Atomistry » Magnesium » PDB 5btm-5c25 » 5byr
Atomistry »
  Magnesium »
    PDB 5btm-5c25 »
      5byr »

Magnesium in PDB 5byr: Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor

Enzymatic activity of Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor

All present enzymatic activity of Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor:
1.12.7.2;

Protein crystallography data

The structure of Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor, PDB code: 5byr was solved by J.Esselborn, N.Muraki, V.Engelbrecht, E.Hofmann, G.Kurisu, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.58 / 1.82
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.470, 72.070, 102.710, 90.00, 100.86, 90.00
R / Rfree (%) 15.6 / 19.2

Other elements in 5byr:

The structure of Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor also contains other interesting chemical elements:

Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor (pdb code 5byr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor, PDB code: 5byr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5byr

Go back to Magnesium Binding Sites List in 5byr
Magnesium binding site 1 out of 5 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:25.7
occ:1.00
 O A:HOH823 2.0 28.0 1.0
O A:HOH777 2.1 23.9 1.0
O A:LEU218 2.1 24.1 1.0
O A:HOH743 2.1 21.1 1.0
O A:HOH795 2.1 25.8 1.0
O A:HOH923 2.2 26.4 1.0
C A:LEU218 3.1 25.9 1.0
HA A:LEU218 3.3 29.3 1.0
CA A:LEU218 3.7 24.4 1.0
OD2 A:ASP263 4.0 23.0 1.0
O A:ALA220 4.1 23.9 1.0
HB3 A:LEU218 4.1 27.3 1.0
HA A:ASN219 4.1 30.9 1.0
O A:HOH816 4.2 24.2 1.0
N A:ASN219 4.2 26.4 1.0
O A:LYS223 4.3 19.8 1.0
HG23 A:VAL225 4.3 23.8 1.0
OD1 A:ASP263 4.3 24.6 1.0
O A:ALA217 4.3 21.9 1.0
O A:HOH1108 4.4 42.1 1.0
CB A:LEU218 4.5 22.8 1.0
O A:GLY261 4.5 24.9 1.0
O A:HOH825 4.5 40.4 1.0
HD23 A:LEU218 4.6 31.8 1.0
CA A:ASN219 4.6 25.8 1.0
CG A:ASP263 4.6 25.7 1.0
HG21 A:VAL225 4.7 23.8 1.0
C A:ASN219 4.8 25.8 1.0
H A:ALA220 4.9 28.2 1.0
HD22 A:LEU218 4.9 31.8 1.0
N A:ALA220 4.9 23.5 1.0
N A:LEU218 4.9 20.2 1.0
O A:HOH901 4.9 38.5 1.0
HA A:PRO221 4.9 32.2 1.0
C A:ALA220 4.9 26.8 1.0
CG2 A:VAL225 4.9 19.8 1.0
H A:ASN219 5.0 31.6 1.0

Magnesium binding site 2 out of 5 in 5byr

Go back to Magnesium Binding Sites List in 5byr
Magnesium binding site 2 out of 5 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:45.4
occ:1.00
 O A:HOH749 2.1 40.4 1.0
HG A:SER320 2.5 34.3 1.0
O A:HOH724 2.7 41.6 1.0
OG A:SER320 2.8 28.6 1.0
NE2 A:HIS565 2.9 39.2 1.0
HD2 A:HIS565 3.0 48.3 1.0
O A:HOH708 3.1 35.5 1.0
CD A:GLU282 3.2 34.2 1.0
CD2 A:HIS565 3.3 40.2 1.0
HE1 A:HIS569 3.3 34.3 1.0
OE2 A:GLU282 3.3 36.6 1.0
OE1 A:GLU282 3.4 34.9 1.0
HB2 A:GLU282 3.6 35.0 1.0
ND1 A:HIS569 3.6 27.2 1.0
HG3 A:GLU282 3.6 41.9 1.0
CE1 A:HIS569 3.7 28.6 1.0
CG A:GLU282 3.9 34.9 1.0
H A:SER320 4.0 31.6 1.0
CB A:SER320 4.1 28.1 1.0
CE1 A:HIS565 4.1 38.8 1.0
O A:HOH1008 4.2 38.9 1.0
HB3 A:SER320 4.2 33.7 1.0
CB A:GLU282 4.2 29.2 1.0
OE1 A:GLN285 4.5 43.9 1.0
HE1 A:HIS565 4.6 46.6 1.0
CG A:HIS565 4.6 38.2 1.0
HB2 A:SER320 4.6 33.7 1.0
HA A:GLU282 4.7 34.6 1.0
N A:SER320 4.8 26.3 1.0
HG2 A:GLU282 4.8 41.9 1.0
CG A:HIS569 4.8 29.0 1.0
NE2 A:HIS569 4.8 28.7 1.0
HA2 A:GLY560 4.9 43.4 1.0
CA A:SER320 4.9 28.8 1.0
HB3 A:GLU282 4.9 35.0 1.0

Magnesium binding site 3 out of 5 in 5byr

Go back to Magnesium Binding Sites List in 5byr
Magnesium binding site 3 out of 5 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg609

b:25.6
occ:1.00
 O A:HOH933 1.9 24.1 1.0
OD1 A:ASP42 1.9 24.3 1.0
O A:HOH769 2.1 21.5 1.0
OD1 A:ASN40 2.1 21.8 1.0
O A:HOH943 2.2 24.6 1.0
O A:HOH931 2.3 27.3 1.0
CG A:ASP42 3.1 26.0 1.0
CG A:ASN40 3.2 21.5 1.0
H A:ASN40 3.2 23.7 1.0
HD21 A:ASN40 3.5 27.8 1.0
OD2 A:ASP42 3.7 31.1 1.0
ND2 A:ASN40 3.8 23.1 1.0
HB2 A:ASP63 3.9 27.1 1.0
O A:HOH711 3.9 28.1 1.0
HB3 A:ASP63 3.9 27.1 1.0
HA A:ASP42 4.0 30.8 1.0
N A:ASN40 4.0 19.8 1.0
O B:HOH711 4.1 34.6 1.0
OD1 B:ASN452 4.2 27.3 1.0
O A:HOH896 4.2 32.5 1.0
O A:HOH1003 4.2 32.4 1.0
OD2 A:ASP63 4.3 23.6 1.0
CB A:ASP42 4.3 25.7 1.0
HB3 B:ASN452 4.3 26.7 1.0
O A:ASN40 4.3 19.5 1.0
CB A:ASP63 4.4 22.6 1.0
CB A:ASN40 4.4 18.7 1.0
O B:HOH738 4.4 31.8 1.0
C A:ASN40 4.5 18.9 1.0
CA A:ASN40 4.5 20.7 1.0
HA A:CYS39 4.6 28.9 1.0
CA A:ASP42 4.6 25.7 1.0
HB3 A:ASP42 4.6 30.8 1.0
CG B:ASN452 4.6 27.3 1.0
HD22 A:ASN40 4.6 27.8 1.0
HB2 A:CYS39 4.7 36.6 1.0
HB3 A:ASN40 4.7 22.4 1.0
N A:ASP42 4.8 21.4 1.0
O B:HOH980 4.8 20.6 1.0
H A:ASP42 4.9 25.6 1.0
CG A:ASP63 4.9 24.5 1.0
HE2 A:LYS45 4.9 41.5 1.0
H B:GLY453 5.0 20.9 1.0
CB B:ASN452 5.0 22.2 1.0

