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

Protein crystallography data

The structure of Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Active Oxidized State, PDB code: 2ohh 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) 10.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.740, 120.860, 92.690, 90.00, 110.40, 90.00
R / Rfree (%) 18.4 / 21.8

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 2ohh

Go back to Iron Binding Sites List in 2ohh
Iron binding site 1 out of 8 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Active 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, Active Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:26.7
occ:1.00
 OD1 A:ASP170 1.8 23.7 0.3
NE2 A:HIS88 1.9 27.5 1.0
NE2 A:HIS233 2.0 28.1 1.0
OD1 A:ASP170 2.1 31.0 0.7
OD2 A:ASP170 2.5 30.4 0.7
CG A:ASP170 2.7 30.1 0.7
OD2 A:ASP87 2.7 40.1 1.0
CG A:ASP170 2.8 26.9 0.3
CE1 A:HIS88 2.9 30.1 1.0
CD2 A:HIS88 2.9 27.4 1.0
CD2 A:HIS233 3.0 25.4 1.0
CE1 A:HIS233 3.0 25.6 1.0
OD2 A:ASP170 3.2 26.3 0.3
O A:HOH944 3.3 40.7 1.0
CG A:ASP87 3.5 34.2 1.0
OD1 A:ASP87 3.6 38.6 1.0
FE A:FE502 3.6 30.6 0.4
OG A:SER232 3.9 20.4 0.3
ND1 A:HIS88 4.0 26.5 1.0
CG A:HIS88 4.0 27.5 1.0
ND1 A:HIS233 4.1 22.7 1.0
CG A:HIS233 4.1 23.6 1.0
CB A:ASP170 4.2 26.6 1.0
CE1 A:HIS83 4.3 18.4 0.3
O A:HOH920 4.3 43.1 1.0
OE2 A:GLU85 4.4 49.9 1.0
ND1 A:HIS83 4.6 21.9 0.3
CD2 A:HIS83 4.7 37.7 0.7
CB A:ASP87 4.8 29.6 1.0
CB A:SER232 4.8 24.2 0.7
CB A:SER232 4.8 23.2 0.3
CA A:ASP170 4.9 26.7 1.0
NE2 A:HIS83 4.9 36.5 0.7
CD A:GLU85 4.9 47.0 1.0

Iron binding site 2 out of 8 in 2ohh

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Iron binding site 2 out of 8 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Active 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, Active Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:30.6
occ:0.40
 OE2 A:GLU85 1.9 49.9 1.0
NE2 A:HIS151 2.2 34.8 0.5
NE2 A:HIS83 2.3 36.5 0.7
OD2 A:ASP170 2.3 26.3 0.3
CD2 A:HIS151 2.8 32.5 0.5
OD2 A:ASP170 2.9 30.4 0.7
CD2 A:HIS83 3.0 37.7 0.7
CD A:GLU85 3.2 47.0 1.0
CG A:ASP170 3.2 26.9 0.3
CE1 A:HIS151 3.2 33.7 0.5
CE1 A:HIS83 3.3 38.2 0.7
CG A:ASP170 3.5 30.1 0.7
OD1 A:ASP170 3.6 23.7 0.3
FE A:FE501 3.6 26.7 1.0
O A:HOH944 3.8 40.7 1.0
CB A:GLU85 3.8 30.4 1.0
CG A:HIS151 3.9 33.2 0.5
OE1 A:GLU85 4.0 48.5 1.0
OD1 A:ASP170 4.0 31.0 0.7
O A:HOH724 4.1 37.2 1.0
CG A:GLU85 4.1 36.2 1.0
ND1 A:HIS151 4.1 32.6 0.5
CG A:HIS83 4.2 34.0 0.7
ND1 A:HIS83 4.2 21.9 0.3
ND1 A:HIS83 4.3 34.6 0.7
CB A:ASP170 4.3 26.6 1.0
CD2 A:HIS88 4.5 27.4 1.0
NE2 A:HIS88 4.6 27.5 1.0
OD1 A:ASP87 4.6 38.6 1.0
NE1 A:TRP152 4.6 30.0 0.5
CE2 A:TRP152 4.7 29.9 0.5
CD1 A:TRP152 4.9 28.6 0.5
CE1 A:HIS83 4.9 18.4 0.3
O A:HOH920 4.9 43.1 1.0

Iron binding site 3 out of 8 in 2ohh

Go back to Iron Binding Sites List in 2ohh
Iron binding site 3 out of 8 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Active 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, Active Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1501

