SER320 2.8 28.6 1.0
NE2 A:HIS565 2.9 39.2 1.0
HD2 A:HIS565 3.0 48.3 1.0
O A:HOH708 3.1 35.5 1.0
CD A:GLU282 3.2 34.2 1.0
CD2 A:HIS565 3.3 40.2 1.0
HE1 A:HIS569 3.3 34.3 1.0
OE2 A:GLU282 3.3 36.6 1.0
OE1 A:GLU282 3.4 34.9 1.0
HB2 A:GLU282 3.6 35.0 1.0
ND1 A:HIS569 3.6 27.2 1.0
HG3 A:GLU282 3.6 41.9 1.0
CE1 A:HIS569 3.7 28.6 1.0
CG A:GLU282 3.9 34.9 1.0
H A:SER320 4.0 31.6 1.0
CB A:SER320 4.1 28.1 1.0
CE1 A:HIS565 4.1 38.8 1.0
O A:HOH1008 4.2 38.9 1.0
HB3 A:SER320 4.2 33.7 1.0
CB A:GLU282 4.2 29.2 1.0
OE1 A:GLN285 4.5 43.9 1.0
HE1 A:HIS565 4.6 46.6 1.0
CG A:HIS565 4.6 38.2 1.0
HB2 A:SER320 4.6 33.7 1.0
HA A:GLU282 4.7 34.6 1.0
N A:SER320 4.8 26.3 1.0
HG2 A:GLU282 4.8 41.9 1.0
CG A:HIS569 4.8 29.0 1.0
NE2 A:HIS569 4.8 28.7 1.0
HA2 A:GLY560 4.9 43.4 1.0
CA A:SER320 4.9 28.8 1.0
HB3 A:GLU282 4.9 35.0 1.0

Magnesium binding site 3 out of 5 in 5byr

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Magnesium binding site 3 out of 5 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-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 Propane-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg609

b:25.6
occ:1.00
 O A:HOH933 1.9 24.1 1.0
OD1 A:ASP42 1.9 24.3 1.0
O A:HOH769 2.1 21.5 1.0
OD1 A:ASN40 2.1 21.8 1.0
O A:HOH943 2.2 24.6 1.0
O A:HOH931 2.3 27.3 1.0
CG A:ASP42 3.1 26.0 1.0
CG A:ASN40 3.2 21.5 1.0
H A:ASN40 3.2 23.7 1.0
HD21 A:ASN40 3.5 27.8 1.0
OD2 A:ASP42 3.7 31.1 1.0
ND2 A:ASN40 3.8 23.1 1.0
HB2 A:ASP63 3.9 27.1 1.0
O A:HOH711 3.9 28.1 1.0
HB3 A:ASP63 3.9 27.1 1.0
HA A:ASP42 4.0 30.8 1.0
N A:ASN40 4.0 19.8 1.0
O B:HOH711 4.1 34.6 1.0
OD1 B:ASN452 4.2 27.3 1.0
O A:HOH896 4.2 32.5 1.0
O A:HOH1003 4.2 32.4 1.0
OD2 A:ASP63 4.3 23.6 1.0
CB A:ASP42 4.3 25.7 1.0
HB3 B:ASN452 4.3 26.7 1.0
O A:ASN40 4.3 19.5 1.0
CB A:ASP63 4.4 22.6 1.0
CB A:ASN40 4.4 18.7 1.0
O B:HOH738 4.4 31.8 1.0
C A:ASN40 4.5 18.9 1.0
CA A:ASN40 4.5 20.7 1.0
HA A:CYS39 4.6 28.9 1.0
CA A:ASP42 4.6 25.7 1.0
HB3 A:ASP42 4.6 30.8 1.0
CG B:ASN452 4.6 27.3 1.0
HD22 A:ASN40 4.6 27.8 1.0
HB2 A:CYS39 4.7 36.6 1.0
HB3 A:ASN40 4.7 22.4 1.0
N A:ASP42 4.8 21.4 1.0
O B:HOH980 4.8 20.6 1.0
H A:ASP42 4.9 25.6 1.0
CG A:ASP63 4.9 24.5 1.0
HE2 A:LYS45 4.9 41.5 1.0
H B:GLY453 5.0 20.9 1.0
CB B:ASN452 5.0 22.2 1.0

