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Iron in PDB 8rja: Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum

Enzymatic activity of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum

All present enzymatic activity of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum:
1.2.7.12; 1.6.5.11; 3.5.2.5;

Protein crystallography data

The structure of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum, PDB code: 8rja was solved by O.N.Lemaire, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.38 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.627, 135.636, 149.902, 90, 90.49, 90
R / Rfree (%) 17.6 / 21

Other elements in 8rja:

The structure of Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 4 atoms
Zinc (Zn) 4 atoms
Tungsten (W) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum (pdb code 8rja). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 48 binding sites of Iron where determined in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum, PDB code: 8rja:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 48 in 8rja

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Iron binding site 1 out of 48 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


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 the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:11.7
occ:1.00
FE1 B:SF4501 0.0 11.7 1.0
S4 B:SF4501 2.3 12.5 1.0
S2 B:SF4501 2.3 10.4 1.0
S3 B:SF4501 2.3 12.9 1.0
SG B:CYS12 2.4 15.9 1.0
FE2 B:SF4501 2.7 8.6 1.0
FE4 B:SF4501 2.7 10.9 1.0
FE3 B:SF4501 2.7 11.0 1.0
CB B:CYS12 3.1 9.5 1.0
N B:CYS12 3.7 13.2 1.0
CA B:CYS12 3.9 9.9 1.0
S1 B:SF4501 4.0 14.3 1.0
CB B:SER14 4.1 12.5 1.0
OG B:SER14 4.3 12.3 1.0
O B:CYS12 4.3 11.5 1.0
C B:CYS12 4.3 13.3 1.0
SG B:CYS35 4.6 14.1 1.0
SG B:CYS9 4.7 13.5 1.0
SG B:CYS16 4.7 15.2 1.0
CD B:PRO156 4.8 18.5 1.0
N B:SER14 4.8 8.9 1.0
CD1 B:PHE11 4.8 13.8 1.0
C B:PHE11 4.9 10.8 1.0
CB B:PHE11 4.9 12.6 1.0
CA B:SER14 5.0 10.6 1.0

Iron binding site 2 out of 48 in 8rja

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Iron binding site 2 out of 48 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


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 the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:8.6
occ:1.00
FE2 B:SF4501 0.0 8.6 1.0
SG B:CYS9 2.2 13.5 1.0
S1 B:SF4501 2.3 14.3 1.0
S4 B:SF4501 2.3 12.5 1.0
S3 B:SF4501 2.4 12.9 1.0
FE4 B:SF4501 2.6 10.9 1.0
FE1 B:SF4501 2.7 11.7 1.0
FE3 B:SF4501 2.7 11.0 1.0
CB B:CYS9 3.0 15.5 1.0
S2 B:SF4501 3.8 10.4 1.0
CA B:GLY38 4.1 16.1 1.0
CB B:PHE11 4.3 12.6 1.0
N B:GLY38 4.4 16.6 1.0
N B:CYS12 4.5 13.2 1.0
CA B:CYS9 4.5 13.3 1.0
SG B:CYS35 4.6 14.1 1.0
SG B:CYS16 4.7 15.2 1.0
N B:PHE11 4.8 10.8 1.0
SG B:CYS12 4.9 15.9 1.0
CB B:CYS16 4.9 15.4 1.0
C B:CYS9 5.0 12.5 1.0
CA B:PHE11 5.0 12.2 1.0

Iron binding site 3 out of 48 in 8rja

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Iron binding site 3 out of 48 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


