Magnesium in PDB 8aj6: Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi)

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

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

Protein crystallography data

The structure of Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), PDB code: 8aj6 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) 47.62 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.18, 72.48, 103.71, 90, 98.01, 90
R / Rfree (%) 17.5 / 19.9

Other elements in 8aj6:

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

Chlorine (Cl) 1 atom
Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) (pdb code 8aj6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), PDB code: 8aj6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8aj6

Go back to Magnesium Binding Sites List in 8aj6
Magnesium binding site 1 out of 4 in the Cyanide-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 Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:25.1
occ:1.00
 O A:HOH915 2.0 26.6 1.0
O A:HOH780 2.1 22.9 1.0
O A:HOH795 2.1 26.8 1.0
O A:HOH946 2.1 29.9 1.0
O A:HOH996 2.1 26.9 1.0
O A:LEU218 2.2 26.0 1.0
C A:LEU218 3.2 23.8 1.0
CA A:LEU218 3.8 23.1 1.0
OD2 A:ASP263 4.0 22.9 1.0
O A:HOH1265 4.0 46.7 1.0
O A:ALA220 4.1 24.8 1.0
O A:HOH818 4.2 23.4 1.0
O A:LYS223 4.2 20.6 1.0
O A:ALA217 4.3 25.0 1.0
OD1 A:ASP263 4.3 26.2 1.0
O A:HOH968 4.3 39.1 1.0
N A:ASN219 4.4 23.4 1.0
O A:GLY261 4.5 24.6 1.0
CG A:ASP263 4.6 26.1 1.0
CB A:LEU218 4.6 23.2 1.0
CA A:ASN219 4.8 26.2 1.0
C A:ASN219 4.9 26.8 1.0
N A:LEU218 4.9 22.4 1.0
N A:ALA220 5.0 22.0 1.0
CG2 A:VAL225 5.0 22.3 1.0
C A:ALA220 5.0 25.9 1.0

Magnesium binding site 2 out of 4 in 8aj6

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Magnesium binding site 2 out of 4 in the Cyanide-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 Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:23.9
occ:1.00
 OD1 A:ASP42 2.0 25.6 1.0
O A:HOH955 2.0 24.2 1.0
OD1 A:ASN40 2.1 22.2 1.0
O A:HOH1088 2.1 28.4 1.0
O A:HOH1051 2.1 26.5 1.0
O A:HOH804 2.2 23.7 1.0
CG A:ASP42 3.0 27.9 1.0
CG A:ASN40 3.3 24.4 1.0
OD2 A:ASP42 3.4 33.2 1.0
N A:ASN40 3.9 20.1 1.0
O A:HOH709 4.0 30.2 1.0
ND2 A:ASN40 4.0 21.1 1.0
O A:ASN40 4.1 22.8 1.0
O B:HOH892 4.2 27.6 1.0
CB A:ASP42 4.4 23.8 1.0
OD2 A:ASP63 4.4 22.1 1.0
CB A:ASN40 4.4 21.9 1.0
CA A:ASN40 4.5 22.6 1.0
C A:ASN40 4.5 22.7 1.0
CB A:ASP63 4.5 22.3 1.0
CG B:ASN452 4.6 28.3 1.0
CA A:ASP42 4.7 21.7 1.0
OD1 B:ASN452 4.7 35.6 1.0
ND2 B:ASN452 4.9 26.9 1.0
N A:ASP42 4.9 21.9 1.0
CB B:ASN452 4.9 22.6 1.0
O B:HOH1060 4.9 31.6 1.0
CG A:ASP63 5.0 24.6 1.0
O A:HOH1002 5.0 42.0 1.0
C A:CYS39 5.0 23.9 1.0

Magnesium binding site 3 out of 4 in 8aj6

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Magnesium binding site 3 out of 4 in the Cyanide-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 Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:25.0
occ:1.00
 O B:HOH1028 2.0 28.7 1.0
O B:HOH991 2.0 25.6 1.0
O B:HOH1003 2.1 24.8 1.0
O B:HOH830 2.1 21.9 1.0
O B:HOH772 2.1 22.2 1.0
O B:LEU218 2.2 25.6 1.0
C B:LEU218 3.3 26.2 1.0
CA B:LEU218 3.8 23.3 1.0
OD2 B:ASP263 4.0 23.2 1.0
O B:HOH889 4.1 38.8 1.0
O B:ALA220 4.1 25.4 1.0
O B:HOH798 4.2 25.3 1.0
O B:LYS223 4.3 23.2 1.0
OD1 B:ASP263 4.3 25.6 1.0
O B:ALA217 4.3 22.6 1.0
N B:ASN219 4.4 25.1 1.0
O B:GLY261 4.6 21.9 1.0
CG B:ASP263 4.6 23.6 1.0
CB B:LEU218 4.7 23.2 1.0
CA B:ASN219 4.8 28.5 1.0
O B:HOH982 4.8 43.6 1.0
O B:HOH788 4.9 39.0 1.0
C B:ASN219 4.9 25.6 1.0
CD2 B:LEU218 5.0 25.3 1.0
N B:LEU218 5.0 21.6 1.0

Magnesium binding site 4 out of 4 in 8aj6

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Magnesium binding site 4 out of 4 in the Cyanide-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 Cyanide-Bound [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg610

b:30.9
occ:1.00
 OD1 B:ASN40 2.0 28.6 1.0
O B:HOH979 2.0 28.7 1.0
O B:HOH926 2.1 28.4 1.0
O B:HOH809 2.1 31.4 1.0
O B:HOH1010 2.1 36.0 1.0
OD1 B:ASP42 2.1 31.2 1.0
CG B:ASP42 3.1 31.3 1.0
CG B:ASN40 3.2 29.4 1.0
OD2 B:ASP42 3.5 37.6 1.0
ND2 B:ASN40 3.8 29.8 1.0
O A:HOH1145 3.9 40.1 1.0
N B:ASN40 3.9 26.4 1.0
O A:HOH879 4.0 30.0 1.0
O B:HOH701 4.1 29.4 1.0
O B:ASN40 4.3 24.0 1.0
OD2 B:ASP63 4.3 29.4 1.0
ND2 A:ASN452 4.4 31.6 1.0
CB B:ASN40 4.4 26.4 1.0
CB B:ASP42 4.5 27.6 1.0
CA B:ASN40 4.5 26.8 1.0
CB B:ASP63 4.5 31.6 1.0
CG A:ASN452 4.6 31.5 1.0
C B:ASN40 4.6 24.9 1.0
CA B:ASP42 4.8 29.8 1.0
OD1 A:ASN452 4.9 34.0 1.0
CB A:ASN452 4.9 27.2 1.0
CG B:ASP63 5.0 30.3 1.0
C B:CYS39 5.0 30.2 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: Fri Apr 7 06:06:33 2023

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