Magnesium binding site 4 out of 5 in 5byr

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Magnesium binding site 4 out of 5 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-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 Propane-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:25.3
occ:1.00
 O B:HOH720 2.0 21.1 1.0
O B:HOH752 2.1 19.2 1.0
O B:LEU218 2.1 24.2 1.0
O B:HOH929 2.1 24.0 1.0
O B:HOH891 2.2 26.2 1.0
O B:HOH787 2.3 21.5 1.0
C B:LEU218 3.1 23.2 1.0
HA B:LEU218 3.2 30.2 1.0
CA B:LEU218 3.7 25.2 1.0
OD2 B:ASP263 3.9 21.1 1.0
O B:ALA220 4.0 23.6 1.0
O B:ALA217 4.1 21.6 1.0
O B:LYS223 4.1 17.4 1.0
O B:HOH814 4.1 21.6 1.0
HG23 B:VAL225 4.2 23.4 1.0
HB3 B:LEU218 4.3 23.2 1.0
O B:HOH1100 4.3 44.1 1.0
N B:ASN219 4.3 25.8 1.0
HA B:ASN219 4.3 30.0 1.0
OD1 B:ASP263 4.4 21.9 1.0
O B:GLY261 4.5 21.9 1.0
HD23 B:LEU218 4.5 27.1 1.0
CG B:ASP263 4.6 23.3 1.0
HG21 B:VAL225 4.6 23.4 1.0
CB B:LEU218 4.6 19.3 1.0
H B:ALA220 4.7 27.0 1.0
CA B:ASN219 4.7 25.0 1.0
O B:HOH930 4.7 39.5 1.0
HA B:PRO221 4.7 30.2 1.0
N B:LEU218 4.8 20.1 1.0
C B:ALA220 4.8 25.5 1.0
CG2 B:VAL225 4.8 19.5 1.0
O B:HOH1022 4.8 40.3 1.0
N B:ALA220 4.8 22.5 1.0
C B:ALA217 4.8 23.3 1.0
HD22 B:LEU218 4.9 27.1 1.0
C B:ASN219 4.9 28.5 1.0

Magnesium binding site 5 out of 5 in 5byr

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:29.8
occ:1.00
 OD1 B:ASP42 2.0 24.4 1.0
O B:HOH914 2.0 30.8 1.0
O B:HOH884 2.1 29.4 1.0
OD1 B:ASN40 2.1 22.1 1.0
O B:HOH868 2.2 27.9 1.0
O B:HOH815 2.2 31.8 1.0
CG B:ASP42 3.1 30.0 1.0
CG B:ASN40 3.2 27.9 1.0
H B:ASN40 3.3 27.5 1.0
HD21 B:ASN40 3.5 32.7 1.0
OD2 B:ASP42 3.6 34.8 1.0
ND2 B:ASN40 3.8 27.2 1.0
O B:HOH705 3.9 34.6 1.0
HA B:ASP42 3.9 33.4 1.0
O B:HOH717 4.0 40.9 1.0
HB3 B:ASP63 4.0 39.9 1.0
N B:ASN40 4.1 22.9 1.0
O A:HOH748 4.2 36.6 1.0
HB3 A:ASN452 4.2 31.6 1.0
HB2 B:ASP63 4.3 39.9 1.0
OD1 A:ASN452 4.3 34.3 1.0
CB B:ASP42 4.3 30.5 1.0
OD2 B:ASP63 4.4 34.0 1.0
O B:ASN40 4.4 23.2 1.0
CB B:ASN40 4.5 22.6 1.0
CA B:ASP42 4.5 27.9 1.0
CB B:ASP63 4.6 33.2 1.0
C B:ASN40 4.6 24.6 1.0
CA B:ASN40 4.6 24.3 1.0
CG A:ASN452 4.6 27.7 1.0
HB3 B:ASP42 4.7 36.6 1.0
HD22 B:ASN40 4.7 32.7 1.0
HA B:CYS39 4.7 32.7 1.0
H A:GLY453 4.9 27.1 1.0
N B:ASP42 4.9 29.4 1.0
O A:HOH970 4.9 25.5 1.0
HB3 B:ASN40 4.9 27.2 1.0
CB A:ASN452 4.9 26.4 1.0
H B:ASP42 4.9 35.3 1.0
HE2 B:LYS45 4.9 52.1 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 06:09:38 2025

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