Iron in PDB 2ohi: Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced State

The structure of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced State, PDB code: 2ohi 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)	20.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	97.798, 123.113, 135.864, 90.00, 103.40, 90.00
R / Rfree (%)	20.3 / 26.9

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

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced State (pdb code 2ohi). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced State, PDB code: 2ohi:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced 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, Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:45.1 occ:1.00 NE2 A:HIS88 2.0 48.1 1.0 OD1 A:ASP170 2.2 45.0 1.0 NE2 A:HIS233 2.3 46.4 1.0 OD1 A:ASP87 2.6 48.4 1.0 CE1 A:HIS88 2.9 47.1 1.0 CG A:ASP170 2.9 45.7 1.0 OD2 A:ASP170 3.0 48.7 1.0 CD2 A:HIS233 3.0 44.7 1.0 CD2 A:HIS88 3.1 46.5 1.0 FE A:FE503 3.5 47.2 0.4 CE1 A:HIS233 3.5 44.3 1.0 CG A:ASP87 3.6 47.5 1.0 OD2 A:ASP87 3.9 49.5 1.0 ND1 A:HIS88 4.0 46.2 1.0 OH A:TYR25 4.1 59.9 1.0 CG A:HIS88 4.2 44.9 1.0 OG A:SER232 4.2 42.4 1.0 CG A:HIS233 4.3 43.2 1.0 CB A:ASP170 4.4 44.2 1.0 ND1 A:HIS233 4.5 44.4 1.0 O A:HOH745 4.7 40.9 1.0 CE2 A:TYR25 4.8 58.9 1.0 ND2 A:ASN169 4.9 45.7 0.7 OE1 A:GLU85 4.9 50.2 1.0 CB A:ASP87 4.9 46.0 1.0 CD2 A:HIS83 4.9 53.0 1.0 CA A:ASP170 5.0 44.2 1.0 CZ A:TYR25 5.0 59.3 1.0

Iron binding site 2 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced 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, Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:47.2 occ:0.40 OE1 A:GLU85 2.0 50.2 1.0 OD2 A:ASP170 2.1 48.7 1.0 NE2 A:HIS83 2.7 54.1 1.0 CD A:GLU85 2.9 49.5 1.0 CD2 A:HIS83 3.2 53.0 1.0 O A:HOH745 3.2 40.9 1.0 CG A:ASP170 3.3 45.7 1.0 ND1 A:HIS151 3.4 64.1 1.0 FE A:FE501 3.5 45.1 1.0 CE1 A:HIS151 3.5 64.7 1.0 OE2 A:GLU85 3.6 51.8 1.0 CE1 A:HIS83 3.7 53.8 1.0 CB A:GLU85 3.8 48.4 1.0 OD1 A:ASP170 3.9 45.0 1.0 CG A:GLU85 3.9 49.3 1.0 CG A:HIS83 4.3 51.5 1.0 NE2 A:HIS88 4.3 48.1 1.0 CB A:ASP170 4.4 44.2 1.0 CD2 A:HIS88 4.4 46.5 1.0 OD2 A:ASP87 4.5 49.5 1.0 ND1 A:HIS83 4.6 53.2 1.0 CG A:HIS151 4.7 63.8 1.0 NE1 A:TRP152 4.8 63.6 1.0 OH A:TYR25 4.8 59.9 1.0 NE2 A:HIS151 4.8 64.6 1.0 OD1 A:ASP87 4.8 48.4 1.0 CE2 A:TRP152 4.8 63.7 1.0

