Atomistry » Iron » PDB 2nwf-2oof » 2ohh
Atomistry »
  Iron »
    PDB 2nwf-2oof »
      2ohh »

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

Go back to Iron Binding Sites List in 2ohh
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

Go back to Iron Binding Sites List in 2ohh
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

Go back to Iron Binding Sites List in 2ohh
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

Go back to Iron Binding Sites List in 2ohh
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy