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Magnesium in PDB 7qhf: [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S

Enzymatic activity of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S

All present enzymatic activity of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S:
1.12.7.2;

Protein crystallography data

The structure of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S, PDB code: 7qhf was solved by C.Brocks, J.Duan, E.Hofmann, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.53 / 1.63
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.49, 72.22, 102.92, 90, 97.32, 90
R / Rfree (%) 16.9 / 19.2

Other elements in 7qhf:

The structure of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S also contains other interesting chemical elements:

Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S (pdb code 7qhf). 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 I From Clostridium Pasteurianum (Cpi), Variant G302S, PDB code: 7qhf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7qhf

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Magnesium binding site 1 out of 4 in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:35.2
occ:1.00
 O A:HOH801 2.0 31.9 1.0
O A:HOH894 2.0 36.2 1.0
O A:LEU218 2.0 31.2 1.0
O A:HOH761 2.1 28.3 1.0
O A:HOH915 2.1 32.2 1.0
O A:HOH892 2.1 33.8 1.0
C A:LEU218 3.1 30.9 1.0
CA A:LEU218 3.7 27.9 1.0
O A:ALA220 4.0 31.4 1.0
OD2 A:ASP263 4.0 29.2 1.0
O A:HOH763 4.1 28.5 1.0
O A:ALA217 4.2 27.1 1.0
N A:ASN219 4.3 28.9 1.0
O A:LYS223 4.3 27.8 1.0
OD1 A:ASP263 4.4 31.3 1.0
CB A:LEU218 4.5 25.6 1.0
O A:HOH1105 4.5 49.8 1.0
O A:GLY261 4.6 29.8 1.0
CG A:ASP263 4.7 32.6 1.0
CA A:ASN219 4.7 34.1 1.0
C A:ASN219 4.8 31.8 1.0
N A:LEU218 4.8 26.0 1.0
N A:ALA220 4.8 29.0 1.0
C A:ALA220 4.9 31.1 1.0
CG2 A:VAL225 4.9 26.4 1.0
C A:ALA217 4.9 28.9 1.0

Magnesium binding site 2 out of 4 in 7qhf

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Magnesium binding site 2 out of 4 in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg609

b:27.8
occ:1.00
 OD1 A:ASP42 2.0 29.6 1.0
O A:HOH830 2.0 30.4 1.0
OD1 A:ASN40 2.0 27.3 1.0
O A:HOH859 2.1 29.9 1.0
O A:HOH964 2.1 32.1 1.0
O A:HOH888 2.2 31.4 1.0
CG A:ASP42 3.1 34.3 1.0
CG A:ASN40 3.2 27.8 1.0
OD2 A:ASP42 3.7 40.1 1.0
ND2 A:ASN40 3.8 28.0 1.0
O A:HOH713 3.9 32.4 1.0
N A:ASN40 4.0 26.0 1.0
O B:HOH723 4.1 38.3 1.0
O A:HOH1031 4.2 38.3 1.0
O A:ASN40 4.2 27.3 1.0
O A:HOH918 4.3 38.2 1.0
CB A:ASP42 4.3 29.3 1.0
OD2 A:ASP63 4.3 30.0 1.0
O B:HOH720 4.4 41.1 1.0
OD1 B:ASN452 4.4 38.7 1.0
CB A:ASN40 4.4 25.6 1.0
CB A:ASP63 4.4 28.1 1.0
C A:ASN40 4.4 26.8 1.0
CA A:ASP42 4.5 30.0 1.0
CA A:ASN40 4.5 25.7 1.0
CG B:ASN452 4.6 34.0 1.0
N A:ASP42 4.7 27.2 1.0
O B:HOH942 4.8 31.6 1.0
CB B:ASN452 4.9 26.3 1.0
CG A:ASP63 4.9 29.4 1.0

Magnesium binding site 3 out of 4 in 7qhf

Go back to Magnesium Binding Sites List in 7qhf
Magnesium binding site 3 out of 4 in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:32.2
occ:1.00
 O B:HOH823 1.9 26.2 1.0
O B:HOH944 2.0 32.4 1.0
O B:HOH798 2.1 27.7 1.0
O B:HOH907 2.1 35.1 1.0
O B:LEU218 2.2 29.9 1.0
O B:HOH841 2.3 33.3 1.0
C B:LEU218 3.2 27.7 1.0
CA B:LEU218 3.8 25.9 1.0
O B:HOH783 4.0 29.7 1.0
OD2 B:ASP263 4.0 28.1 1.0
O B:ALA220 4.0 30.6 1.0
O B:LYS223 4.1 28.5 1.0
O B:ALA217 4.2 28.5 1.0
OD1 B:ASP263 4.3 28.3 1.0
N B:ASN219 4.4 27.9 1.0
CG B:ASP263 4.6 31.1 1.0
CB B:LEU218 4.7 27.7 1.0
O B:GLY261 4.7 28.4 1.0
CA B:ASN219 4.8 33.3 1.0
C B:ASN219 4.8 33.0 1.0
O B:HOH741 4.8 42.1 1.0
N B:ALA220 4.9 30.2 1.0
C B:ALA220 4.9 33.5 1.0
N B:LEU218 4.9 24.0 1.0
CG2 B:VAL225 4.9 26.7 1.0
O B:HOH972 5.0 47.9 1.0
C B:ALA217 5.0 28.9 1.0

Magnesium binding site 4 out of 4 in 7qhf

Go back to Magnesium Binding Sites List in 7qhf
Magnesium binding site 4 out of 4 in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg609

b:38.4
occ:1.00
 O B:HOH970 1.9 42.8 1.0
O B:HOH817 2.0 35.0 1.0
OD1 B:ASP42 2.0 36.5 1.0
OD1 B:ASN40 2.1 32.4 1.0
O B:HOH967 2.2 37.4 1.0
O B:HOH761 2.3 41.7 1.0
CG B:ASP42 3.2 36.0 1.0
CG B:ASN40 3.2 31.3 1.0
O B:HOH707 3.7 41.0 1.0
OD2 B:ASP42 3.8 41.3 1.0
ND2 B:ASN40 3.9 34.2 1.0
N B:ASN40 4.0 29.3 1.0
O B:ASN40 4.2 29.5 1.0
OD2 B:ASP63 4.3 36.6 1.0
O A:HOH819 4.3 38.5 1.0
CB B:ASP42 4.4 35.2 1.0
CB B:ASN40 4.4 26.0 1.0
C B:ASN40 4.5 25.2 1.0
CA B:ASN40 4.5 29.4 1.0
CA B:ASP42 4.5 32.5 1.0
ND2 A:ASN452 4.6 40.2 1.0
CG A:ASN452 4.7 36.4 1.0
CB B:ASP63 4.8 35.9 1.0
N B:ASP42 4.8 29.1 1.0
OD1 A:ASN452 4.9 39.4 1.0
O A:HOH984 4.9 38.1 1.0
CB A:ASN452 5.0 30.5 1.0

Reference:

C.Brocks, C.K.Das, J.Duan, E.Hofmann, M.Winkler, L.Schaefer, V.Engelbrecht, T.Happe. Intruder Protection: Manipulating the Pathways of Ros Diffusion in [Fefe]-Hydrogenases To Be Published.
Page generated: Thu Dec 28 07:49:08 2023

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