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 the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:11.0
occ:1.00
FE3 B:SF4501 0.0 11.0 1.0
S2 B:SF4501 2.3 10.4 1.0
S1 B:SF4501 2.3 14.3 1.0
S4 B:SF4501 2.3 12.5 1.0
SG B:CYS35 2.3 14.1 1.0
FE4 B:SF4501 2.7 10.9 1.0
FE2 B:SF4501 2.7 8.6 1.0
FE1 B:SF4501 2.7 11.7 1.0
CB B:CYS35 3.4 15.5 1.0
N B:CYS35 4.0 15.6 1.0
S3 B:SF4501 4.0 12.9 1.0
CA B:CYS35 4.2 14.8 1.0
CD B:ARG157 4.3 15.3 1.0
CG B:ARG157 4.4 16.7 1.0
CD B:PRO156 4.4 18.5 1.0
N B:GLY38 4.4 16.6 1.0
N B:ARG157 4.6 14.6 1.0
CB B:PRO156 4.7 13.3 1.0
CG B:PRO156 4.7 13.0 1.0
CB B:ARG157 4.7 15.8 1.0
SG B:CYS9 4.7 13.5 1.0
SG B:CYS16 4.8 15.2 1.0
CA B:GLY38 4.8 16.1 1.0
C B:CYS35 4.9 16.6 1.0
SG B:CYS12 4.9 15.9 1.0
N B:PRO156 4.9 16.8 1.0
CB B:LEU37 5.0 13.8 1.0

Iron binding site 4 out of 48 in 8rja

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Iron binding site 4 out of 48 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


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 the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:10.9
occ:1.00
FE4 B:SF4501 0.0 10.9 1.0
S2 B:SF4501 2.3 10.4 1.0
S3 B:SF4501 2.3 12.9 1.0
SG B:CYS16 2.3 15.2 1.0
S1 B:SF4501 2.4 14.3 1.0
FE2 B:SF4501 2.6 8.6 1.0
FE3 B:SF4501 2.7 11.0 1.0
FE1 B:SF4501 2.7 11.7 1.0
CB B:CYS16 3.3 15.4 1.0
S4 B:SF4501 3.9 12.5 1.0
N B:CYS16 4.0 10.6 1.0
CB B:SER14 4.1 12.5 1.0
CD B:ARG157 4.2 15.3 1.0
CA B:CYS16 4.3 17.2 1.0
CB B:ARG157 4.4 15.8 1.0
CB B:CYS9 4.4 15.5 1.0
SG B:CYS12 4.5 15.9 1.0
SG B:CYS9 4.6 13.5 1.0
NH1 B:ARG157 4.6 18.4 1.0
CG B:ARG157 4.6 16.7 1.0
OG B:SER14 4.8 12.3 1.0
N B:LEU15 4.9 11.4 1.0
SG B:CYS35 5.0 14.1 1.0

Iron binding site 5 out of 48 in 8rja

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Iron binding site 5 out of 48 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


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 the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1101

b:24.9
occ:1.00
FE1 E:SF41101 0.0 24.9 1.0
SG E:CYS276 2.3 29.1 1.0
S2 E:SF41101 2.3 23.1 1.0
S4 E:SF41101 2.3 23.3 1.0
S3 E:SF41101 2.4 24.8 1.0
FE4 E:SF41101 2.6 23.1 1.0
FE3 E:SF41101 2.7 22.0 1.0
FE2 E:SF41101 2.8 28.3 1.0
CB E:CYS276 2.9 26.9 1.0
NZ E:LYS340 3.4 28.5 1.0
S1 E:SF41101 3.9 21.6 1.0
CE E:LYS340 4.3 27.2 1.0
CB E:CYS187 4.4 19.1 1.0
NH2 E:ARG70 4.4 27.8 1.0
CA E:CYS276 4.4 25.2 1.0
O E:HOH1351 4.6 23.3 1.0
CA E:CYS273 4.6 25.3 1.0
O E:ASP278 4.6 24.9 1.0
SG E:CYS187 4.7 25.6 1.0
SG E:CYS273 4.8 29.2 1.0
N E:CYS187 4.9 19.2 1.0
CB E:CYS273 4.9 21.8 1.0
O E:CYS273 4.9 25.6 1.0
SG E:CYS219 4.9 20.2 1.0

Iron binding site 6 out of 48 in 8rja

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Iron binding site 6 out of 48 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


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 the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1101

b:28.3
occ:1.00
FE2 E:SF41101 0.0 28.3 1.0
SG E:CYS273 2.2 29.2 1.0
S4 E:SF41101 2.3 23.3 1.0
S3 E:SF41101 2.3 24.8 1.0
S1 E:SF41101 2.3 21.6 1.0
FE4 E:SF41101 2.6 23.1 1.0
FE1 E:SF41101 2.8 24.9 1.0
FE3 E:SF41101 2.8 22.0 1.0
CB E:CYS273 3.0 21.8 1.0
CA E:CYS273 3.4 25.3 1.0
O E:HOH1266 3.8 19.8 1.0
S2 E:SF41101 4.0 23.1 1.0
N E:CYS273 4.1 30.0 1.0
N E:GLU222 4.2 27.2 1.0
O E:HOH1231 4.3 25.8 1.0
CB E:GLU222 4.5 22.1 1.0
CA E:GLU221 4.5 21.4 1.0
SG E:CYS219 4.6 20.2 1.0
CB E:CYS276 4.6 26.9 1.0
C E:CYS273 4.7 24.4 1.0
C E:GLU221 4.7 21.9 1.0
SG E:CYS276 4.8 29.1 1.0
C E:GLY272 4.8 26.4 1.0
O E:CYS273 4.9 25.6 1.0
CG E:GLU222 4.9 22.6 1.0
O E:GLY272 4.9 27.8 1.0
CA E:GLU222 5.0 21.7 1.0

Iron binding site 7 out of 48 in 8rja

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Iron binding site 7 out of 48 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


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 the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1101

b:22.0
occ:1.00
FE3 E:SF41101 0.0 22.0 1.0
S4 E:SF41101 2.2 23.3 1.0
S1 E:SF41101 2.3 21.6 1.0
S2 E:SF41101 2.3 23.1 1.0
SG E:CYS187 2.4 25.6 1.0
FE1 E:SF41101 2.7 24.9 1.0
FE4 E:SF41101 2.7 23.1 1.0
FE2 E:SF41101 2.8 28.3 1.0
CB E:CYS187 3.1 19.1 1.0
OG1 E:THR185 3.8 27.4 1.0
O E:HOH1246 3.9 23.8 1.0
S3 E:SF41101 4.0 24.8 1.0
N E:CYS187 4.1 19.2 1.0
CB E:THR185 4.1 23.9 1.0
O E:HOH1231 4.2 25.8 1.0
CA E:CYS187 4.2 19.7 1.0
SG E:CYS276 4.7 29.1 1.0
SG E:CYS273 4.8 29.2 1.0
O E:HOH1266 4.8 19.8 1.0
CG1 E:VAL19 4.8 20.6 1.0
SG E:CYS219 4.8 20.2 1.0
CG2 E:THR185 4.8 20.7 1.0
CB E:VAL19 4.8 20.5 1.0

Iron binding site 8 out of 48 in 8rja

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Iron binding site 8 out of 48 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


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 the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1101

b:23.1
occ:1.00
FE4 E:SF41101 0.0 23.1 1.0
S3 E:SF41101 2.3 24.8 1.0
S1 E:SF41101 2.3 21.6 1.0
S2 E:SF41101 2.4 23.1 1.0
SG E:CYS219 2.4 20.2 1.0
FE2 E:SF41101 2.6 28.3 1.0
FE1 E:SF41101 2.6 24.9 1.0
FE3 E:SF41101 2.7 22.0 1.0
CB E:CYS219 3.4 20.6 1.0
S4 E:SF41101 3.8 23.3 1.0
NZ E:LYS340 3.9 28.5 1.0
CB E:THR185 4.3 23.9 1.0
O E:CYS219 4.4 24.8 1.0
CA E:GLU221 4.5 21.4 1.0
C E:CYS219 4.5 24.3 1.0
SG E:CYS273 4.5 29.2 1.0
CA E:CYS219 4.5 23.1 1.0
CG2 E:THR185 4.6 20.7 1.0
N E:GLU221 4.6 23.0 1.0
CD E:PRO186 4.6 22.2 1.0
SG E:CYS276 4.7 29.1 1.0
C E:GLU221 4.7 21.9 1.0
N E:GLU222 4.9 27.2 1.0
CG E:GLU222 4.9 22.6 1.0
OG1 E:THR185 4.9 27.4 1.0
SG E:CYS187 4.9 25.6 1.0
C E:ALA220 5.0 22.4 1.0

