Iron in PDB 2ohj: Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State

The structure of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State, PDB code: 2ohj was solved by H.Seedorf, E.Warkentin, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.11 / 2.26
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.700, 88.700, 450.400, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.4

The structure of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State (pdb code 2ohj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State, PDB code: 2ohj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:17.6 occ:1.00 OD2 A:ASP170 1.9 29.9 1.0 NE2 A:HIS88 2.0 22.0 1.0 NE2 A:HIS233 2.1 18.2 1.0 OD1 A:ASP170 2.4 28.5 1.0 CG A:ASP170 2.5 25.6 1.0 CD2 A:HIS233 2.9 19.4 1.0 CE1 A:HIS88 3.0 22.6 1.0 CD2 A:HIS88 3.0 22.8 1.0 CE1 A:HIS233 3.2 17.9 1.0 CB A:ASP170 4.0 23.6 1.0 OD1 A:ASP87 4.1 25.2 1.0 CG A:HIS233 4.1 20.1 1.0 ND1 A:HIS88 4.1 22.2 1.0 CG A:HIS88 4.2 22.0 1.0 ND1 A:HIS233 4.2 19.2 1.0 CG A:GLU85 4.3 27.4 1.0 CE1 A:HIS83 4.4 25.8 1.0 CB A:ASP87 4.4 23.6 1.0 CB A:SER232 4.7 19.9 1.0 ND1 A:HIS83 4.8 24.3 1.0 CG A:ASP87 4.8 24.5 1.0 CA A:ASP170 5.0 23.4 1.0

Iron binding site 2 out of 12 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:21.5 occ:1.00 O A:HOH792 1.8 21.4 1.0 NE2 B:HIS267 1.9 24.4 1.0 NE2 A:HIS26 2.0 33.2 1.0 OE1 A:GLU85 2.1 32.8 1.0 CE1 B:HIS267 2.7 24.4 1.0 OE2 A:GLU85 2.8 31.2 1.0 CE1 A:HIS26 2.8 33.0 1.0 CD A:GLU85 2.8 30.5 1.0 CD2 B:HIS267 3.0 23.9 1.0 CD2 A:HIS26 3.2 31.0 1.0 OD2 A:ASP87 3.8 27.1 1.0 ND1 B:HIS267 3.9 25.6 1.0 ND1 A:HIS26 4.0 32.5 1.0 CG B:HIS267 4.0 24.2 1.0 CG A:ASP87 4.1 24.5 1.0 CG A:HIS26 4.2 30.6 1.0 CG A:GLU85 4.3 27.4 1.0 OD1 A:ASP87 4.3 25.2 1.0 CE1 A:TYR25 4.4 28.9 1.0 CG A:LYS86 4.4 24.2 1.0 CD1 A:TYR25 4.7 27.6 1.0 N A:ASP87 4.7 23.7 1.0 N A:LYS86 4.9 24.9 1.0 CB A:ASP87 4.9 23.6 1.0

Iron binding site 3 out of 12 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe511 b:26.0 occ:1.00 OD2 A:ASP320 1.9 23.0 1.0 NE2 B:HIS151 2.0 29.1 1.0 O B:HOH1778 2.1 12.7 1.0 O B:HOH1779 2.4 19.1 1.0 CG A:ASP320 2.8 20.4 1.0 CD2 B:HIS151 2.9 27.9 1.0 CE1 B:HIS151 3.1 28.8 1.0 OD1 A:ASP320 3.1 20.5 1.0 NZ B:LYS337 3.8 23.0 1.0 CG B:HIS151 4.1 28.8 1.0 CB A:ASP320 4.1 19.7 1.0 ND1 B:HIS151 4.2 28.6 1.0 CE B:LYS337 4.3 22.4 1.0 CD2 B:LEU150 4.4 30.4 1.0 O A:TYR319 4.7 20.5 1.0 C A:TYR319 4.7 19.8 1.0 CG B:LEU150 4.7 30.2 1.0 NH1 B:ARG340 4.7 20.2 1.0 N A:ASP320 4.9 19.9 1.0

