Atomistry » Magnesium » PDB 5btn-5c28 » 5bys
Atomistry »
  Magnesium »
    PDB 5btn-5c28 »
      5bys »

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

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

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

Protein crystallography data

The structure of Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-Dithiolato-Bridged [2FE] Cofactor, PDB code: 5bys 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) 48.05 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.830, 73.130, 103.040, 90.00, 96.60, 90.00
R / Rfree (%) 15.8 / 18.8

Other elements in 5bys:

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

Magnesium binding site 1 out of 4 in 5bys

Go back to Magnesium Binding Sites List in 5bys
Magnesium binding site 1 out of 4 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-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 Sulfur-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:27.5
occ:1.00
 O A:HOH795 2.0 21.6 1.0
O A:LEU218 2.1 25.0 1.0
O A:HOH922 2.1 26.6 1.0
O A:HOH743 2.2 24.1 1.0
O A:HOH842 2.2 26.5 1.0
O A:HOH841 2.2 25.4 1.0
C A:LEU218 3.2 25.0 1.0
HA A:LEU218 3.2 26.4 1.0
CA A:LEU218 3.7 22.0 1.0
OD2 A:ASP263 3.9 25.7 1.0
O A:HOH1138 3.9 41.8 1.0
O A:ALA220 4.0 23.7 1.0
O A:LYS223 4.1 22.5 1.0
O A:ALA217 4.2 24.1 1.0
OD1 A:ASP263 4.2 25.5 1.0
O A:HOH852 4.3 25.5 1.0
HG23 A:VAL225 4.3 25.2 1.0
N A:ASN219 4.3 26.9 1.0
HB3 A:LEU218 4.3 27.4 1.0
HA A:ASN219 4.4 35.5 1.0
HD23 A:LEU218 4.4 24.5 1.0
CG A:ASP263 4.5 24.5 1.0
O A:GLY261 4.5 24.3 1.0
CB A:LEU218 4.7 22.9 1.0
O A:HOH853 4.7 36.9 1.0
HG21 A:VAL225 4.7 25.2 1.0
CA A:ASN219 4.8 29.6 1.0
HD22 A:LEU218 4.8 24.5 1.0
N A:LEU218 4.8 21.4 1.0
C A:ALA220 4.9 26.7 1.0
C A:ASN219 4.9 29.9 1.0
C A:ALA217 4.9 23.9 1.0
CG2 A:VAL225 5.0 21.0 1.0
H A:ALA220 5.0 31.4 1.0
N A:ALA220 5.0 26.2 1.0

Magnesium binding site 2 out of 4 in 5bys

Go back to Magnesium Binding Sites List in 5bys
Magnesium binding site 2 out of 4 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-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 Sulfur-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:24.5
occ:1.00
 OD1 A:ASN40 1.9 21.5 1.0
OD1 A:ASP42 2.0 27.3 1.0
O A:HOH908 2.1 27.3 1.0
O A:HOH916 2.1 24.8 1.0
O A:HOH949 2.1 25.2 1.0
O A:HOH791 2.2 24.2 1.0
CG A:ASN40 3.1 23.6 1.0
H A:ASN40 3.2 27.6 1.0
CG A:ASP42 3.2 27.6 1.0
HD21 A:ASN40 3.5 29.6 1.0
ND2 A:ASN40 3.7 24.7 1.0
OD2 A:ASP42 3.8 30.0 1.0
HB3 A:ASP63 3.9 26.4 1.0
HA A:ASP42 4.0 29.9 1.0
O B:HOH775 4.0 36.9 1.0
N A:ASN40 4.0 23.0 1.0
O A:HOH751 4.1 28.2 1.0
HB2 A:ASP63 4.1 26.4 1.0
O A:HOH1051 4.1 36.3 1.0
O A:ASN40 4.2 22.1 1.0
CB A:ASN40 4.3 26.3 1.0
O B:HOH729 4.3 31.9 1.0
HB3 B:ASN452 4.4 23.6 1.0
OD2 A:ASP63 4.4 25.0 1.0
CB A:ASP42 4.4 23.1 1.0
C A:ASN40 4.4 22.1 1.0
OD1 B:ASN452 4.4 26.1 1.0
CB A:ASP63 4.4 22.0 1.0
CA A:ASN40 4.4 22.6 1.0
CA A:ASP42 4.6 25.0 1.0
HD22 A:ASN40 4.6 29.6 1.0
HA A:CYS39 4.6 29.6 1.0
HB3 A:ASN40 4.6 31.6 1.0
CG B:ASN452 4.7 26.9 1.0
HB3 A:ASP42 4.7 27.7 1.0
O A:HOH871 4.7 31.3 1.0
HE2 A:LYS45 4.8 37.5 1.0
O B:HOH979 4.8 25.4 1.0
N A:ASP42 4.8 21.3 1.0
H A:ASP42 4.9 25.5 1.0
CG A:ASP63 5.0 24.8 1.0

Magnesium binding site 3 out of 4 in 5bys

Go back to Magnesium Binding Sites List in 5bys
Magnesium binding site 3 out of 4 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-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 Sulfur-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:26.4
occ:1.00
 O B:HOH809 2.0 19.9 1.0
O B:HOH918 2.1 21.3 1.0
O B:HOH770 2.1 22.5 1.0
O B:HOH815 2.1 20.5 1.0
O B:HOH928 2.2 24.3 1.0
O B:LEU218 2.2 25.5 1.0
C B:LEU218 3.3 25.2 1.0
HA B:LEU218 3.3 25.5 1.0
CA B:LEU218 3.8 21.2 1.0
OD2 B:ASP263 3.9 21.1 1.0
O B:HOH852 4.0 22.0 1.0
O B:ALA220 4.1 24.8 1.0
O B:LYS223 4.2 20.8 1.0
OD1 B:ASP263 4.2 21.8 1.0
HB3 B:LEU218 4.3 27.8 1.0
O B:ALA217 4.3 22.0 1.0
HG23 B:VAL225 4.3 22.3 1.0
N B:ASN219 4.3 25.4 1.0
HA B:ASN219 4.4 32.1 1.0
HD23 B:LEU218 4.5 23.5 1.0
CG B:ASP263 4.5 22.7 1.0
O B:GLY261 4.5 19.3 1.0
CB B:LEU218 4.6 23.2 1.0
CA B:ASN219 4.8 26.8 1.0
HG21 B:VAL225 4.8 22.3 1.0
O B:HOH1051 4.8 38.2 1.0
HD22 B:LEU218 4.8 23.5 1.0
H B:ALA220 4.9 25.1 1.0
C B:ASN219 4.9 24.5 1.0
N B:LEU218 4.9 21.6 1.0

Magnesium binding site 4 out of 4 in 5bys

Go back to Magnesium Binding Sites List in 5bys
Magnesium binding site 4 out of 4 in the Semisynthetic [Fefe]-Hydrogenase Cpi with Sulfur-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 Sulfur-Dithiolato-Bridged [2FE] Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg608

b:31.1
occ:1.00
 O B:HOH984 2.0 28.3 1.0
OD1 B:ASP42 2.1 28.6 1.0
O B:HOH752 2.1 32.1 1.0
O B:HOH961 2.2 32.1 1.0
OD1 B:ASN40 2.2 27.1 1.0
O B:HOH966 2.3 29.3 1.0
CG B:ASP42 3.2 28.3 1.0
H B:ASN40 3.2 33.7 1.0
CG B:ASN40 3.3 27.2 1.0
OD2 B:ASP42 3.6 36.8 1.0
HD21 B:ASN40 3.8 35.9 1.0
ND2 B:ASN40 4.0 29.9 1.0
N B:ASN40 4.1 28.1 1.0
HA B:ASP42 4.1 34.0 1.0
HB3 B:ASP63 4.1 37.6 1.0
HB3 A:ASN452 4.2 34.0 1.0
HB2 B:ASP63 4.3 37.6 1.0
O B:ASN40 4.3 23.7 1.0
O A:HOH715 4.4 36.4 1.0
OD2 B:ASP63 4.4 30.0 1.0
OD1 A:ASN452 4.4 34.9 1.0
CB B:ASP42 4.4 28.1 1.0
CG A:ASN452 4.5 28.6 1.0
CB B:ASN40 4.5 25.5 1.0
HA B:CYS39 4.5 34.6 1.0
C B:ASN40 4.5 24.8 1.0
CA B:ASN40 4.6 25.8 1.0
CB B:ASP63 4.6 31.3 1.0
CA B:ASP42 4.7 28.3 1.0
HB3 B:ASP42 4.7 33.8 1.0
H A:GLY453 4.8 24.1 1.0
O A:HOH995 4.8 31.9 1.0
CB A:ASN452 4.8 28.3 1.0
ND2 A:ASN452 4.8 37.5 1.0
HD22 B:ASN40 4.8 35.9 1.0
HB3 B:ASN40 4.9 30.6 1.0
H A:ILE454 5.0 23.4 1.0
HD21 A:ASN452 5.0 45.0 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 01:48:41 2024

Last articles

Fe in 6RR1
Fe in 6RQY
Fe in 6RQ9
Fe in 6RQE
Fe in 6RQD
Fe in 6RQ8
Fe in 6RQB
Fe in 6RQ6
Fe in 6RQ5
Fe in 6RPE
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy