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Magnesium in PDB 8aio: Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi)

Enzymatic activity of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi)

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

Protein crystallography data

The structure of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), PDB code: 8aio was solved by 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) 40.03 / 1.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.6, 72.16, 103.21, 90, 101.94, 90
R / Rfree (%) 16.7 / 19.2

Other elements in 8aio:

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

Iron (Fe) 40 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) (pdb code 8aio). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), PDB code: 8aio:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8aio

Go back to Magnesium Binding Sites List in 8aio
Magnesium binding site 1 out of 4 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:24.2
occ:1.00
 O A:HOH867 2.0 28.1 1.0
O A:HOH796 2.1 22.6 1.0
O A:HOH797 2.1 22.8 1.0
O A:LEU218 2.1 23.3 1.0
O A:HOH792 2.1 25.6 1.0
O A:HOH860 2.1 26.3 1.0
C A:LEU218 3.2 22.9 1.0
HA A:LEU218 3.3 26.4 1.0
CA A:LEU218 3.7 22.0 1.0
OD2 A:ASP263 3.9 22.6 1.0
O A:ALA220 4.1 23.6 1.0
O A:HOH1098 4.1 47.3 1.0
O A:HOH774 4.2 22.7 1.0
O A:ALA217 4.2 21.7 1.0
HA A:ASN219 4.2 30.9 1.0
OD1 A:ASP263 4.2 24.4 1.0
HB3 A:LEU218 4.2 27.4 1.0
O A:LYS223 4.3 23.1 1.0
N A:ASN219 4.3 21.4 1.0
HG23 A:VAL225 4.3 23.1 1.0
O A:HOH1012 4.3 47.6 1.0
HD21 A:LEU218 4.5 30.5 1.0
CG A:ASP263 4.5 27.6 1.0
O A:GLY261 4.6 23.4 1.0
CB A:LEU218 4.6 22.8 1.0
CA A:ASN219 4.7 25.7 1.0
HD23 A:LEU218 4.7 30.5 1.0
C A:ASN219 4.8 24.7 1.0
N A:LEU218 4.9 22.1 1.0
HG21 A:VAL225 4.9 23.1 1.0
O A:HOH946 5.0 45.4 1.0
HA A:PRO221 5.0 32.7 1.0
H A:ALA220 5.0 28.1 1.0
N A:ALA220 5.0 23.4 1.0

Magnesium binding site 2 out of 4 in 8aio

Go back to Magnesium Binding Sites List in 8aio
Magnesium binding site 2 out of 4 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi)


Mono view


Stereo pair view

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

b:21.4
occ:1.00
 OD1 A:ASP42 2.0 24.7 1.0
OD1 A:ASN40 2.0 23.0 1.0
O B:HOH936 2.1 25.1 1.0
O A:HOH856 2.1 22.8 1.0
O A:HOH872 2.1 24.1 1.0
O A:HOH862 2.1 20.9 1.0
CG A:ASP42 3.2 27.7 1.0
CG A:ASN40 3.2 24.0 1.0
H A:ASN40 3.3 25.3 1.0
HD21 A:ASN40 3.6 29.2 1.0
OD2 A:ASP42 3.7 34.0 1.0
ND2 A:ASN40 3.8 24.3 1.0
HB3 A:ASP63 3.9 24.8 1.0
HA A:ASP42 3.9 25.7 1.0
HB2 A:ASP63 3.9 24.8 1.0
O A:HOH718 4.0 28.3 1.0
OD1 B:ASN452 4.1 28.7 1.0
N A:ASN40 4.1 21.1 1.0
O A:HOH1002 4.2 30.2 1.0
HB3 B:ASN452 4.2 24.5 1.0
O B:HOH726 4.3 32.1 1.0
O A:HOH863 4.3 33.2 1.0
CB A:ASP42 4.3 23.4 1.0
CB A:ASP63 4.4 20.7 1.0
O A:ASN40 4.4 20.7 1.0
OD2 A:ASP63 4.4 23.6 1.0
CB A:ASN40 4.4 19.6 1.0
CG B:ASN452 4.5 28.5 1.0
O B:HOH725 4.5 29.8 1.0
CA A:ASP42 4.5 21.4 1.0
C A:ASN40 4.5 21.6 1.0
HB3 A:ASP42 4.5 28.1 1.0
CA A:ASN40 4.6 21.3 1.0
HA A:CYS39 4.6 25.0 0.5
O B:HOH982 4.6 23.7 1.0
HD22 A:ASN40 4.7 29.2 1.0
HA A:CYS39 4.7 25.1 0.5
HB3 A:ASN40 4.7 23.5 1.0
HB2 A:CYS39 4.8 31.3 0.5
CB B:ASN452 4.9 20.4 1.0
N A:ASP42 4.9 21.8 1.0
H B:GLY453 4.9 22.3 1.0
CG A:ASP63 4.9 21.9 1.0
H A:ASP42 5.0 26.2 1.0