Iron binding site 9 out of 48 in 8rja

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Iron binding site 9 out of 48 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


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 the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1102

b:14.5
occ:1.00
FE1 E:SF41102 0.0 14.5 1.0
S4 E:SF41102 2.2 13.7 1.0
S3 E:SF41102 2.3 13.4 1.0
SG E:CYS61 2.3 16.5 1.0
S2 E:SF41102 2.4 15.6 1.0
FE3 E:SF41102 2.6 15.8 1.0
FE4 E:SF41102 2.7 16.0 1.0
FE2 E:SF41102 2.7 16.7 1.0
CB E:CYS61 3.3 21.5 1.0
S1 E:SF41102 3.9 17.4 1.0
O E:HOH1293 4.0 19.4 1.0
N E:LEU63 4.0 17.5 1.0
N E:ASN62 4.0 19.1 1.0
CD E:PRO29 4.2 22.8 1.0
CB E:LEU63 4.5 20.6 1.0
CA E:CYS61 4.5 21.5 1.0
C E:CYS61 4.6 19.4 1.0
N E:CYS64 4.6 22.3 1.0
CA E:CYS58 4.7 21.4 1.0
SG E:CYS58 4.7 25.4 1.0
SG E:CYS64 4.7 16.1 1.0
CA E:ASN62 4.7 18.2 1.0
CG E:PRO29 4.7 20.3 1.0
SG E:CYS28 4.7 23.5 1.0
CA E:LEU63 4.8 17.2 1.0
C E:ASN62 4.8 18.6 1.0
O E:ALA57 4.9 19.4 1.0
CB E:CYS58 4.9 22.7 1.0

Iron binding site 10 out of 48 in 8rja

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Iron binding site 10 out of 48 in the Crystal Structure of the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum


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 the F420-Reducing Formylmethanofuran Dehydrogenase Complex From the Ethanotroph Candidatus Ethanoperedens Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1102

b:16.7
occ:1.00
FE2 E:SF41102 0.0 16.7 1.0
SG E:CYS64 2.2 16.1 1.0
S3 E:SF41102 2.3 13.4 1.0
S1 E:SF41102 2.3 17.4 1.0
S4 E:SF41102 2.4 13.7 1.0
FE4 E:SF41102 2.7 16.0 1.0
FE1 E:SF41102 2.7 14.5 1.0
FE3 E:SF41102 2.8 15.8 1.0
CB E:CYS64 3.1 16.8 1.0
N E:CYS64 3.7 22.3 1.0
S2 E:SF41102 4.0 15.6 1.0
N E:TYR5 4.0 21.6 1.0
CA E:CYS64 4.1 18.9 1.0
CA E:GLY4 4.3 20.1 1.0
CD1 E:ILE33 4.5 28.6 1.0
C E:GLY4 4.5 20.1 1.0
N E:LEU63 4.6 17.5 1.0
CB E:TYR5 4.7 24.9 1.0
SG E:CYS58 4.8 25.4 1.0
SG E:CYS28 4.8 23.5 1.0
CA E:TYR5 4.8 21.4 1.0
SG E:CYS61 4.8 16.5 1.0
CA E:ASN62 4.9 18.2 1.0
C E:LEU63 4.9 19.0 1.0
C E:ASN62 4.9 18.6 1.0
N E:ASN62 5.0 19.1 1.0

Reference:

O.N.Lemaire, G.Wegener, T.Wagner. F420 Reduction As A Cellular Driver For Anaerobic Ethanotrophy To Be Published.
Page generated: Thu Oct 31 20:29:23 2024

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