Magnesium in PDB 8pvm: Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D

Enzymatic activity of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D

All present enzymatic activity of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D:
1.12.7.2;

Protein crystallography data

The structure of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D, PDB code: 8pvm 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) 45.06 / 1.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.65, 69.83, 102.89, 90, 102.74, 90
R / Rfree (%) 14.3 / 17.5

Other elements in 8pvm:

The structure of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D also contains other interesting chemical elements:

Iron (Fe) 40 atoms
Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D (pdb code 8pvm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D, PDB code: 8pvm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8pvm

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Magnesium binding site 1 out of 5 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg611

b:16.2
occ:1.00
 OD1 A:ASP42 2.0 18.2 1.0
O A:HOH1022 2.1 19.0 1.0
OD1 A:ASN40 2.1 17.2 1.0
O A:HOH835 2.1 16.7 1.0
O A:HOH875 2.1 17.4 1.0
O A:HOH972 2.1 17.4 1.0
CG A:ASP42 3.2 20.0 1.0
CG A:ASN40 3.2 15.3 1.0
OD2 A:ASP42 3.7 25.2 1.0
ND2 A:ASN40 3.9 14.4 1.0
N A:ASN40 4.1 15.5 1.0
O B:HOH711 4.1 44.8 1.0
O A:HOH701 4.1 31.3 1.0
OD1 B:ASN452 4.2 19.4 1.0
O A:HOH976 4.2 23.6 1.0
O A:HOH892 4.3 24.0 1.0
O A:ASN40 4.3 16.2 1.0
CB A:ASP42 4.3 18.2 1.0
OD2 A:ASP63 4.3 16.8 1.0
CB A:ASP63 4.3 16.1 1.0
O B:HOH799 4.4 21.6 1.0
CB A:ASN40 4.4 15.0 1.0
CG B:ASN452 4.5 17.4 1.0
C A:ASN40 4.5 15.9 1.0
CA A:ASP42 4.5 15.9 1.0
CA A:ASN40 4.5 14.5 1.0
O B:HOH1049 4.7 24.2 1.0
N A:ASP42 4.8 14.9 1.0
CB B:ASN452 4.8 15.3 1.0
CG A:ASP63 4.9 15.9 1.0

Magnesium binding site 2 out of 5 in 8pvm

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Magnesium binding site 2 out of 5 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg612

b:21.4
occ:1.00
 O A:HOH795 2.0 19.8 1.0
O A:HOH964 2.1 29.5 1.0
O A:HOH834 2.1 20.3 1.0
O A:LEU218 2.1 20.1 1.0
O A:HOH905 2.1 21.0 1.0
O A:HOH919 2.1 21.6 1.0
C A:LEU218 3.2 18.7 1.0
CA A:LEU218 3.7 16.8 1.0
OD2 A:ASP263 4.0 19.0 1.0
O A:ALA220 4.1 20.3 1.0
O A:HOH768 4.1 20.7 1.0
O A:ALA217 4.2 18.4 1.0
O A:LYS223 4.2 19.0 1.0
OD1 A:ASP263 4.3 20.1 1.0
N A:ASN219 4.3 18.5 1.0
O A:HOH983 4.4 45.1 1.0
CB A:LEU218 4.6 15.6 1.0
O A:GLY261 4.6 19.4 1.0
CG A:ASP263 4.6 17.9 1.0
CA A:ASN219 4.7 20.7 1.0
O A:HOH884 4.7 51.3 1.0
C A:ASN219 4.8 21.1 1.0
N A:LEU218 4.9 17.1 1.0
N A:ALA220 4.9 19.6 1.0
C A:ALA220 5.0 19.4 1.0
C A:ALA217 5.0 17.2 1.0
CD2 A:LEU218 5.0 17.1 1.0

Magnesium binding site 3 out of 5 in 8pvm

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Magnesium binding site 3 out of 5 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg612

b:25.6
occ:1.00
 OD1 B:ASN40 2.0 23.6 1.0
OD1 B:ASP42 2.0 26.5 1.0
O B:HOH1037 2.0 32.5 1.0
O B:HOH880 2.1 23.6 1.0
O B:HOH785 2.1 27.8 1.0
O B:HOH936 2.1 26.7 1.0
CG B:ASN40 3.1 20.8 1.0
CG B:ASP42 3.2 27.2 1.0
ND2 B:ASN40 3.8 23.1 1.0
OD2 B:ASP42 3.8 30.9 1.0
N B:ASN40 4.1 18.6 1.0
O B:HOH1002 4.1 29.8 1.0
OD1 A:ASN452 4.3 28.4 1.0
CB B:ASN40 4.3 19.2 1.0
O B:ASN40 4.3 19.3 1.0
CB B:ASP42 4.4 24.1 1.0
OD2 B:ASP63 4.4 32.5 1.0
O A:HOH724 4.4 33.1 1.0
CA B:ASN40 4.5 17.7 1.0
CA B:ASP42 4.5 22.2 1.0
C B:ASN40 4.5 17.7 1.0
O A:HOH996 4.5 31.4 1.0
CG A:ASN452 4.5 25.3 1.0
CB B:ASP63 4.6 30.1 1.0
N B:ASP42 4.8 20.8 1.0
CB A:ASN452 4.9 20.6 1.0

Magnesium binding site 4 out of 5 in 8pvm

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Magnesium binding site 4 out of 5 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg613

b:19.2
occ:1.00
 O B:HOH887 2.0 18.8 1.0
O B:HOH938 2.0 20.5 1.0
O B:HOH950 2.1 24.1 1.0
O B:HOH810 2.1 16.7 1.0
O B:HOH901 2.1 19.2 1.0
O B:LEU218 2.1 18.4 1.0
C B:LEU218 3.2 17.2 1.0
CA B:LEU218 3.7 14.8 1.0
OD2 B:ASP263 4.0 17.5 1.0
O B:HOH1224 4.1 45.8 1.0
O B:HOH850 4.1 18.6 1.0
O B:ALA220 4.1 17.7 1.0
O B:ALA217 4.3 16.1 1.0
O B:LYS223 4.3 17.2 1.0
OD1 B:ASP263 4.3 19.2 1.0
N B:ASN219 4.4 17.1 1.0
O B:GLY261 4.5 18.0 1.0
CB B:LEU218 4.6 15.6 1.0
CG B:ASP263 4.6 17.6 1.0
O B:HOH1008 4.6 43.7 1.0
CA B:ASN219 4.8 17.4 1.0
N B:LEU218 4.9 15.2 1.0
O B:HOH994 4.9 33.3 1.0
CD2 B:LEU218 4.9 16.2 1.0
C B:ASN219 4.9 18.6 1.0
CG2 B:VAL225 5.0 14.3 1.0

Magnesium binding site 5 out of 5 in 8pvm

Go back to Magnesium Binding Sites List in 8pvm
Magnesium binding site 5 out of 5 in the Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Formaldehyde-Inhibited [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant C299D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg614

b:27.1
occ:1.00
 O B:HOH969 2.0 29.1 1.0
O B:HOH830 2.1 27.5 1.0
O B:ASN309 3.9 23.4 1.0
OD1 B:ASN189 4.1 20.9 1.0
O B:HOH1153 4.5 49.8 1.0
C B:ASN309 4.9 17.2 1.0

Reference:

J.Duan, A.Veliju, O.Lampret, L.Liu, S.Yadav, U.P.Apfel, F.A.Armstrong, A.Hemschemeier, E.Hofmann. Insights Into the Molecular Mechanism of Formaldehyde Inhibition of [Fefe]-Hydrogenases J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
DOI: 10.1021/JACS.3C07800
Page generated: Fri Oct 4 16:15:30 2024

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