Magnesium binding site 3 out of 4 in 8aio

Go back to Magnesium Binding Sites List in 8aio
Magnesium binding site 3 out of 4 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi)


Mono view


Stereo pair view

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

b:26.0
occ:1.00
 O B:HOH764 2.1 21.6 1.0
O B:HOH843 2.1 22.9 1.0
O B:HOH887 2.1 28.5 1.0
O B:HOH759 2.1 22.5 1.0
O B:HOH909 2.1 26.1 1.0
O B:LEU218 2.1 22.7 1.0
C B:LEU218 3.2 20.4 1.0
HA B:LEU218 3.3 25.8 1.0
CA B:LEU218 3.8 21.5 1.0
OD2 B:ASP263 4.0 21.2 1.0
O B:ALA220 4.0 24.9 1.0
HG22 B:VAL225 4.1 23.9 1.0
O B:HOH830 4.1 22.5 1.0
O B:ALA217 4.2 22.6 1.0
O B:LYS223 4.2 21.1 1.0
OD1 B:ASP263 4.3 23.7 1.0
HB3 B:LEU218 4.3 28.8 1.0
HA B:ASN219 4.3 30.1 1.0
N B:ASN219 4.3 23.6 1.0
HD23 B:LEU218 4.5 28.2 1.0
O B:GLY261 4.6 21.0 1.0
CG B:ASP263 4.6 24.7 1.0
CB B:LEU218 4.7 24.0 1.0
HD22 B:LEU218 4.7 28.2 1.0
CA B:ASN219 4.7 25.1 1.0
HA B:PRO221 4.9 34.6 1.0
H B:ALA220 4.9 26.9 1.0
C B:ASN219 4.9 28.6 1.0
N B:LEU218 4.9 20.9 1.0
N B:ALA220 5.0 22.4 1.0
C B:ALA220 5.0 24.4 1.0
CD2 B:LEU218 5.0 23.5 1.0

Magnesium binding site 4 out of 4 in 8aio

Go back to Magnesium Binding Sites List in 8aio
Magnesium binding site 4 out of 4 in the Co-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi)


Mono view


Stereo pair view

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

b:30.7
occ:1.00
 OD1 B:ASP42 2.0 29.2 1.0
O B:HOH890 2.1 35.1 1.0
O B:HOH974 2.1 35.6 1.0
O B:HOH836 2.1 32.7 1.0
OD1 B:ASN40 2.1 27.6 1.0
O B:HOH889 2.1 32.2 1.0
CG B:ASP42 3.1 29.9 1.0
CG B:ASN40 3.2 27.5 1.0
ND2 B:ASN40 3.8 29.0 1.0
OD2 B:ASP42 3.8 38.4 1.0
HA B:ASP42 3.9 34.5 1.0
HB3 B:ASP63 4.1 33.7 1.0
N B:ASN40 4.1 29.4 1.0
CB B:ASP42 4.3 28.6 1.0
OD1 A:ASN452 4.3 37.3 1.0
O A:HOH755 4.3 37.8 1.0
O B:ASN40 4.4 26.2 1.0
HB2 B:ASP63 4.4 33.7 1.0
CB B:ASN40 4.4 23.3 1.0
OD2 B:ASP63 4.4 31.7 1.0
CA B:ASP42 4.5 28.8 1.0
HB3 B:ASP42 4.5 34.4 1.0
HB3 A:ASN452 4.5 33.6 1.0
C B:ASN40 4.6 25.9 1.0
CA B:ASN40 4.6 24.1 1.0
HA B:CYS39 4.6 34.0 0.3
CG A:ASN452 4.7 31.9 1.0
CB B:ASP63 4.7 28.1 1.0
HA B:CYS39 4.7 34.0 0.7
HE2 B:LYS45 4.8 58.8 1.0
N B:ASP42 4.8 27.4 1.0
O A:HOH977 4.8 31.4 1.0
H B:ASP42 4.9 32.9 1.0
H A:GLY453 4.9 24.1 1.0

Reference:

J.Duan, A.Hemschemeier, D.J.Burr, S.T.Stripp, E.Hofmann, T.Happe. Cyanide Binding to [Fefe]-Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway. Angew.Chem.Int.Ed.Engl. 2022.
ISSN: ESSN 1521-3773
PubMed: 36464641
DOI: 10.1002/ANIE.202216903
Page generated: Thu Oct 3 18:08:00 2024

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