Iron binding site 3 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced 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, Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1501 b:36.9 occ:1.00 NE2 B:HIS88 2.0 40.2 1.0 OD1 B:ASP170 2.1 48.1 1.0 NE2 B:HIS233 2.1 43.4 1.0 O B:HOH1739 2.5 44.4 1.0 OD2 B:ASP87 2.7 54.9 1.0 CE1 B:HIS88 2.9 41.0 1.0 CD2 B:HIS233 3.0 41.6 1.0 CD2 B:HIS88 3.1 41.0 1.0 CG B:ASP170 3.1 46.9 1.0 CE1 B:HIS233 3.2 42.5 1.0 OD2 B:ASP170 3.4 49.6 1.0 FE B:FE1503 3.7 45.6 0.4 CG B:ASP87 3.8 50.1 1.0 ND1 B:HIS88 4.1 40.2 1.0 OG B:SER232 4.1 43.9 1.0 CG B:HIS233 4.1 42.2 1.0 CG B:HIS88 4.2 41.3 1.0 OD1 B:ASP87 4.2 54.8 1.0 ND1 B:HIS233 4.2 43.6 1.0 OE2 B:GLU85 4.3 54.8 1.0 CB B:ASP170 4.5 44.5 1.0 OH B:TYR25 4.6 59.5 1.0 CD B:GLU85 4.8 51.5 1.0 ND2 B:ASN169 4.8 49.5 1.0 CA B:ASP170 5.0 44.3 1.0 CB B:ASP87 5.0 47.1 1.0

Iron binding site 4 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced 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, Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1503 b:45.6 occ:0.40 OD2 B:ASP170 2.1 49.6 1.0 NE2 B:HIS151 2.3 66.5 1.0 OE1 B:GLU85 2.4 55.3 1.0 NE2 B:HIS83 2.6 52.9 1.0 CD B:GLU85 3.0 51.5 1.0 CD2 B:HIS151 3.0 66.7 1.0 CG B:ASP170 3.1 46.9 1.0 CD2 B:HIS83 3.2 50.5 1.0 OE2 B:GLU85 3.4 54.8 1.0 CE1 B:HIS151 3.5 65.4 1.0 OD1 B:ASP170 3.6 48.1 1.0 O B:HOH1739 3.6 44.4 1.0 FE B:FE1501 3.7 36.9 1.0 CB B:GLU85 3.8 48.8 1.0 CE1 B:HIS83 3.8 53.6 1.0 CG B:GLU85 3.9 50.9 1.0 CG B:HIS151 4.3 65.3 1.0 CB B:ASP170 4.4 44.5 1.0 ND1 B:HIS151 4.5 65.5 1.0 CG B:HIS83 4.5 50.5 1.0 CD2 B:HIS88 4.7 41.0 1.0 NE2 B:HIS88 4.7 40.2 1.0 ND1 B:HIS83 4.7 52.1 1.0 CE2 B:TRP152 4.8 65.5 1.0 NE1 B:TRP152 4.8 65.4 1.0 ND2 B:ASN169 4.9 49.5 1.0 CD2 B:TRP152 5.0 65.2 1.0

Iron binding site 5 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced 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, Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe2501 b:39.1 occ:1.00 NE2 D:HIS88 2.1 44.4 1.0 NE2 D:HIS233 2.2 42.1 1.0 OD1 D:ASP170 2.3 48.7 1.0 OD2 D:ASP87 2.5 52.3 1.0 O D:HOH2743 2.8 42.8 1.0 CD2 D:HIS233 2.9 40.5 1.0 CE1 D:HIS88 3.0 46.2 1.0 CG D:ASP170 3.1 46.8 1.0 CD2 D:HIS88 3.1 44.4 1.0 OD2 D:ASP170 3.2 51.7 1.0 CE1 D:HIS233 3.3 41.6 1.0 CG D:ASP87 3.5 50.0 1.0 FE D:FE2503 3.8 36.5 0.4 OD1 D:ASP87 3.9 55.0 1.0 CG D:HIS233 4.1 41.3 1.0 ND1 D:HIS88 4.2 45.4 1.0 OE2 D:GLU85 4.2 58.9 1.0 CG D:HIS88 4.2 44.5 1.0 OG D:SER232 4.3 43.7 1.0 ND1 D:HIS233 4.3 42.4 1.0 CB D:ASP170 4.5 44.5 1.0 CE1 D:HIS83 4.6 46.1 0.3 CB D:ASP87 4.6 46.8 1.0 O D:HOH2747 4.7 50.7 1.0 OH D:TYR25 4.8 61.5 1.0 ND1 D:HIS83 4.8 45.9 0.3 CD D:GLU85 4.9 55.7 1.0

