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Magnesium in PDB 5oef: Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Diselenato- Bridged [2FE] Cofactor

Enzymatic activity of Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Diselenato- Bridged [2FE] Cofactor

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

Protein crystallography data

The structure of Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Diselenato- Bridged [2FE] Cofactor, PDB code: 5oef was solved by L.Kertess, J.Esselborn, T.Happe, E.Hofmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.46 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.350, 72.880, 103.100, 90.00, 98.70, 90.00
R / Rfree (%) 23.2 / 26.9

Other elements in 5oef:

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

Iron (Fe) 40 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 5 in 5oef

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Magnesium binding site 1 out of 5 in the Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Diselenato- 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 Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Diselenato- Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:35.8
occ:1.00
 O A:HOH800 2.1 27.1 1.0
O A:HOH775 2.2 34.0 1.0
O A:LEU218 2.4 37.1 1.0
O A:HOH715 2.4 30.6 1.0
O A:HOH717 2.5 29.3 1.0
C A:LEU218 3.5 35.8 1.0
HA A:LEU218 3.7 43.2 1.0
O A:HOH761 3.8 32.9 1.0
OD1 A:ASP263 4.1 34.6 1.0
CA A:LEU218 4.2 36.0 1.0
O A:GLY261 4.2 27.1 1.0
HB3 A:LEU218 4.3 43.4 1.0
OD2 A:ASP263 4.3 30.6 1.0
HA A:ASN219 4.4 50.5 1.0
O A:ALA220 4.5 32.2 1.0
HD23 A:LEU218 4.6 40.0 1.0
N A:ASN219 4.6 36.0 1.0
CG A:ASP263 4.6 34.0 1.0
HD22 A:LEU218 4.7 40.0 1.0
HG23 A:VAL225 4.8 41.6 1.0
CB A:LEU218 4.8 36.2 1.0
O A:LYS223 4.8 29.7 1.0
CA A:ASN219 4.9 42.0 1.0

Magnesium binding site 2 out of 5 in 5oef

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

b:33.9
occ:1.00
 O A:HOH793 2.1 32.3 1.0
O A:HOH884 2.2 29.8 1.0
O A:HOH864 2.2 33.9 1.0
O B:HOH935 2.3 35.5 1.0
OD1 A:ASN40 2.3 30.7 1.0
OD1 A:ASP42 2.4 36.0 1.0
H A:ASN40 3.2 39.9 1.0
CG A:ASN40 3.4 34.7 1.0
CG A:ASP42 3.5 33.3 1.0
HD21 A:ASN40 3.8 43.5 1.0
O A:HOH774 3.9 30.4 1.0
HB3 A:ASP63 4.0 45.8 1.0
OD2 A:ASP42 4.1 36.7 1.0
N A:ASN40 4.1 33.2 1.0
ND2 A:ASN40 4.1 36.2 1.0
HA A:CYS39 4.1 46.5 1.0
HB3 B:ASN452 4.1 35.3 1.0
HB2 A:ASP63 4.4 45.8 1.0
HA A:ASP42 4.4 47.8 1.0
OD1 B:ASN452 4.4 40.0 1.0
O B:HOH815 4.5 37.5 1.0
O A:ASN40 4.5 37.6 1.0
CG B:ASN452 4.6 35.3 1.0
CB A:ASP63 4.6 38.1 1.0
CB A:ASN40 4.6 33.7 1.0
OD2 A:ASP63 4.7 39.8 1.0
CB A:ASP42 4.7 37.1 1.0
O B:HOH894 4.7 33.9 1.0
CA A:ASN40 4.7 35.3 1.0
HB2 A:CYS39 4.8 48.5 1.0
CB B:ASN452 4.8 29.4 1.0
C A:ASN40 4.8 35.1 1.0
HB3 A:ASP42 4.9 44.5 1.0
HB3 A:ASN40 4.9 40.5 1.0
CA A:CYS39 4.9 38.7 1.0
O A:HOH820 4.9 35.8 1.0
HD22 A:ASN40 4.9 43.5 1.0
H B:GLY453 5.0 35.3 1.0
CA A:ASP42 5.0 39.8 1.0
H B:ILE454 5.0 37.5 1.0

Magnesium binding site 3 out of 5 in 5oef

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Magnesium binding site 3 out of 5 in the Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Diselenato- 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 Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Diselenato- Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:33.4
occ:1.00
 O B:HOH772 2.0 26.6 1.0
O B:HOH717 2.1 27.9 1.0
O B:LEU218 2.2 36.0 1.0
O B:HOH745 2.3 24.9 1.0
HA B:LEU218 3.2 38.2 1.0
C B:LEU218 3.2 32.2 1.0
O B:HOH798 3.7 25.2 1.0
CA B:LEU218 3.7 31.8 1.0
O B:ALA220 3.8 32.9 1.0
O B:HOH932 3.9 37.6 1.0
OD2 B:ASP263 4.0 28.4 1.0
O B:LYS223 4.1 29.3 1.0
OD1 B:ASP263 4.1 30.5 1.0
HG23 B:VAL225 4.2 37.0 1.0
HB3 B:LEU218 4.2 41.1 1.0
O B:ALA217 4.3 31.7 1.0
N B:ASN219 4.4 31.8 1.0
HD23 B:LEU218 4.4 39.7 1.0
HA B:PRO221 4.4 45.5 1.0
CG B:ASP263 4.5 31.5 1.0
HA B:ASN219 4.5 44.0 1.0
CB B:LEU218 4.6 34.3 1.0
HG21 B:VAL225 4.7 37.0 1.0
O B:GLY261 4.7 33.9 1.0
C B:ALA220 4.7 35.0 1.0
CA B:ASN219 4.8 36.7 1.0
N B:LEU218 4.9 33.0 1.0
C B:ASN219 4.9 33.6 1.0
CG2 B:VAL225 4.9 30.8 1.0
HD22 B:LEU218 4.9 39.7 1.0
N B:ALA220 5.0 33.7 1.0

Magnesium binding site 4 out of 5 in 5oef

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Magnesium binding site 4 out of 5 in the Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Diselenato- 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 Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Diselenato- Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:53.4
occ:1.00
 O B:HOH906 4.0 36.8 1.0
OD1 B:ASN309 4.0 30.1 1.0
HA B:ASN309 4.4 39.3 1.0
OD1 B:ASN189 4.7 35.2 1.0
O B:HOH859 4.7 34.2 1.0
CG B:ASN309 4.9 35.2 1.0

Magnesium binding site 5 out of 5 in 5oef

Go back to Magnesium Binding Sites List in 5oef
Magnesium binding site 5 out of 5 in the Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Diselenato- 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 Active Semisynthetic [Fefe]-Hydrogenase Cpi with Aza-Diselenato- Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg609

b:56.1
occ:1.00
 OD1 B:ASN44 3.2 56.7 1.0
HA B:ASN44 3.3 57.0 1.0
O A:HOH736 3.3 47.0 1.0
O B:HOH899 3.9 47.9 1.0
OE1 A:GLU456 4.1 48.5 1.0
OE2 A:GLU456 4.1 47.2 1.0
H B:LYS45 4.2 51.0 1.0
CA B:ASN44 4.2 47.5 1.0
CG B:ASN44 4.3 56.2 1.0
O B:ILE43 4.4 52.3 1.0
CD A:GLU456 4.5 43.7 1.0
N B:LYS45 4.6 42.5 1.0
CB B:ASN44 4.7 50.4 1.0
O A:HOH953 4.7 47.7 1.0
C B:ASN44 4.8 44.9 1.0
HB2 B:ASN44 4.8 60.5 1.0
O B:LYS45 4.9 43.7 1.0

Reference:

L.Kertess, F.Wittkamp, C.Sommer, J.Esselborn, O.Rudiger, E.J.Reijerse, E.Hofmann, W.Lubitz, M.Winkler, T.Happe, U.P.Apfel. Chalcogenide Substitution in the [2FE] Cluster of [Fefe]-Hydrogenases Conserves High Enzymatic Activity. Dalton Trans V. 46 16947 2017.
ISSN: ESSN 1477-9234
PubMed: 29177350
DOI: 10.1039/C7DT03785F
Page generated: Mon Dec 14 20:59:39 2020

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