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Iron in PDB 5t5i: Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A

Enzymatic activity of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A

All present enzymatic activity of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A:
1.2.99.5;

Protein crystallography data

The structure of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A, PDB code: 5t5i was solved by T.Wagner, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.49 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.644, 174.576, 205.425, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 17.2

Other elements in 5t5i:

The structure of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A also contains other interesting chemical elements:

Tungsten (W) 2 atoms
Magnesium (Mg) 2 atoms
Potassium (K) 18 atoms
Zinc (Zn) 4 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 5 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 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 88;

Binding sites:

The binding sites of Iron atom in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A (pdb code 5t5i). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 88 binding sites of Iron where determined in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A, PDB code: 5t5i:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 88 in 5t5i

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Iron binding site 1 out of 88 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:22.7
occ:1.00
 FE1 B:SF4501 0.0 22.7 1.0
S4 B:SF4501 2.2 22.9 1.0
S2 B:SF4501 2.3 22.6 1.0
SG B:CYS16 2.3 22.6 1.0
S3 B:SF4501 2.3 22.4 1.0
FE4 B:SF4501 2.7 22.3 1.0
FE2 B:SF4501 2.7 20.2 1.0
FE3 B:SF4501 2.8 20.6 1.0
CB B:CYS16 3.3 19.2 1.0
S1 B:SF4501 3.7 20.7 1.0
CD B:ARG159 4.0 26.9 1.0
N B:CYS16 4.0 18.6 1.0
CA B:CYS16 4.3 19.0 1.0
CB B:THR14 4.4 24.1 1.0
CG B:ARG159 4.4 23.7 1.0
CB B:ARG159 4.4 19.4 1.0
CG2 B:THR14 4.6 24.6 1.0
CB B:CYS9 4.6 20.7 1.0
SG B:CYS9 4.7 23.5 1.0
NH1 B:ARG159 4.7 26.2 1.0
SG B:CYS12 4.7 21.4 1.0
N B:LEU15 5.0 17.2 1.0

Iron binding site 2 out of 88 in 5t5i

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Iron binding site 2 out of 88 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:20.2
occ:1.00
 FE2 B:SF4501 0.0 20.2 1.0
S1 B:SF4501 2.2 20.7 1.0
S3 B:SF4501 2.2 22.4 1.0
SG B:CYS12 2.2 21.4 1.0
S4 B:SF4501 2.3 22.9 1.0
FE1 B:SF4501 2.7 22.7 1.0
FE4 B:SF4501 2.8 22.3 1.0
FE3 B:SF4501 2.9 20.6 1.0
CB B:CYS12 3.5 18.8 1.0
N B:CYS12 3.7 18.9 1.0
S2 B:SF4501 3.9 22.6 1.0
CA B:CYS12 4.0 19.1 1.0
CB B:THR14 4.2 24.1 1.0
O B:CYS12 4.4 21.0 1.0
OG1 B:THR14 4.4 25.0 1.0
C B:CYS12 4.4 22.4 1.0
CD B:PRO158 4.6 20.2 1.0
CD2 B:PHE11 4.7 24.2 1.0
SG B:CYS9 4.8 23.5 1.0
SG B:CYS16 4.8 22.6 1.0
SG B:CYS35 4.8 22.0 1.0
N B:THR14 4.8 19.5 1.0
CB B:PHE11 4.9 22.3 1.0
N B:LEU15 4.9 17.2 1.0
C B:PHE11 4.9 22.6 1.0

Iron binding site 3 out of 88 in 5t5i

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Iron binding site 3 out of 88 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:20.6
occ:1.00
 FE3 B:SF4501 0.0 20.6 1.0
S2 B:SF4501 2.2 22.6 1.0
S1 B:SF4501 2.3 20.7 1.0
S4 B:SF4501 2.3 22.9 1.0
SG B:CYS35 2.3 22.0 1.0
FE4 B:SF4501 2.8 22.3 1.0
FE1 B:SF4501 2.8 22.7 1.0
FE2 B:SF4501 2.9 20.2 1.0
CB B:CYS35 3.4 19.4 1.0
N B:CYS35 3.9 20.3 1.0
S3 B:SF4501 4.0 22.4 1.0
CD B:PRO158 4.2 20.2 1.0
CA B:CYS35 4.2 20.6 1.0
CG B:ARG159 4.3 23.7 1.0
CD B:ARG159 4.3 26.9 1.0
N B:GLY38 4.3 21.3 1.0
CA B:GLY38 4.6 20.8 1.0
CG B:PRO158 4.7 24.6 1.0
N B:ARG159 4.7 18.7 1.0
CB B:PRO158 4.7 20.9 1.0
SG B:CYS9 4.8 23.5 1.0
N B:PRO158 4.8 18.1 1.0
SG B:CYS12 4.9 21.4 1.0
SG B:CYS16 4.9 22.6 1.0
CB B:ARG159 4.9 19.4 1.0
C B:CYS35 5.0 23.7 1.0

Iron binding site 4 out of 88 in 5t5i

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Iron binding site 4 out of 88 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:22.3
occ:1.00
 FE4 B:SF4501 0.0 22.3 1.0
S1 B:SF4501 2.2 20.7 1.0
SG B:CYS9 2.2 23.5 1.0
S2 B:SF4501 2.3 22.6 1.0
S3 B:SF4501 2.3 22.4 1.0
FE1 B:SF4501 2.7 22.7 1.0
FE3 B:SF4501 2.8 20.6 1.0
FE2 B:SF4501 2.8 20.2 1.0
CB B:CYS9 3.1 20.7 1.0
S4 B:SF4501 3.8 22.9 1.0
CA B:GLY38 4.0 20.8 1.0
CB B:PHE11 4.3 22.3 1.0
CA B:CYS9 4.5 20.4 1.0
N B:GLY38 4.5 21.3 1.0
N B:CYS12 4.6 18.9 1.0
SG B:CYS35 4.7 22.0 1.0
SG B:CYS16 4.8 22.6 1.0
O B:CYS9 4.8 22.7 1.0
N B:PHE11 4.8 20.0 1.0
C B:CYS9 4.8 23.1 1.0
CB B:CYS16 4.9 19.2 1.0
SG B:CYS12 4.9 21.4 1.0
CA B:PHE11 5.0 20.0 1.0

Iron binding site 5 out of 88 in 5t5i

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Iron binding site 5 out of 88 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:26.1
occ:1.00
 FE1 F:SF4401 0.0 26.1 1.0
S4 F:SF4401 2.2 27.4 1.0
S3 F:SF4401 2.3 26.8 1.0
S2 F:SF4401 2.3 27.1 1.0
SG F:CYS308 2.3 28.6 1.0
FE2 F:SF4401 2.8 24.0 1.0
FE4 F:SF4401 2.8 25.9 1.0
FE3 F:SF4401 2.9 26.6 1.0
CB F:CYS308 3.5 24.7 1.0
S1 F:SF4401 3.8 25.6 1.0
CA F:CYS308 3.9 24.7 1.0
N F:TYR310 4.0 25.0 1.0
N F:ILE309 4.0 25.7 1.0
CG2 F:VAL285 4.1 25.6 1.0
CD2 F:LEU264 4.3 38.9 1.0
CD1 F:LEU264 4.4 32.9 1.0
C F:CYS308 4.4 29.4 1.0
CA F:TYR310 4.5 25.4 1.0
CB F:VAL285 4.7 25.1 1.0
N F:CYS311 4.8 25.5 1.0
CG F:LEU264 4.8 33.9 1.0
CG1 F:VAL285 4.8 25.2 1.0
SG F:CYS281 4.8 24.9 1.0
SG F:CYS314 4.8 27.2 1.0
C F:ILE309 5.0 28.1 1.0

Iron binding site 6 out of 88 in 5t5i

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Iron binding site 6 out of 88 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:24.0
occ:1.00
 FE2 F:SF4401 0.0 24.0 1.0
S1 F:SF4401 2.2 25.6 1.0
S3 F:SF4401 2.2 26.8 1.0
S4 F:SF4401 2.3 27.4 1.0
SG F:CYS281 2.3 24.9 1.0
FE1 F:SF4401 2.8 26.1 1.0
FE4 F:SF4401 2.8 25.9 1.0
FE3 F:SF4401 2.9 26.6 1.0
CB F:CYS281 3.2 22.1 1.0
CA F:CYS281 3.9 22.5 1.0
S2 F:SF4401 3.9 27.1 1.0
CG2 F:VAL285 3.9 25.6 1.0
CB F:VAL285 4.1 25.1 1.0
CD F:PRO282 4.3 27.6 1.0
C F:CYS281 4.5 27.1 1.0
N F:PRO282 4.6 25.9 1.0
CB F:CYS283 4.7 24.6 1.0
N F:CYS283 4.8 25.1 1.0
SG F:CYS314 4.8 27.2 1.0
SG F:CYS311 4.8 27.2 1.0
CG1 F:VAL285 4.9 25.2 1.0
CD1 F:LEU286 4.9 25.6 1.0
SG F:CYS308 4.9 28.6 1.0
CB F:CYS314 5.0 23.9 1.0

Iron binding site 7 out of 88 in 5t5i

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Iron binding site 7 out of 88 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:26.6
occ:1.00
 FE3 F:SF4401 0.0 26.6 1.0
S2 F:SF4401 2.2 27.1 1.0
S4 F:SF4401 2.3 27.4 1.0
SG F:CYS311 2.3 27.2 1.0
S1 F:SF4401 2.3 25.6 1.0
FE4 F:SF4401 2.8 25.9 1.0
FE2 F:SF4401 2.9 24.0 1.0
FE1 F:SF4401 2.9 26.1 1.0
CB F:CYS311 3.6 24.6 1.0
N F:CYS311 3.6 25.5 1.0
N F:GLY312 3.8 26.4 1.0
S3 F:SF4401 3.9 26.8 1.0
CA F:CYS311 4.0 24.8 1.0
N F:ALA313 4.2 24.4 1.0
C F:CYS311 4.3 29.3 1.0
CD F:PRO282 4.5 27.6 1.0
N F:TYR310 4.5 25.0 1.0
C F:TYR310 4.6 29.8 1.0
CG1 F:ILE309 4.7 27.9 1.0
CB F:ALA313 4.8 24.4 1.0
CA F:GLY312 4.8 25.6 1.0
SG F:CYS314 4.8 27.2 1.0
CA F:TYR310 4.8 25.4 1.0
SG F:CYS308 4.9 28.6 1.0
SG F:CYS281 4.9 24.9 1.0
N F:CYS314 4.9 24.0 1.0
C F:GLY312 4.9 28.1 1.0

Iron binding site 8 out of 88 in 5t5i

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Iron binding site 8 out of 88 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:25.9
occ:1.00
 FE4 F:SF4401 0.0 25.9 1.0
SG F:CYS314 2.2 27.2 1.0
S3 F:SF4401 2.3 26.8 1.0
S2 F:SF4401 2.3 27.1 1.0
S1 F:SF4401 2.3 25.6 1.0
FE1 F:SF4401 2.8 26.1 1.0
FE2 F:SF4401 2.8 24.0 1.0
FE3 F:SF4401 2.8 26.6 1.0
CB F:CYS314 3.2 23.9 1.0
N F:CYS314 3.8 24.0 1.0
S4 F:SF4401 3.8 27.4 1.0
CA F:CYS314 4.1 23.9 1.0
CD2 F:LEU264 4.4 38.9 1.0
CG2 F:VAL325 4.6 32.9 1.0
N F:ALA313 4.7 24.4 1.0
SG F:CYS311 4.7 27.2 1.0
N F:GLY312 4.8 26.4 1.0
SG F:CYS308 4.8 28.6 1.0
CD1 F:LEU286 4.8 25.6 1.0
SG F:CYS281 4.8 24.9 1.0
C F:GLY312 5.0 28.1 1.0
C F:ALA313 5.0 26.0 1.0

Iron binding site 9 out of 88 in 5t5i

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Iron binding site 9 out of 88 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe402

b:24.1
occ:1.00
 FE1 F:SF4402 0.0 24.1 1.0
S4 F:SF4402 2.2 25.1 1.0
S3 F:SF4402 2.3 23.9 1.0
S2 F:SF4402 2.3 23.7 1.0
SG F:CYS318 2.3 26.2 1.0
FE4 F:SF4402 2.8 25.2 1.0
FE2 F:SF4402 2.8 24.4 1.0
FE3 F:SF4402 2.9 23.4 1.0
CB F:CYS318 3.3 23.1 1.0
S1 F:SF4402 3.9 26.3 1.0
CA F:CYS318 4.0 22.9 1.0
CG2 F:VAL320 4.1 25.9 1.0
CB F:ALA322 4.3 26.2 1.0
CD F:PRO319 4.6 26.1 1.0
SG F:CYS274 4.6 24.5 1.0
C F:CYS318 4.8 27.3 1.0
N F:ALA322 4.8 24.6 1.0
CG2 F:ILE323 4.8 31.7 1.0
N F:PRO319 4.9 25.0 1.0
SG F:CYS277 4.9 24.7 1.0
SG F:CYS271 4.9 24.3 1.0

Iron binding site 10 out of 88 in 5t5i

Go back to Iron Binding Sites List in 5t5i
Iron binding site 10 out of 88 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe402

b:24.4
occ:1.00
 FE2 F:SF4402 0.0 24.4 1.0
S3 F:SF4402 2.2 23.9 1.0
S1 F:SF4402 2.2 26.3 1.0
S4 F:SF4402 2.2 25.1 1.0
SG F:CYS271 2.3 24.3 1.0
FE3 F:SF4402 2.8 23.4 1.0
FE1 F:SF4402 2.8 24.1 1.0
FE4 F:SF4402 2.9 25.2 1.0
CB F:CYS271 3.2 22.1 1.0
CA F:CYS271 3.6 22.4 1.0
S2 F:SF4402 3.8 23.7 1.0
N F:ALA273 3.8 24.8 1.0
N F:GLN272 3.9 24.4 1.0
C F:CYS271 4.2 26.8 1.0
CA F:ALA273 4.2 24.3 1.0
CD2 F:LEU301 4.6 28.9 1.0
N F:CYS274 4.6 22.8 1.0
SG F:CYS277 4.8 24.7 1.0
CB F:ALA322 4.8 26.2 1.0
C F:GLN272 4.8 26.1 1.0
N F:CYS271 4.9 23.0 1.0
SG F:CYS318 5.0 26.2 1.0
C F:ALA273 5.0 26.5 1.0

Reference:

T.Wagner, U.Ermler, S.Shima. The Methanogenic CO2 Reducing-and-Fixing Enzyme Is Bifunctional and Contains 46 [4FE-4S] Clusters. Science V. 354 114 2016.
ISSN: ESSN 1095-9203
PubMed: 27846502
DOI: 10.1126/SCIENCE.AAF9284
Page generated: Tue Aug 6 08:53:20 2024

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