Atomistry » Magnesium » PDB 8qf1-8qmi » 8qm3
Atomistry »
  Magnesium »
    PDB 8qf1-8qmi »
      8qm3 »

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

Go back to Magnesium Binding Sites List in 8qm3
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

Go back to Magnesium Binding Sites List in 8qm3
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

Go back to Magnesium Binding Sites List in 8qm3
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

Go back to Magnesium Binding Sites List in 8qm3
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy