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Magnesium in PDB 6gm4: [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A

Enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A

All present enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A:
1.12.7.2;

Protein crystallography data

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A, PDB code: 6gm4 was solved by J.Duan, J.Esselborn, E.Hofmann, M.Winkler, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.84 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.070, 73.330, 103.250, 90.00, 96.46, 90.00
R / Rfree (%) 16.4 / 20.2

Other elements in 6gm4:

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A also contains other interesting chemical elements:

Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A (pdb code 6gm4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A, PDB code: 6gm4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6gm4

Go back to Magnesium Binding Sites List in 6gm4
Magnesium binding site 1 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:25.6
occ:1.00
 O A:HOH921 2.1 27.9 1.0
OD1 A:ASP42 2.1 26.8 1.0
O A:HOH774 2.1 22.9 1.0
O A:HOH805 2.1 22.7 1.0
O A:HOH881 2.1 24.3 1.0
OD1 A:ASN40 2.1 24.8 1.0
CG A:ASN40 3.2 25.3 1.0
CG A:ASP42 3.2 31.3 1.0
ND2 A:ASN40 3.8 20.1 1.0
OD2 A:ASP42 3.8 31.6 1.0
O A:HOH704 4.0 29.1 1.0
OD1 B:ASN452 4.1 32.5 1.0
O B:HOH716 4.2 34.2 1.0
N A:ASN40 4.2 18.8 1.0
O A:HOH918 4.3 38.4 1.0
O A:ASN40 4.4 24.8 1.0
CB A:ASP42 4.4 24.1 1.0
CB A:ASN40 4.5 22.2 1.0
CB A:ASP63 4.5 21.0 1.0
CG B:ASN452 4.5 33.3 1.0
OD2 A:ASP63 4.5 26.7 1.0
CA A:ASP42 4.6 26.0 1.0
C A:ASN40 4.6 24.8 1.0
CA A:ASN40 4.7 26.7 1.0
O B:HOH933 4.7 25.0 1.0
O A:HOH882 4.7 32.3 1.0
N A:ASP42 4.8 25.5 1.0
CB B:ASN452 4.9 20.2 1.0
O A:HOH807 5.0 37.7 1.0

Magnesium binding site 2 out of 4 in 6gm4

Go back to Magnesium Binding Sites List in 6gm4
Magnesium binding site 2 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:27.5
occ:0.86
 O A:HOH862 2.1 27.0 1.0
O A:HOH731 2.1 19.9 1.0
O A:HOH756 2.1 29.8 1.0
O A:HOH865 2.1 28.6 1.0
O A:HOH883 2.1 25.8 1.0
O A:LEU218 2.1 28.7 1.0
C A:LEU218 3.2 25.5 1.0
CA A:LEU218 3.8 24.2 1.0
O A:ALA220 4.0 26.0 1.0
OD2 A:ASP263 4.1 25.8 1.0
O A:LYS223 4.2 21.6 1.0
O A:HOH851 4.2 23.1 1.0
O A:ALA217 4.3 23.6 1.0
OD1 A:ASP263 4.3 25.0 1.0
N A:ASN219 4.3 26.6 1.0
CG A:ASP263 4.6 25.3 1.0
CA A:ASN219 4.6 30.0 1.0
CB A:LEU218 4.7 19.2 1.0
O A:GLY261 4.7 27.3 1.0
O A:HOH738 4.8 41.5 1.0
C A:ASN219 4.8 29.4 1.0
C A:ALA220 4.8 26.3 1.0
N A:ALA220 4.8 23.2 1.0
N A:LEU218 4.9 20.2 1.0
CG2 A:VAL225 5.0 22.6 1.0

Magnesium binding site 3 out of 4 in 6gm4

Go back to Magnesium Binding Sites List in 6gm4
Magnesium binding site 3 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:26.5
occ:1.00
 O B:HOH790 2.1 20.3 1.0
O B:HOH812 2.1 27.7 1.0
O B:HOH930 2.1 24.7 1.0
O B:HOH740 2.1 25.6 1.0
O B:HOH873 2.1 24.4 1.0
O B:LEU218 2.1 29.4 1.0
C B:LEU218 3.2 24.7 1.0
CA B:LEU218 3.8 24.6 1.0
OD2 B:ASP263 4.0 21.3 1.0
O B:HOH784 4.1 23.2 1.0
O B:ALA220 4.1 25.4 1.0
O B:LYS223 4.2 26.0 1.0
O B:ALA217 4.3 26.1 1.0
OD1 B:ASP263 4.3 22.2 1.0
N B:ASN219 4.3 25.1 1.0
O B:HOH931 4.5 42.0 1.0
CG B:ASP263 4.5 24.3 1.0
O B:GLY261 4.6 21.8 1.0
CB B:LEU218 4.7 25.4 1.0
CA B:ASN219 4.7 30.1 1.0
O B:HOH1056 4.8 49.2 1.0
C B:ASN219 4.8 26.7 1.0
C B:ALA220 4.9 26.4 1.0
N B:ALA220 4.9 22.7 1.0
N B:LEU218 4.9 15.3 1.0
CG2 B:VAL225 5.0 19.3 1.0

Magnesium binding site 4 out of 4 in 6gm4

Go back to Magnesium Binding Sites List in 6gm4
Magnesium binding site 4 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:22.1
occ:0.77
 ND2 B:ASN40 1.9 37.3 1.0
O B:HOH732 2.1 34.1 1.0
O B:HOH701 2.1 30.2 1.0
OD1 B:ASP42 2.1 29.1 1.0
O B:HOH809 2.1 26.3 1.0
O B:HOH748 2.1 32.3 1.0
OD1 B:ASN40 2.1 42.2 1.0
CG B:ASN40 2.3 19.7 1.0
CG B:ASP42 3.2 31.0 1.0
CB B:ASN40 3.7 28.8 1.0
OD2 B:ASP42 3.8 39.8 1.0
N B:ASN40 3.9 24.2 1.0
CA B:ASN40 4.3 28.6 1.0
OD2 B:ASP63 4.3 32.1 1.0
O B:ASN40 4.3 26.0 1.0
C B:ASN40 4.4 24.2 1.0
OD1 A:ASN452 4.4 32.5 1.0
CB B:ASP42 4.4 28.6 1.0
CB B:ASP63 4.4 31.3 1.0
O A:HOH720 4.5 37.0 1.0
CA B:ASP42 4.5 27.6 1.0
CG A:ASN452 4.6 29.5 1.0
N B:ASP42 4.7 24.5 1.0
CG B:ASP63 4.9 33.6 1.0
O A:HOH941 5.0 29.6 1.0

Reference:

J.Duan, M.Senger, J.Esselborn, V.Engelbrecht, F.Wittkamp, U.P.Apfel, E.Hofmann, S.T.Stripp, T.Happe, M.Winkler. Crystallographic and Spectroscopic Assignment of the Proton Transfer Pathway in [Fefe]-Hydrogenases. Nat Commun V. 9 4726 2018.
ISSN: ESSN 2041-1723
PubMed: 30413719
DOI: 10.1038/S41467-018-07140-X
Page generated: Tue Oct 1 01:15:56 2024

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