Atomistry » Magnesium » PDB 6gg6-6gof » 6gm4
Atomistry »
  Magnesium »
    PDB 6gg6-6gof »
      6gm4 »

Magnesium in PDB 6gm4: [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A

Enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A

All present enzymatic activity of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A:
1.12.7.2;

Protein crystallography data

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A, PDB code: 6gm4 was solved by J.Duan, J.Esselborn, E.Hofmann, M.Winkler, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.84 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.070, 73.330, 103.250, 90.00, 96.46, 90.00
R / Rfree (%) 16.4 / 20.2

Other elements in 6gm4:

The structure of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A also contains other interesting chemical elements:

Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A (pdb code 6gm4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A, PDB code: 6gm4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6gm4

Go back to Magnesium Binding Sites List in 6gm4
Magnesium binding site 1 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:25.6
occ:1.00
 O A:HOH921 2.1 27.9 1.0
OD1 A:ASP42 2.1 26.8 1.0
O A:HOH774 2.1 22.9 1.0
O A:HOH805 2.1 22.7 1.0
O A:HOH881 2.1 24.3 1.0
OD1 A:ASN40 2.1 24.8 1.0
CG A:ASN40 3.2 25.3 1.0
CG A:ASP42 3.2 31.3 1.0
ND2 A:ASN40 3.8 20.1 1.0
OD2 A:ASP42 3.8 31.6 1.0
O A:HOH704 4.0 29.1 1.0
OD1 B:ASN452 4.1 32.5 1.0
O B:HOH716 4.2 34.2 1.0
N A:ASN40 4.2 18.8 1.0
O A:HOH918 4.3 38.4 1.0
O A:ASN40 4.4 24.8 1.0
CB A:ASP42 4.4 24.1 1.0
CB A:ASN40 4.5 22.2 1.0
CB A:ASP63 4.5 21.0 1.0
CG B:ASN452 4.5 33.3 1.0
OD2 A:ASP63 4.5 26.7 1.0
CA A:ASP42 4.6 26.0 1.0
C A:ASN40 4.6 24.8 1.0
CA A:ASN40 4.7 26.7 1.0
O B:HOH933 4.7 25.0 1.0
O A:HOH882 4.7 32.3 1.0
N A:ASP42 4.8 25.5 1.0
CB B:ASN452 4.9 20.2 1.0
O A:HOH807 5.0 37.7 1.0

Magnesium binding site 2 out of 4 in 6gm4

Go back to Magnesium Binding Sites List in 6gm4
Magnesium binding site 2 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:27.5
occ:0.86
 O A:HOH862 2.1 27.0 1.0
O A:HOH731 2.1 19.9 1.0
O A:HOH756 2.1 29.8 1.0
O A:HOH865 2.1 28.6 1.0
O A:HOH883 2.1 25.8 1.0
O A:LEU218 2.1 28.7 1.0
C A:LEU218 3.2 25.5 1.0
CA A:LEU218 3.8 24.2 1.0
O A:ALA220 4.0 26.0 1.0
OD2 A:ASP263 4.1 25.8 1.0
O A:LYS223 4.2 21.6 1.0
O A:HOH851 4.2 23.1 1.0
O A:ALA217 4.3 23.6 1.0
OD1 A:ASP263 4.3 25.0 1.0
N A:ASN219 4.3 26.6 1.0
CG A:ASP263 4.6 25.3 1.0
CA A:ASN219 4.6 30.0 1.0
CB A:LEU218 4.7 19.2 1.0
O A:GLY261 4.7 27.3 1.0
O A:HOH738 4.8 41.5 1.0
C A:ASN219 4.8 29.4 1.0
C A:ALA220 4.8 26.3 1.0
N A:ALA220 4.8 23.2 1.0
N A:LEU218 4.9 20.2 1.0
CG2 A:VAL225 5.0 22.6 1.0

Magnesium binding site 3 out of 4 in 6gm4

Go back to Magnesium Binding Sites List in 6gm4
Magnesium binding site 3 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:26.5
occ:1.00
 O B:HOH790 2.1 20.3 1.0
O B:HOH812 2.1 27.7 1.0
O B:HOH930 2.1 24.7 1.0
O B:HOH740 2.1 25.6 1.0
O B:HOH873 2.1 24.4 1.0
O B:LEU218 2.1 29.4 1.0
C B:LEU218 3.2 24.7 1.0
CA B:LEU218 3.8 24.6 1.0
OD2 B:ASP263 4.0 21.3 1.0
O B:HOH784 4.1 23.2 1.0
O B:ALA220 4.1 25.4 1.0
O B:LYS223 4.2 26.0 1.0
O B:ALA217 4.3 26.1 1.0
OD1 B:ASP263 4.3 22.2 1.0
N B:ASN219 4.3 25.1 1.0
O B:HOH931 4.5 42.0 1.0
CG B:ASP263 4.5 24.3 1.0
O B:GLY261 4.6 21.8 1.0
CB B:LEU218 4.7 25.4 1.0
CA B:ASN219 4.7 30.1 1.0
O B:HOH1056 4.8 49.2 1.0
C B:ASN219 4.8 26.7 1.0
C B:ALA220 4.9 26.4 1.0
N B:ALA220 4.9 22.7 1.0
N B:LEU218 4.9 15.3 1.0
CG2 B:VAL225 5.0 19.3 1.0

Magnesium binding site 4 out of 4 in 6gm4

Go back to Magnesium Binding Sites List in 6gm4
Magnesium binding site 4 out of 4 in the [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of [Fefe]-Hydrogenase Cpi From Clostridium Pasteurianum, Variant S319A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:22.1
occ:0.77
 ND2 B:ASN40 1.9 37.3 1.0
O B:HOH732 2.1 34.1 1.0
O B:HOH701 2.1 30.2 1.0
OD1 B:ASP42 2.1 29.1 1.0
O B:HOH809 2.1 26.3 1.0
O B:HOH748 2.1 32.3 1.0
OD1 B:ASN40 2.1 42.2 1.0
CG B:ASN40 2.3 19.7 1.0
CG B:ASP42 3.2 31.0 1.0
CB B:ASN40 3.7 28.8 1.0
OD2 B:ASP42 3.8 39.8 1.0
N B:ASN40 3.9 24.2 1.0
CA B:ASN40 4.3 28.6 1.0
OD2 B:ASP63 4.3 32.1 1.0
O B:ASN40 4.3 26.0 1.0
C B:ASN40 4.4 24.2 1.0
OD1 A:ASN452 4.4 32.5 1.0
CB B:ASP42 4.4 28.6 1.0
CB B:ASP63 4.4 31.3 1.0
O A:HOH720 4.5 37.0 1.0
CA B:ASP42 4.5 27.6 1.0
CG A:ASN452 4.6 29.5 1.0
N B:ASP42 4.7 24.5 1.0
CG B:ASP63 4.9 33.6 1.0
O A:HOH941 5.0 29.6 1.0

Reference:

J.Duan, M.Senger, J.Esselborn, V.Engelbrecht, F.Wittkamp, U.P.Apfel, E.Hofmann, S.T.Stripp, T.Happe, M.Winkler. Crystallographic and Spectroscopic Assignment of the Proton Transfer Pathway in [Fefe]-Hydrogenases. Nat Commun V. 9 4726 2018.
ISSN: ESSN 2041-1723
PubMed: 30413719
DOI: 10.1038/S41467-018-07140-X
Page generated: Tue Oct 1 01:15:56 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