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Magnesium in PDB 8qm3: Formaldehyde-Inhibited [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi)

Enzymatic activity of Formaldehyde-Inhibited [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi)

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

Protein crystallography data

The structure of Formaldehyde-Inhibited [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), PDB code: 8qm3 was solved by J.Duan, E.Hofmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.95 / 1.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.29, 69.77, 102.64, 90, 102.74, 90
R / Rfree (%) 16.2 / 19.4

Other elements in 8qm3:

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

Chlorine (Cl) 7 atoms
Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Formaldehyde-Inhibited [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) (pdb code 8qm3). 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 I From Clostridium Pasteurianum (Cpi), PDB code: 8qm3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8qm3

Go back to Magnesium Binding Sites List in 8qm3
Magnesium binding site 1 out of 5 in the Formaldehyde-Inhibited [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 Formaldehyde-Inhibited [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg615

b:24.6
occ:1.00
 O A:HOH866 2.0 23.8 1.0
O A:HOH758 2.1 22.5 1.0
O A:HOH905 2.1 22.1 1.0
O A:HOH919 2.1 27.0 1.0
O A:LEU218 2.1 23.6 1.0
O A:HOH789 2.1 21.3 1.0
C A:LEU218 3.2 22.1 1.0
HA A:LEU218 3.2 23.0 1.0
CA A:LEU218 3.7 19.1 1.0
OD2 A:ASP263 4.0 21.6 1.0
O A:ALA220 4.1 22.8 1.0
O A:HOH745 4.1 22.9 1.0
O A:HOH1105 4.2 52.6 1.0
O A:ALA217 4.2 20.7 1.0
HG23 A:VAL225 4.2 22.9 1.0
O A:LYS223 4.2 21.0 1.0
HB3 A:LEU218 4.2 26.6 1.0
HA A:ASN219 4.3 26.9 1.0
OD1 A:ASP263 4.3 22.8 1.0
N A:ASN219 4.3 20.9 1.0
HD23 A:LEU218 4.4 24.7 1.0
O A:GLY261 4.6 22.1 1.0
HD22 A:LEU218 4.6 24.7 1.0
CB A:LEU218 4.6 22.1 1.0
CG A:ASP263 4.6 25.3 1.0
CA A:ASN219 4.7 22.4 1.0
O A:HOH1001 4.7 44.0 1.0
C A:ASN219 4.8 25.3 1.0
N A:LEU218 4.9 19.8 1.0
HG21 A:VAL225 4.9 22.9 1.0
HA A:PRO221 4.9 26.0 1.0
CD2 A:LEU218 4.9 20.6 1.0
C A:ALA220 4.9 21.1 1.0
N A:ALA220 5.0 20.7 1.0
CG2 A:VAL225 5.0 19.0 1.0
C A:ALA217 5.0 22.2 1.0
H A:ALA220 5.0 24.8 1.0

Magnesium binding site 2 out of 5 in 8qm3

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Magnesium binding site 2 out of 5 in the Formaldehyde-Inhibited [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 Formaldehyde-Inhibited [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg616

b:19.4
occ:1.00
 OD1 A:ASP42 2.0 22.6 1.0
O B:HOH960 2.1 22.2 1.0
O A:HOH800 2.1 19.2 1.0
OD1 A:ASN40 2.1 18.9 1.0
O A:HOH929 2.1 18.3 1.0
O A:HOH828 2.2 20.1 1.0
CG A:ASP42 3.2 24.2 1.0
H A:ASN40 3.3 22.5 1.0
CG A:ASN40 3.3 18.8 1.0
HD21 A:ASN40 3.7 23.1 1.0
OD2 A:ASP42 3.8 37.0 1.0
HA A:ASP42 3.9 20.9 1.0
ND2 A:ASN40 3.9 19.3 1.0
HB3 A:ASP63 3.9 22.9 1.0
HB2 A:ASP63 4.0 22.9 1.0
N A:ASN40 4.1 18.7 1.0
O A:HOH713 4.1 34.5 1.0
HB3 B:ASN452 4.1 24.6 1.0
O A:HOH726 4.1 32.9 1.0
OD1 B:ASN452 4.1 23.1 1.0
O A:HOH906 4.2 25.0 1.0
O A:ASN40 4.3 20.0 1.0
CB A:ASP42 4.3 20.3 1.0
O A:HOH865 4.3 23.6 1.0
OD2 A:ASP63 4.4 17.8 1.0
CB A:ASP63 4.4 19.1 1.0
HB3 A:ASP42 4.4 24.4 1.0
CG B:ASN452 4.4 23.5 1.0
CB A:ASN40 4.4 17.0 1.0
C A:ASN40 4.5 18.0 1.0
CA A:ASP42 4.5 17.4 1.0
O B:HOH803 4.5 22.5 1.0
CA A:ASN40 4.5 16.1 1.0
HA A:CYS39 4.5 21.4 1.0
O B:HOH1019 4.6 21.8 1.0
HD22 A:ASN40 4.8 23.1 1.0
CB B:ASN452 4.8 20.5 1.0
HB3 A:ASN40 4.8 20.4 1.0
N A:ASP42 4.8 19.2 1.0
H B:GLY453 4.9 21.2 1.0
CG A:ASP63 4.9 21.6 1.0
H A:ASP42 5.0 23.1 1.0

Magnesium binding site 3 out of 5 in 8qm3

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Magnesium binding site 3 out of 5 in the Formaldehyde-Inhibited [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 Formaldehyde-Inhibited [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg615

b:29.9
occ:1.00
 O B:HOH964 2.0 31.7 1.0
O B:HOH778 2.1 29.3 1.0
O B:ASN309 3.9 27.6 1.0
OD1 B:ASN189 4.1 22.0 1.0
HA B:ASN309 4.2 21.8 1.0
O B:HOH961 4.7 37.2 1.0
HB3 B:ASN309 4.7 28.2 1.0
HD21 B:ASN189 4.8 29.0 1.0
C B:ASN309 4.9 21.3 1.0
CA B:ASN309 4.9 18.2 1.0

Magnesium binding site 4 out of 5 in 8qm3

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Magnesium binding site 4 out of 5 in the Formaldehyde-Inhibited [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 Formaldehyde-Inhibited [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg616

b:27.3
occ:1.00
 OD1 B:ASP42 2.0 26.0 1.0
OD1 B:ASN40 2.0 24.3 1.0
O B:HOH999 2.1 33.1 1.0
O B:HOH721 2.1 27.3 1.0
O B:HOH857 2.1 24.5 1.0
O B:HOH856 2.1 31.8 1.0
CG B:ASN40 3.2 22.4 1.0
CG B:ASP42 3.2 28.9 1.0
H B:ASN40 3.3 28.1 1.0
HD21 B:ASN40 3.5 32.4 1.0
ND2 B:ASN40 3.8 27.0 1.0
HA B:ASP42 3.8 32.3 1.0
OD2 B:ASP42 3.9 39.9 1.0
O B:HOH1040 4.0 36.2 1.0
N B:ASN40 4.1 23.4 1.0
HB3 B:ASP63 4.2 38.0 1.0
CB B:ASP42 4.3 27.2 1.0
O B:ASN40 4.3 23.1 1.0
CB B:ASN40 4.4 21.8 1.0
HB3 A:ASN452 4.4 24.7 1.0
OD1 A:ASN452 4.4 35.0 1.0
CA B:ASP42 4.4 26.9 1.0
O A:HOH735 4.4 36.8 1.0
HB2 B:ASP63 4.4 38.0 1.0
C B:ASN40 4.5 19.5 1.0
HB3 B:ASP42 4.5 32.7 1.0
CA B:ASN40 4.5 20.1 1.0
CG A:ASN452 4.6 30.5 1.0
OD2 B:ASP63 4.6 30.2 1.0
HA B:CYS39 4.6 27.7 1.0
HD22 B:ASN40 4.6 32.4 1.0
N B:ASP42 4.7 21.2 1.0
O A:HOH971 4.7 30.7 1.0
CB B:ASP63 4.8 31.6 1.0
HB3 B:ASN40 4.8 26.2 1.0
H B:ASP42 4.8 25.5 1.0
H A:GLY453 4.9 26.8 1.0
ND2 A:ASN452 5.0 40.5 1.0
CB A:ASN452 5.0 20.6 1.0

Magnesium binding site 5 out of 5 in 8qm3

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Magnesium binding site 5 out of 5 in the Formaldehyde-Inhibited [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 5 of Formaldehyde-Inhibited [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg617

b:24.6
occ:1.00
 O B:HOH939 2.0 23.9 1.0
O B:HOH930 2.0 23.7 1.0
O B:HOH792 2.1 21.8 1.0
O B:HOH767 2.1 19.4 1.0
O B:LEU218 2.1 20.1 1.0
O B:HOH909 2.2 25.1 1.0
HA B:LEU218 3.2 21.9 1.0
C B:LEU218 3.2 17.7 1.0
CA B:LEU218 3.7 18.2 1.0
OD2 B:ASP263 4.1 18.8 1.0
O B:HOH804 4.1 19.9 1.0
HB3 B:LEU218 4.2 23.8 1.0
O B:ALA220 4.2 21.2 1.0
O B:ALA217 4.2 17.7 1.0
HD23 B:LEU218 4.3 24.8 1.0
O B:LYS223 4.3 20.2 1.0
HG23 B:VAL225 4.3 17.9 1.0
HA B:ASN219 4.3 20.6 1.0
N B:ASN219 4.3 21.0 1.0
OD1 B:ASP263 4.4 20.2 1.0
O B:GLY261 4.5 20.1 1.0
CB B:LEU218 4.5 19.8 1.0
CG B:ASP263 4.7 21.0 1.0
O B:HOH821 4.7 40.1 1.0
CA B:ASN219 4.7 17.1 1.0
HG21 B:VAL225 4.7 17.9 1.0
O B:HOH1001 4.8 41.3 1.0
HA B:PRO221 4.8 30.8 1.0
HD22 B:LEU218 4.8 24.8 1.0
N B:LEU218 4.9 18.3 1.0
C B:ASN219 4.9 25.3 1.0
CD2 B:LEU218 5.0 20.7 1.0
CG2 B:VAL225 5.0 14.9 1.0
H B:ALA220 5.0 22.9 1.0
C B:ALA220 5.0 19.8 1.0
C B:ALA217 5.0 18.5 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 16:46:23 2024

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