b:33.7
occ:1.00
 NE2 B:HIS88 2.0 34.5 1.0
OD1 B:ASP170 2.0 45.4 1.0
NE2 B:HIS233 2.1 36.7 1.0
OD2 B:ASP87 2.5 46.5 1.0
CE1 B:HIS88 2.9 37.5 1.0
CD2 B:HIS233 2.9 36.5 1.0
CG B:ASP170 3.0 42.9 1.0
CD2 B:HIS88 3.0 37.9 1.0
CE1 B:HIS233 3.2 40.4 1.0
OD2 B:ASP170 3.2 46.1 1.0
CG B:ASP87 3.3 44.2 1.0
FE B:FE1502 3.5 34.5 0.4
OD1 B:ASP87 3.5 46.3 1.0
OG B:SER232 3.9 31.6 0.3
ND1 B:HIS88 4.0 37.0 1.0
CG B:HIS88 4.1 36.4 1.0
CG B:HIS233 4.1 36.1 1.0
ND1 B:HIS233 4.2 36.4 1.0
CB B:ASP170 4.4 38.5 1.0
OE1 B:GLU85 4.5 51.0 1.0
CB B:SER232 4.5 35.9 0.7
CB B:SER232 4.6 34.9 0.3
CB B:ASP87 4.7 42.2 1.0
CD2 B:HIS83 4.7 45.0 0.7
CD B:GLU85 4.8 50.3 1.0
OH B:TYR25 4.9 55.6 1.0
CA B:ASP170 4.9 38.0 1.0
OD1 B:ASN169 5.0 38.5 0.3
CE2 B:TYR25 5.0 53.5 1.0

Iron binding site 4 out of 8 in 2ohh

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Iron binding site 4 out of 8 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Active 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, Active Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1502

b:34.5
occ:0.40
 NE2 B:HIS151 1.9 34.3 0.5
OE1 B:GLU85 1.9 51.0 1.0
OD2 B:ASP170 2.1 46.1 1.0
NE2 B:HIS83 2.2 45.5 0.7
CE1 B:HIS151 2.8 34.1 0.5
CD2 B:HIS83 2.9 45.0 0.7
CD2 B:HIS151 2.9 33.7 0.5
CD B:GLU85 3.1 50.3 1.0
CG B:ASP170 3.2 42.9 1.0
CE1 B:HIS83 3.4 47.8 0.7
FE B:FE1501 3.5 33.7 1.0
OD1 B:ASP170 3.6 45.4 1.0
CB B:GLU85 3.8 42.1 1.0
OE2 B:GLU85 3.8 54.1 1.0
ND1 B:HIS151 3.9 35.6 0.5
CG B:HIS151 4.0 34.9 0.5
CG B:GLU85 4.0 45.6 1.0
CG B:HIS83 4.2 42.6 0.7
ND1 B:HIS83 4.4 45.0 0.7
CB B:ASP170 4.4 38.5 1.0
CD2 B:HIS88 4.4 37.9 1.0
NE2 B:HIS88 4.5 34.5 1.0
OD1 B:ASP87 4.5 46.3 1.0
ND2 B:ASN169 4.8 39.3 0.3
NE1 B:TRP152 4.8 35.1 0.5
OD2 B:ASP87 4.8 46.5 1.0
CE2 B:TRP152 4.8 34.7 0.5

Iron binding site 5 out of 8 in 2ohh

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Iron binding site 5 out of 8 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Active 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, Active Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe2501

b:30.8
occ:1.00
 NE2 D:HIS88 1.8 37.6 1.0
O2 D:SO42414 1.9 45.3 0.5
NE2 D:HIS233 2.1 25.4 1.0
OD1 D:ASP170 2.1 38.3 1.0
OD2 D:ASP87 2.3 44.0 1.0
CD2 D:HIS233 2.8 31.1 1.0
CE1 D:HIS88 2.8 36.0 1.0
CD2 D:HIS88 2.9 37.6 1.0
CG D:ASP170 3.0 39.7 1.0
S D:SO42414 3.2 47.1 0.5
CE1 D:HIS233 3.2 31.9 1.0
OD2 D:ASP170 3.2 43.7 1.0
CG D:ASP87 3.3 41.9 1.0
O3 D:SO42414 3.5 46.3 0.5
OD1 D:ASP87 3.6 44.2 1.0
FE D:FE2502 3.7 31.8 0.4
OG D:SER232 3.8 28.1 0.3
O1 D:SO42414 3.8 47.3 0.5
ND1 D:HIS88 3.9 36.9 1.0
CG D:HIS88 4.0 36.1 1.0
CG D:HIS233 4.0 28.6 1.0
ND1 D:HIS233 4.2 29.1 1.0
O4 D:SO42414 4.3 44.0 0.5
CB D:ASP170 4.3 34.7 1.0
CB D:ASP87 4.6 35.6 1.0
CB D:SER232 4.6 30.3 0.3
CB D:SER232 4.7 30.8 0.7
CD2 D:HIS83 4.8 45.2 0.7
CD D:GLU85 4.9 49.9 1.0
OE1 D:GLU85 4.9 52.4 1.0
CA D:ASP170 4.9 34.4 1.0
OE2 D:GLU85 5.0 49.7 1.0