Iron binding site 6 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced 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, Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe2503 b:36.5 occ:0.40 NE2 D:HIS151 2.0 63.0 0.7 OD2 D:ASP170 2.3 51.7 1.0 CE1 D:HIS83 2.6 50.6 0.7 OE1 D:GLU85 2.7 57.2 1.0 CE1 D:HIS151 2.9 63.7 0.7 CD2 D:HIS151 3.1 63.5 0.7 ND1 D:HIS83 3.2 51.1 0.7 O D:HOH2747 3.2 50.7 1.0 CD D:GLU85 3.2 55.7 1.0 CG D:ASP170 3.4 46.8 1.0 OE2 D:GLU85 3.5 58.9 1.0 NE2 D:HIS83 3.6 50.3 0.7 FE D:FE2501 3.8 39.1 1.0 O D:HOH2743 3.9 42.8 1.0 OD1 D:ASP170 4.0 48.7 1.0 ND1 D:HIS151 4.0 63.7 0.7 CB D:GLU85 4.1 49.3 1.0 CG D:HIS151 4.2 63.4 0.7 CG D:GLU85 4.2 52.2 1.0 NE1 D:TRP152 4.3 65.5 1.0 CG D:HIS83 4.4 50.6 0.7 ND1 D:HIS83 4.4 45.9 0.3 CB D:ASP170 4.4 44.5 1.0 CD2 D:HIS83 4.6 51.1 0.7 CD1 D:TRP152 4.6 65.2 1.0 CE2 D:TRP152 4.6 65.7 1.0 CD2 D:HIS88 4.8 44.4 1.0 NE2 D:HIS88 4.8 44.4 1.0 ND2 D:ASN169 4.8 48.9 0.7 OD1 D:ASP87 4.9 55.0 1.0 OD2 D:ASP87 4.9 52.3 1.0 CG D:TRP152 5.0 64.2 1.0 CD2 D:TRP152 5.0 65.5 1.0

Iron binding site 7 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced 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, Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe3501 b:44.8 occ:1.00 OD1 E:ASP170 2.2 47.5 1.0 NE2 E:HIS88 2.2 43.5 1.0 NE2 E:HIS233 2.3 38.6 1.0 CG E:ASP170 3.0 46.8 1.0 OD2 E:ASP87 3.0 50.5 1.0 CD2 E:HIS233 3.1 37.9 1.0 OD2 E:ASP170 3.1 48.8 1.0 CE1 E:HIS88 3.2 44.1 1.0 CD2 E:HIS88 3.2 43.1 1.0 CE1 E:HIS233 3.5 37.5 1.0 OD1 E:ASP87 3.5 50.5 1.0 CG E:ASP87 3.7 48.2 1.0 FE E:FE3503 3.9 58.1 0.4 OG E:SER232 4.2 43.6 1.0 CG E:HIS233 4.3 38.8 1.0 ND1 E:HIS88 4.3 42.8 1.0 CG E:HIS88 4.4 42.9 1.0 CB E:ASP170 4.4 44.8 1.0 ND1 E:HIS233 4.5 38.6 1.0 OE2 E:GLU85 4.7 52.6 1.0 CD2 E:HIS83 4.8 50.1 1.0 ND2 E:ASN169 4.9 50.1 1.0 CD E:GLU85 5.0 49.7 1.0

Iron binding site 8 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced 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, Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe3503 b:58.1 occ:0.40 NE2 E:HIS83 2.2 51.8 1.0 OD2 E:ASP170 2.5 48.8 1.0 OE1 E:GLU85 2.6 50.4 1.0 CD2 E:HIS83 2.8 50.1 1.0 CD2 E:HIS151 2.9 62.4 0.3 CD E:GLU85 3.3 49.7 1.0 NE2 E:HIS151 3.4 62.1 0.3 CE1 E:HIS83 3.4 52.0 1.0 CG E:ASP170 3.6 46.8 1.0 CB E:GLU85 3.9 48.3 1.0 FE E:FE3501 3.9 44.8 1.0 OE2 E:GLU85 3.9 52.6 1.0 CG E:HIS83 4.1 50.0 1.0 CG E:HIS151 4.2 62.5 0.3 CG E:GLU85 4.2 49.4 1.0 OD1 E:ASP170 4.2 47.5 1.0 ND1 E:HIS83 4.4 51.2 1.0 CD2 E:HIS151 4.4 63.4 0.7 CE2 E:TRP152 4.5 65.3 1.0 NE1 E:TRP152 4.6 65.4 1.0 CE1 E:HIS151 4.6 62.2 0.3 CB E:ASP170 4.7 44.8 1.0 CD2 E:TRP152 4.7 65.3 1.0 CZ2 E:TRP152 4.7 64.3 1.0 CG E:HIS151 4.8 63.4 0.7 CD1 E:TRP152 4.9 64.9 1.0 CB E:HIS151 5.0 63.0 0.7 CD2 E:HIS88 5.0 43.1 1.0 CB E:HIS151 5.0 62.7 0.3 CG E:TRP152 5.0 63.9 1.0

Iron binding site 9 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced 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, Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe501 b:37.9 occ:1.00 NE2 G:HIS88 2.2 44.7 1.0 NE2 G:HIS233 2.2 42.7 1.0 OD1 G:ASP170 2.2 47.4 1.0 OD2 G:ASP87 2.8 52.5 1.0 CD2 G:HIS233 3.0 42.6 1.0 CG G:ASP170 3.0 47.0 1.0 CD2 G:HIS88 3.1 42.0 1.0 OD2 G:ASP170 3.2 49.0 1.0 CE1 G:HIS88 3.2 43.6 1.0 CE1 G:HIS233 3.3 43.7 1.0 O G:HOH741 3.6 53.0 1.0 CG G:ASP87 3.7 49.1 1.0 FE G:FE503 3.7 32.6 0.4 OD1 G:ASP87 3.9 51.1 1.0 OE2 G:GLU85 4.2 55.5 1.0 CG G:HIS88 4.2 42.9 1.0 CG G:HIS233 4.3 41.6 1.0 ND1 G:HIS88 4.3 43.7 1.0 OG G:SER232 4.3 44.7 1.0 ND1 G:HIS233 4.4 43.6 1.0 CB G:ASP170 4.4 45.1 1.0 OH G:TYR25 4.6 60.1 1.0 ND2 G:ASN169 4.9 45.8 0.7 CD G:GLU85 5.0 54.0 1.0 CD2 G:HIS83 5.0 53.5 1.0 CG G:GLU85 5.0 51.8 1.0 CB G:ASP87 5.0 46.0 1.0

Iron binding site 10 out of 16 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Reduced 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, Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe503 b:32.6 occ:0.40 OD2 G:ASP170 2.2 49.0 1.0 NE2 G:HIS83 2.3 54.6 1.0 NE2 G:HIS151 2.6 66.9 1.0 CD2 G:HIS83 2.9 53.5 1.0 OE2 G:GLU85 3.1 55.5 1.0 CD G:GLU85 3.1 54.0 1.0 CD2 G:HIS151 3.2 66.2 1.0 CG G:ASP170 3.4 47.0 1.0 CE1 G:HIS83 3.4 54.8 1.0 CB G:GLU85 3.6 49.1 1.0 OE1 G:GLU85 3.6 55.5 1.0 CG G:GLU85 3.6 51.8 1.0 FE G:FE501 3.7 37.9 1.0 CE1 G:HIS151 3.8 67.2 1.0 O G:HOH709 3.9 68.0 1.0 OD1 G:ASP170 3.9 47.4 1.0 CG G:HIS83 4.1 51.8 1.0 ND1 G:HIS83 4.3 54.0 1.0 CG G:HIS151 4.5 65.1 1.0 CB G:ASP170 4.5 45.1 1.0 ND2 G:ASN169 4.6 45.8 0.7 CD2 G:HIS88 4.7 42.0 1.0 O G:HOH741 4.8 53.0 1.0 ND1 G:HIS151 4.8 67.0 1.0 OD1 G:ASP87 4.8 51.1 1.0 NE2 G:HIS88 4.9 44.7 1.0 CE2 G:TRP152 4.9 64.2 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