Magnesium binding site 4 out of 5 in 5byr

Go back to Magnesium Binding Sites List in 5byr
Magnesium binding site 4 out of 5 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:25.3
occ:1.00
 O B:HOH720 2.0 21.1 1.0
O B:HOH752 2.1 19.2 1.0
O B:LEU218 2.1 24.2 1.0
O B:HOH929 2.1 24.0 1.0
O B:HOH891 2.2 26.2 1.0
O B:HOH787 2.3 21.5 1.0
C B:LEU218 3.1 23.2 1.0
HA B:LEU218 3.2 30.2 1.0
CA B:LEU218 3.7 25.2 1.0
OD2 B:ASP263 3.9 21.1 1.0
O B:ALA220 4.0 23.6 1.0
O B:ALA217 4.1 21.6 1.0
O B:LYS223 4.1 17.4 1.0
O B:HOH814 4.1 21.6 1.0
HG23 B:VAL225 4.2 23.4 1.0
HB3 B:LEU218 4.3 23.2 1.0
O B:HOH1100 4.3 44.1 1.0
N B:ASN219 4.3 25.8 1.0
HA B:ASN219 4.3 30.0 1.0
OD1 B:ASP263 4.4 21.9 1.0
O B:GLY261 4.5 21.9 1.0
HD23 B:LEU218 4.5 27.1 1.0
CG B:ASP263 4.6 23.3 1.0
HG21 B:VAL225 4.6 23.4 1.0
CB B:LEU218 4.6 19.3 1.0
H B:ALA220 4.7 27.0 1.0
CA B:ASN219 4.7 25.0 1.0
O B:HOH930 4.7 39.5 1.0
HA B:PRO221 4.7 30.2 1.0
N B:LEU218 4.8 20.1 1.0
C B:ALA220 4.8 25.5 1.0
CG2 B:VAL225 4.8 19.5 1.0
O B:HOH1022 4.8 40.3 1.0
N B:ALA220 4.8 22.5 1.0
C B:ALA217 4.8 23.3 1.0
HD22 B:LEU218 4.9 27.1 1.0
C B:ASN219 4.9 28.5 1.0

Magnesium binding site 5 out of 5 in 5byr

Go back to Magnesium Binding Sites List in 5byr
Magnesium binding site 5 out of 5 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Semisynthetic [Fefe]-Hydrogenase Cpi with Propane-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:29.8
occ:1.00
 OD1 B:ASP42 2.0 24.4 1.0
O B:HOH914 2.0 30.8 1.0
O B:HOH884 2.1 29.4 1.0
OD1 B:ASN40 2.1 22.1 1.0
O B:HOH868 2.2 27.9 1.0
O B:HOH815 2.2 31.8 1.0
CG B:ASP42 3.1 30.0 1.0
CG B:ASN40 3.2 27.9 1.0
H B:ASN40 3.3 27.5 1.0
HD21 B:ASN40 3.5 32.7 1.0
OD2 B:ASP42 3.6 34.8 1.0
ND2 B:ASN40 3.8 27.2 1.0
O B:HOH705 3.9 34.6 1.0
HA B:ASP42 3.9 33.4 1.0
O B:HOH717 4.0 40.9 1.0
HB3 B:ASP63 4.0 39.9 1.0
N B:ASN40 4.1 22.9 1.0
O A:HOH748 4.2 36.6 1.0
HB3 A:ASN452 4.2 31.6 1.0
HB2 B:ASP63 4.3 39.9 1.0
OD1 A:ASN452 4.3 34.3 1.0
CB B:ASP42 4.3 30.5 1.0
OD2 B:ASP63 4.4 34.0 1.0
O B:ASN40 4.4 23.2 1.0
CB B:ASN40 4.5 22.6 1.0
CA B:ASP42 4.5 27.9 1.0
CB B:ASP63 4.6 33.2 1.0
C B:ASN40 4.6 24.6 1.0
CA B:ASN40 4.6 24.3 1.0
CG A:ASN452 4.6 27.7 1.0
HB3 B:ASP42 4.7 36.6 1.0
HD22 B:ASN40 4.7 32.7 1.0
HA B:CYS39 4.7 32.7 1.0
H A:GLY453 4.9 27.1 1.0
N B:ASP42 4.9 29.4 1.0
O A:HOH970 4.9 25.5 1.0
HB3 B:ASN40 4.9 27.2 1.0
CB A:ASN452 4.9 26.4 1.0
H B:ASP42 4.9 35.3 1.0
HE2 B:LYS45 4.9 52.1 1.0

Reference:

J.Esselborn, N.Muraki, K.Klein, V.Engelbrecht, N.Metzler-Nolte, U.P.Apfel, E.Hofmann, G.Kurisu, T.Happe. A Structural View of Synthetic Cofactor Integration Into [Fefe]-Hydrogenases. Chem Sci V. 7 959 2016.
ISSN: ISSN 2041-6520
PubMed: 29896366
DOI: 10.1039/C5SC03397G
Page generated: Sun Sep 29 01:48:39 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