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Iron in PDB 1b25: Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus

Protein crystallography data

The structure of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, PDB code: 1b25 was solved by Y.L.Hu, S.Faham, R.Roy, M.W.W.Adams, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.340, 170.850, 180.640, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 22

Other elements in 1b25:

The structure of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus also contains other interesting chemical elements:

Tungsten (W) 4 atoms
Magnesium (Mg) 4 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus (pdb code 1b25). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus, PDB code: 1b25:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 1b25

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Iron binding site 1 out of 16 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe700

b:17.4
occ:1.00
FE1 A:SF4700 0.0 17.4 1.0
S4 A:SF4700 2.3 18.3 1.0
S2 A:SF4700 2.3 19.4 1.0
SG A:CYS284 2.3 19.1 1.0
S3 A:SF4700 2.3 18.4 1.0
FE2 A:SF4700 2.7 17.6 1.0
FE4 A:SF4700 2.7 21.6 1.0
FE3 A:SF4700 2.7 17.6 1.0
CB A:CYS284 3.3 15.3 1.0
N A:CYS284 3.7 19.7 1.0
NH2 A:ARG180 3.8 20.3 1.0
NZ A:LYS75 3.9 15.8 1.0
S1 A:SF4700 3.9 19.8 1.0
CE A:LYS75 4.0 15.7 1.0
CA A:CYS284 4.1 18.7 1.0
CZ A:ARG180 4.5 18.5 1.0
SG A:CYS291 4.6 19.5 1.0
SG A:CYS287 4.6 18.8 1.0
SG A:CYS491 4.7 17.0 1.0
C A:GLY283 4.8 21.0 1.0
CB A:CYS287 4.9 14.6 1.0
O A:HOH1078 4.9 30.5 1.0
CA A:GLY283 5.0 22.8 1.0

Iron binding site 2 out of 16 in 1b25

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Iron binding site 2 out of 16 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe700

b:17.6
occ:1.00
FE2 A:SF4700 0.0 17.6 1.0
S1 A:SF4700 2.3 19.8 1.0
S3 A:SF4700 2.3 18.4 1.0
S4 A:SF4700 2.3 18.3 1.0
SG A:CYS291 2.3 19.5 1.0
FE4 A:SF4700 2.6 21.6 1.0
FE1 A:SF4700 2.7 17.4 1.0
FE3 A:SF4700 2.7 17.6 1.0
CB A:CYS291 3.5 15.3 1.0
N A:CYS291 3.8 17.6 1.0
S2 A:SF4700 3.8 19.4 1.0
CA A:CYS291 4.2 13.1 1.0
O A:MET289 4.3 18.0 1.0
CD1 A:LEU493 4.4 15.8 1.0
O A:HOH820 4.5 17.9 1.0
NH2 A:ARG180 4.5 20.3 1.0
CZ2 A:TRP235 4.6 19.1 1.0
SG A:CYS287 4.7 18.8 1.0
C A:PRO290 4.7 23.0 1.0
SG A:CYS284 4.8 19.1 1.0
C A:CYS291 4.8 17.8 1.0
SG A:CYS491 4.8 17.0 1.0

Iron binding site 3 out of 16 in 1b25

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Iron binding site 3 out of 16 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe700

b:17.6
occ:1.00
FE3 A:SF4700 0.0 17.6 1.0
S2 A:SF4700 2.2 19.4 1.0
SG A:CYS491 2.3 17.0 1.0
S4 A:SF4700 2.3 18.3 1.0
S1 A:SF4700 2.3 19.8 1.0
FE4 A:SF4700 2.6 21.6 1.0
FE1 A:SF4700 2.7 17.4 1.0
FE2 A:SF4700 2.7 17.6 1.0
CB A:CYS491 3.3 14.5 1.0
S3 A:SF4700 3.9 18.4 1.0
CE A:LYS75 4.0 15.7 1.0
CD1 A:LEU493 4.1 15.8 1.0
NZ A:LYS75 4.3 15.8 1.0
CB A:LEU493 4.3 13.2 1.0
N33 A:PTT800 4.4 17.4 1.0
CG A:LEU493 4.4 8.8 1.0
C34 A:PTT800 4.5 16.1 1.0
SG A:CYS287 4.6 18.8 1.0
CA A:CYS491 4.7 19.6 1.0
SG A:CYS291 4.7 19.5 1.0
SG A:CYS284 4.7 19.1 1.0
CB A:SER72 4.8 13.4 1.0
O22 A:PTT800 4.8 21.5 1.0
CD A:PRO494 4.9 22.8 1.0
OG A:SER72 4.9 17.9 1.0

Iron binding site 4 out of 16 in 1b25

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Iron binding site 4 out of 16 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe700

b:21.6
occ:1.00
FE4 A:SF4700 0.0 21.6 1.0
S1 A:SF4700 2.3 19.8 1.0
SG A:CYS287 2.3 18.8 1.0
S2 A:SF4700 2.3 19.4 1.0
S3 A:SF4700 2.3 18.4 1.0
FE2 A:SF4700 2.6 17.6 1.0
FE3 A:SF4700 2.6 17.6 1.0
FE1 A:SF4700 2.7 17.4 1.0
CB A:CYS287 3.3 14.6 1.0
S4 A:SF4700 3.8 18.3 1.0
O A:MET289 3.9 18.0 1.0
OG A:SER72 4.2 17.9 1.0
C A:MET289 4.3 18.8 1.0
SG A:CYS491 4.6 17.0 1.0
CA A:PRO290 4.6 20.0 1.0
CG A:MET289 4.6 21.0 1.0
CB A:SER72 4.7 13.4 1.0
CA A:CYS287 4.7 17.5 1.0
SG A:CYS284 4.7 19.1 1.0
N A:PRO290 4.7 21.3 1.0
N A:CYS284 4.7 19.7 1.0
SG A:CYS291 4.8 19.5 1.0
N A:CYS291 4.8 17.6 1.0
CB A:CYS284 4.9 15.3 1.0

Iron binding site 5 out of 16 in 1b25

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Iron binding site 5 out of 16 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:19.5
occ:1.00
FE1 B:SF4701 0.0 19.5 1.0
S2 B:SF4701 2.3 18.5 1.0
S4 B:SF4701 2.3 19.0 1.0
S3 B:SF4701 2.3 19.9 1.0
SG B:CYS284 2.3 20.6 1.0
FE4 B:SF4701 2.7 18.5 1.0
FE2 B:SF4701 2.7 21.2 1.0
FE3 B:SF4701 2.7 20.8 1.0
CB B:CYS284 3.3 16.2 1.0
N B:CYS284 3.7 24.2 1.0
NZ B:LYS75 3.9 18.3 1.0
S1 B:SF4701 3.9 19.0 1.0
NH2 B:ARG180 3.9 21.1 1.0
CA B:CYS284 4.1 20.2 1.0
CE B:LYS75 4.2 18.9 1.0
CZ B:ARG180 4.6 19.0 1.0
SG B:CYS291 4.7 19.1 1.0
SG B:CYS287 4.7 21.2 1.0
SG B:CYS491 4.7 19.3 1.0
C B:GLY283 4.7 27.6 1.0
O B:HOH919 4.8 34.9 1.0
CB B:CYS287 4.9 19.5 1.0
CA B:GLY283 4.9 27.8 1.0

Iron binding site 6 out of 16 in 1b25

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Iron binding site 6 out of 16 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:21.2
occ:1.00
FE2 B:SF4701 0.0 21.2 1.0
SG B:CYS291 2.3 19.1 1.0
S3 B:SF4701 2.3 19.9 1.0
S4 B:SF4701 2.3 19.0 1.0
S1 B:SF4701 2.3 19.0 1.0
FE1 B:SF4701 2.7 19.5 1.0
FE4 B:SF4701 2.7 18.5 1.0
FE3 B:SF4701 2.7 20.8 1.0
CB B:CYS291 3.4 13.2 1.0
N B:CYS291 3.8 20.9 1.0
S2 B:SF4701 3.9 18.5 1.0
CA B:CYS291 4.1 20.7 1.0
CD1 B:LEU493 4.3 20.4 1.0
O B:MET289 4.4 18.9 1.0
O B:HOH837 4.4 21.8 1.0
NH2 B:ARG180 4.5 21.1 1.0
CZ2 B:TRP235 4.6 22.1 1.0
C B:PRO290 4.7 18.7 1.0
C B:CYS291 4.7 21.4 1.0
SG B:CYS284 4.8 20.6 1.0
SG B:CYS287 4.8 21.2 1.0
SG B:CYS491 4.9 19.3 1.0
CA B:PRO290 5.0 22.1 1.0

Iron binding site 7 out of 16 in 1b25

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Iron binding site 7 out of 16 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:20.8
occ:1.00
FE3 B:SF4701 0.0 20.8 1.0
S1 B:SF4701 2.3 19.0 1.0
SG B:CYS491 2.3 19.3 1.0
S2 B:SF4701 2.3 18.5 1.0
S4 B:SF4701 2.3 19.0 1.0
FE4 B:SF4701 2.7 18.5 1.0
FE2 B:SF4701 2.7 21.2 1.0
FE1 B:SF4701 2.7 19.5 1.0
CB B:CYS491 3.3 15.1 1.0
S3 B:SF4701 3.9 19.9 1.0
CD1 B:LEU493 4.2 20.4 1.0
CE B:LYS75 4.2 18.9 1.0
N33 B:PTT801 4.3 15.3 1.0
CB B:LEU493 4.3 18.0 1.0
CG B:LEU493 4.3 23.1 1.0
NZ B:LYS75 4.3 18.3 1.0
C34 B:PTT801 4.4 15.0 1.0
SG B:CYS287 4.6 21.2 1.0
CA B:CYS491 4.7 19.5 1.0
O22 B:PTT801 4.7 18.8 1.0
SG B:CYS291 4.7 19.1 1.0
SG B:CYS284 4.8 20.6 1.0
CB B:SER72 4.8 14.8 1.0
OG B:SER72 4.9 24.1 1.0
CD B:PRO494 5.0 17.8 1.0

Iron binding site 8 out of 16 in 1b25

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Iron binding site 8 out of 16 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:18.5
occ:1.00
FE4 B:SF4701 0.0 18.5 1.0
S2 B:SF4701 2.2 18.5 1.0
SG B:CYS287 2.3 21.2 1.0
S1 B:SF4701 2.3 19.0 1.0
S3 B:SF4701 2.3 19.9 1.0
FE3 B:SF4701 2.7 20.8 1.0
FE1 B:SF4701 2.7 19.5 1.0
FE2 B:SF4701 2.7 21.2 1.0
CB B:CYS287 3.3 19.5 1.0
S4 B:SF4701 3.9 19.0 1.0
O B:MET289 3.9 18.9 1.0
OG B:SER72 4.2 24.1 1.0
C B:MET289 4.4 24.0 1.0
CA B:PRO290 4.6 22.1 1.0
CB B:SER72 4.6 14.8 1.0
CG B:MET289 4.7 24.5 1.0
N B:PRO290 4.7 23.3 1.0
SG B:CYS491 4.7 19.3 1.0
N B:CYS284 4.7 24.2 1.0
CA B:CYS287 4.7 21.6 1.0
SG B:CYS284 4.7 20.6 1.0
N B:CYS291 4.8 20.9 1.0
SG B:CYS291 4.8 19.1 1.0
CB B:CYS284 4.9 16.2 1.0

Iron binding site 9 out of 16 in 1b25

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Iron binding site 9 out of 16 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe702

b:14.7
occ:1.00
FE1 C:SF4702 0.0 14.7 1.0
SG C:CYS284 2.3 14.9 1.0
S4 C:SF4702 2.3 16.6 1.0
S2 C:SF4702 2.3 17.7 1.0
S3 C:SF4702 2.3 15.7 1.0
FE3 C:SF4702 2.7 14.9 1.0
FE2 C:SF4702 2.7 15.9 1.0
FE4 C:SF4702 2.7 14.8 1.0
CB C:CYS284 3.3 11.4 1.0
N C:CYS284 3.7 18.6 1.0
NZ C:LYS75 3.8 12.1 1.0
NH2 C:ARG180 3.8 15.1 1.0
S1 C:SF4702 3.9 15.2 1.0
CE C:LYS75 4.1 12.5 1.0
CA C:CYS284 4.2 16.7 1.0
CZ C:ARG180 4.5 12.0 1.0
SG C:CYS291 4.6 14.8 1.0
SG C:CYS491 4.7 14.2 1.0
SG C:CYS287 4.7 12.6 1.0
O C:HOH891 4.8 25.7 1.0
C C:GLY283 4.8 22.2 1.0
CB C:CYS287 4.9 12.0 1.0
CA C:GLY283 5.0 20.8 1.0

Iron binding site 10 out of 16 in 1b25

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Iron binding site 10 out of 16 in the Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe702

b:15.9
occ:1.00
FE2 C:SF4702 0.0 15.9 1.0
SG C:CYS291 2.3 14.8 1.0
S1 C:SF4702 2.3 15.2 1.0
S3 C:SF4702 2.3 15.7 1.0
S4 C:SF4702 2.3 16.6 1.0
FE4 C:SF4702 2.7 14.8 1.0
FE1 C:SF4702 2.7 14.7 1.0
FE3 C:SF4702 2.8 14.9 1.0
CB C:CYS291 3.4 12.8 1.0
N C:CYS291 3.7 11.1 1.0
S2 C:SF4702 3.9 17.7 1.0
CA C:CYS291 4.1 9.6 1.0
O C:MET289 4.3 12.8 1.0
CD1 C:LEU493 4.4 13.2 1.0
NH2 C:ARG180 4.5 15.1 1.0
O C:HOH836 4.5 16.2 1.0
CZ2 C:TRP235 4.6 13.2 1.0
C C:PRO290 4.6 15.7 1.0
C C:CYS291 4.7 12.1 1.0
SG C:CYS287 4.8 12.6 1.0
SG C:CYS284 4.8 14.9 1.0
CA C:PRO290 4.8 12.6 1.0
SG C:CYS491 4.9 14.2 1.0

Reference:

Y.Hu, S.Faham, R.Roy, M.W.Adams, D.C.Rees. Formaldehyde Ferredoxin Oxidoreductase From Pyrococcus Furiosus: the 1.85 A Resolution Crystal Structure and Its Mechanistic Implications. J.Mol.Biol. V. 286 899 1999.
ISSN: ISSN 0022-2836
PubMed: 10024458
DOI: 10.1006/JMBI.1998.2488
Page generated: Sun Dec 13 14:06:20 2020

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