Iron binding site 4 out of 12 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1501 b:14.6 occ:1.00 OD1 B:ASP170 2.0 28.0 1.0 NE2 B:HIS88 2.1 17.8 1.0 NE2 B:HIS233 2.1 13.8 1.0 CG B:ASP170 2.7 26.6 1.0 OD2 B:ASP170 2.7 33.5 1.0 CE1 B:HIS88 3.0 20.8 1.0 CE1 B:HIS233 3.0 15.8 1.0 CD2 B:HIS88 3.1 20.7 1.0 CD2 B:HIS233 3.2 14.8 1.0 OD1 B:ASP87 3.5 38.5 1.0 O B:HOH1739 3.7 31.9 1.0 ND1 B:HIS88 4.1 21.6 1.0 CB B:ASP170 4.2 24.4 1.0 ND1 B:HIS233 4.2 14.9 1.0 CG B:HIS88 4.2 22.1 1.0 CG B:HIS233 4.3 17.7 1.0 CG B:GLU85 4.3 27.6 1.0 CG B:ASP87 4.4 29.6 1.0 OD2 B:ASP87 4.5 30.4 1.0 NE2 B:HIS83 4.5 32.5 1.0 CB B:SER232 4.7 20.9 1.0 CD2 B:HIS83 4.8 30.5 1.0 O B:HOH1726 4.9 30.3 1.0 CA B:ASP170 4.9 23.1 1.0 CD B:GLU85 5.0 31.0 1.0

Iron binding site 5 out of 12 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1502 b:22.9 occ:1.00 OE2 B:GLU85 2.0 30.9 1.0 NE2 A:HIS267 2.0 23.6 1.0 NE2 B:HIS26 2.1 30.1 1.0 CE1 B:HIS26 2.8 31.4 1.0 CD B:GLU85 2.9 31.0 1.0 CD2 A:HIS267 2.9 23.9 1.0 CE1 A:HIS267 3.0 24.7 1.0 OE1 B:GLU85 3.0 31.0 1.0 CD2 B:HIS26 3.3 30.8 1.0 ND1 B:HIS26 4.0 32.6 1.0 ND1 A:HIS267 4.1 25.6 1.0 CG A:HIS267 4.1 23.8 1.0 OD2 B:ASP87 4.1 30.4 1.0 CG B:LYS86 4.1 26.6 1.0 CG B:GLU85 4.3 27.6 1.0 CG B:HIS26 4.3 30.6 1.0 CE1 B:TYR25 4.3 34.2 1.0 CG B:ASP87 4.5 29.6 1.0 CD1 B:TYR25 4.6 32.0 1.0 CD B:LYS86 4.7 26.5 1.0 N B:ASP87 4.8 25.1 1.0 N B:LYS86 4.8 25.8 1.0

Iron binding site 6 out of 12 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe512 b:19.0 occ:1.00 NE2 A:HIS151 1.8 23.1 1.0 OD2 B:ASP320 2.1 20.7 1.0 O A:HOH753 2.2 3.1 1.0 O B:HOH1833 2.7 27.0 1.0 CG B:ASP320 2.8 19.1 1.0 OD1 B:ASP320 2.8 15.9 1.0 CD2 A:HIS151 2.8 25.1 1.0 CE1 A:HIS151 2.8 24.1 1.0 ND1 A:HIS151 3.9 25.1 1.0 CG A:HIS151 3.9 25.3 1.0 CD2 A:LEU150 4.0 27.9 1.0 NZ A:LYS337 4.2 17.8 1.0 CB B:ASP320 4.2 19.8 1.0 CE A:LYS337 4.3 17.4 1.0 C B:TYR319 4.7 20.6 1.0 NH1 A:ARG340 4.7 17.6 1.0 O B:TYR319 4.7 20.6 1.0 CG A:LEU150 4.7 27.8 1.0 N B:ASP320 4.9 20.6 1.0 O B:HOH1712 4.9 18.3 1.0

Iron binding site 7 out of 12 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe2501 b:13.9 occ:1.00 O D:HOH2799 1.9 21.2 1.0 NE2 D:HIS88 2.1 23.4 1.0 OD1 D:ASP170 2.2 27.4 1.0 NE2 D:HIS233 2.2 20.5 1.0 OD2 D:ASP170 2.3 26.7 1.0 O D:HOH2831 2.5 51.5 1.0 CG D:ASP170 2.6 24.5 1.0 CD2 D:HIS233 3.0 18.9 1.0 CE1 D:HIS88 3.0 24.9 1.0 CD2 D:HIS88 3.2 23.2 1.0 CE1 D:HIS233 3.3 19.4 1.0 CB D:ASP170 4.1 23.3 1.0 ND1 D:HIS88 4.1 23.4 1.0 CG D:HIS233 4.2 19.6 1.0 OD2 D:ASP87 4.2 27.4 1.0 CG D:HIS88 4.3 22.4 1.0 ND1 D:HIS233 4.3 17.6 1.0 CG D:GLU85 4.3 27.5 1.0 NE2 D:HIS83 4.5 28.3 1.0 CB D:ASP87 4.5 23.3 1.0 CB D:SER232 4.6 21.1 1.0 CD2 D:HIS83 4.8 27.1 1.0 CG D:ASP87 4.9 25.1 1.0 CA D:ASP170 4.9 22.9 1.0 CB D:GLU85 5.0 26.2 1.0

Iron binding site 8 out of 12 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe2502 b:17.5 occ:1.00 NE2 D:HIS26 2.0 28.9 1.0 O D:HOH2828 2.0 18.6 1.0 NE2 E:HIS267 2.1 26.2 1.0 OE1 D:GLU85 2.5 29.9 1.0 OE2 D:GLU85 2.6 29.3 1.0 CE1 D:HIS26 2.7 29.5 1.0 CD D:GLU85 2.8 28.5 1.0 CE1 E:HIS267 2.9 26.8 1.0 CD2 E:HIS267 3.1 25.0 1.0 CD2 D:HIS26 3.3 29.3 1.0 OD1 D:ASP87 3.7 26.0 1.0 ND1 D:HIS26 3.9 28.4 1.0 ND1 E:HIS267 4.1 26.7 1.0 CG D:ASP87 4.1 25.1 1.0 CG D:LYS86 4.2 26.1 1.0 CG E:HIS267 4.2 24.2 1.0 O D:HOH2800 4.2 22.4 1.0 CG D:HIS26 4.2 29.2 1.0 OD2 D:ASP87 4.3 27.4 1.0 CG D:GLU85 4.3 27.5 1.0 CE1 D:TYR25 4.4 29.3 1.0 CD1 D:TYR25 4.6 28.2 1.0 N D:ASP87 4.7 23.1 1.0 CD D:LYS86 4.8 27.4 1.0 N D:LYS86 4.9 24.6 1.0

Iron binding site 9 out of 12 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe513 b:13.5 occ:1.00 NE2 D:HIS151 1.9 25.1 1.0 OD2 E:ASP320 2.0 16.9 1.0 O E:HOH3761 2.2 2.0 1.0 CG E:ASP320 2.8 17.5 1.0 CD2 D:HIS151 2.8 25.1 1.0 OD1 E:ASP320 2.9 15.8 1.0 CE1 D:HIS151 3.0 25.0 1.0 CG D:HIS151 4.0 25.1 1.0 CD2 D:LEU150 4.0 24.0 1.0 ND1 D:HIS151 4.0 23.9 1.0 O D:HOH2773 4.1 23.3 1.0 NZ D:LYS337 4.1 21.0 1.0 CB E:ASP320 4.2 18.8 1.0 CE D:LYS337 4.4 20.1 1.0 CG D:LEU150 4.6 24.9 1.0 C E:TYR319 4.6 19.5 1.0 O E:HOH3787 4.7 20.9 1.0 O E:TYR319 4.8 19.6 1.0 N E:ASP320 4.8 19.1 1.0 O E:HOH3733 4.9 20.0 1.0 CA E:TYR319 4.9 19.0 1.0

Iron binding site 10 out of 12 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Inactive Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe3501 b:17.3 occ:1.00 NE2 E:HIS88 1.9 20.7 1.0 OD1 E:ASP170 2.1 27.5 1.0 NE2 E:HIS233 2.2 14.1 1.0 CE1 E:HIS88 2.9 22.2 1.0 CD2 E:HIS88 3.0 21.2 1.0 CG E:ASP170 3.0 27.3 1.0 CD2 E:HIS233 3.1 14.5 1.0 CE1 E:HIS233 3.2 14.8 1.0 OD2 E:ASP170 3.3 33.8 1.0 O E:HOH3702 3.4 21.8 1.0 OD1 E:ASP87 3.4 34.1 1.0 ND1 E:HIS88 4.0 22.2 1.0 CG E:HIS88 4.1 21.4 1.0 ND1 E:HIS233 4.3 15.4 1.0 CG E:ASP87 4.3 28.6 1.0 CG E:HIS233 4.3 17.0 1.0 OD2 E:ASP87 4.4 29.3 1.0 CB E:ASP170 4.4 24.3 1.0 CG E:GLU85 4.6 29.9 1.0 CB E:SER232 4.7 19.5 1.0 CA E:ASP170 4.9 23.6 1.0 CD2 E:HIS83 5.0 34.9 1.0

H.Seedorf, C.H.Hagemeier, S.Shima, R.K.Thauer, E.Warkentin, U.Ermler. Structure of Coenzyme F420H2 Oxidase (Fpra), A Di-Iron Flavoprotein From Methanogenic Archaea Catalyzing the Reduction of O2 to H2O. Febs J. V. 274 1588 2007.
ISSN: ISSN 1742-464X
PubMed: 17480207
DOI: 10.1111/J.1742-4658.2007.05706.X