Iron binding site 6 out of 8 in 2ohh

Go back to Iron Binding Sites List in 2ohh
Iron binding site 6 out of 8 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Active 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, Active Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe2502

b:31.8
occ:0.40
 OD2 D:ASP170 2.0 43.7 1.0
NE2 D:HIS151 2.1 35.1 0.5
OE1 D:GLU85 2.2 52.4 1.0
NE2 D:HIS83 2.3 46.6 0.7
O1 D:SO42414 2.7 47.3 0.5
CD2 D:HIS83 2.9 45.2 0.7
CD2 D:HIS151 2.9 37.6 0.5
CD D:GLU85 3.1 49.9 1.0
CG D:ASP170 3.2 39.7 1.0
CE1 D:HIS151 3.2 35.8 0.5
S D:SO42414 3.6 47.1 0.5
CE1 D:HIS83 3.6 44.9 0.7
O2 D:SO42414 3.6 45.3 0.5
FE D:FE2501 3.7 30.8 1.0
OE2 D:GLU85 3.7 49.7 1.0
OD1 D:ASP170 3.7 38.3 1.0
CB D:GLU85 3.9 38.1 1.0
O3 D:SO42414 3.9 46.3 0.5
CG D:GLU85 4.1 42.3 1.0
CG D:HIS151 4.1 35.6 0.5
CG D:HIS83 4.2 42.3 0.7
ND1 D:HIS151 4.2 36.5 0.5
CB D:ASP170 4.3 34.7 1.0
ND1 D:HIS83 4.5 44.5 0.7
CD2 D:HIS88 4.6 37.6 1.0
NE2 D:HIS88 4.7 37.6 1.0
OD1 D:ASP87 4.7 44.2 1.0
CE2 D:TRP152 4.8 32.8 0.5
NE1 D:TRP152 4.8 34.0 0.5
O4 D:SO42414 4.9 44.0 0.5
OD2 D:ASP87 4.9 44.0 1.0

Iron binding site 7 out of 8 in 2ohh

Go back to Iron Binding Sites List in 2ohh
Iron binding site 7 out of 8 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Active 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, Active Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe3501

b:25.5
occ:1.00
 NE2 E:HIS88 2.0 23.6 1.0
NE2 E:HIS233 2.0 19.4 1.0
OD1 E:ASP170 2.1 31.8 1.0
O E:HOH3971 2.2 38.2 1.0
CD2 E:HIS233 2.9 24.6 1.0
OD2 E:ASP87 2.9 38.2 1.0
CE1 E:HIS88 2.9 27.6 1.0
CG E:ASP170 3.0 33.3 1.0
CD2 E:HIS88 3.0 25.6 1.0
CE1 E:HIS233 3.1 26.0 1.0
O E:HOH3970 3.1 40.2 0.5
OD2 E:ASP170 3.3 40.7 1.0
CG E:ASP87 3.5 34.3 1.0
OD1 E:ASP87 3.6 35.7 1.0
FE E:FE3502 3.6 26.0 0.4
OG E:SER232 4.0 21.9 0.3
CG E:HIS233 4.1 22.6 1.0
ND1 E:HIS88 4.1 23.1 1.0
ND1 E:HIS233 4.1 21.7 1.0
CG E:HIS88 4.1 25.4 1.0
CB E:ASP170 4.3 25.9 1.0
CD2 E:HIS83 4.6 35.0 0.7
OE1 E:GLU85 4.7 40.7 1.0
CB E:SER232 4.8 23.8 0.7
NE2 E:HIS83 4.8 36.9 0.7
CB E:SER232 4.8 23.6 0.3
CB E:ASP87 4.8 27.3 1.0
CA E:ASP170 4.9 26.3 1.0
CD E:GLU85 4.9 40.7 1.0

Iron binding site 8 out of 8 in 2ohh

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Iron binding site 8 out of 8 in the Crystal Structure of Coenzyme F420H2 Oxidase (Fpra), A Diiron Flavoprotein, Active 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, Active Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe3502

b:26.0
occ:0.40
 O E:HOH3971 1.8 38.2 1.0
CE1 E:HIS151 1.8 27.4 0.5
OD2 E:ASP170 2.1 40.7 1.0
OE1 E:GLU85 2.1 40.7 1.0
NE2 E:HIS83 2.1 36.9 0.7
ND1 E:HIS151 2.7 33.8 0.5
NE2 E:HIS151 2.9 34.6 0.5
CD2 E:HIS83 3.0 35.0 0.7
CD E:GLU85 3.1 40.7 1.0
CE1 E:HIS83 3.2 36.1 0.7
CG E:ASP170 3.2 33.3 1.0
O E:HOH3970 3.5 40.2 0.5
FE E:FE3501 3.6 25.5 1.0
OD1 E:ASP170 3.7 31.8 1.0
CG E:HIS151 3.9 32.6 0.5
OE2 E:GLU85 3.9 42.0 1.0
CB E:GLU85 3.9 32.2 1.0
CD2 E:HIS151 4.0 32.2 0.5
CG E:GLU85 4.1 34.9 1.0
CG E:HIS83 4.1 33.1 0.7
ND1 E:HIS83 4.2 35.7 0.7
O E:HOH3744 4.3 40.9 1.0
CB E:ASP170 4.4 25.9 1.0
CD2 E:HIS88 4.6 25.6 1.0
NE2 E:HIS88 4.6 23.6 1.0
OD1 E:ASP87 4.7 35.7 1.0
CE2 E:TRP152 4.9 29.2 0.5
NE1 E:TRP152 5.0 29.5 0.5

Reference:

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
Page generated: Sun Aug 4 00:58:42 2024

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