Atomistry » Magnesium » PDB 5odz-5onh » 5oef
Atomistry »
  Magnesium »
    PDB 5odz-5onh »
      5oef »

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

Go back to Magnesium Binding Sites List in 5oef
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

Go back to Magnesium Binding Sites List in 5oef
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

Go back to Magnesium Binding Sites List in 5oef
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

Go back to Magnesium Binding Sites List in 5oef
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 Sep 30 00:56:59 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy