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Magnesium 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
Potassium (K) 18 atoms
Zinc (Zn) 4 atoms
Iron (Fe) 88 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A, PDB code: 5t5i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5t5i

Go back to Magnesium Binding Sites List in 5t5i
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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
A:Mg603

b:16.3
occ:1.00
OE2 B:GLU138 2.6 30.4 1.0
O A:THR344 2.7 21.5 1.0
O A:VAL340 2.8 21.8 1.0
O A:HOH817 2.9 25.2 1.0
O A:HOH842 2.9 26.5 1.0
C A:THR344 3.6 23.1 1.0
N A:THR344 3.7 21.2 1.0
C A:VAL340 3.7 22.1 1.0
CD B:GLU138 3.8 38.5 1.0
N A:VAL340 3.9 21.2 1.0
NH1 B:ARG142 3.9 26.2 1.0
CA A:THR344 4.1 20.2 1.0
N A:GLU343 4.2 19.2 1.0
OE1 A:GLU186 4.3 23.2 1.0
CA A:VAL340 4.5 19.7 1.0
C A:GLU343 4.5 24.2 1.0
OE1 B:GLU138 4.5 30.5 1.0
C A:ASP339 4.5 24.0 1.0
N A:LEU342 4.5 21.8 1.0
CB A:ASP339 4.6 25.2 1.0
N A:GLU341 4.6 18.4 1.0
N A:GLY345 4.6 22.4 1.0
CA A:ASP339 4.7 22.9 1.0
CA A:GLU341 4.8 18.6 1.0
CG B:GLU138 4.8 27.3 1.0
C A:GLU341 4.9 22.6 1.0
CA A:GLU343 4.9 20.1 1.0
OD1 A:ASP339 4.9 29.3 1.0
C A:LEU342 5.0 23.5 1.0

Magnesium binding site 2 out of 2 in 5t5i

Go back to Magnesium Binding Sites List in 5t5i
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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
I:Mg603

b:13.2
occ:1.00
OE2 J:GLU138 2.6 30.3 1.0
O I:THR344 2.7 22.0 1.0
O I:VAL340 2.8 19.4 1.0
O I:HOH745 2.9 23.2 1.0
O I:HOH895 2.9 22.6 1.0
C I:THR344 3.6 22.5 1.0
N I:THR344 3.7 19.1 1.0
C I:VAL340 3.7 21.5 1.0
CD J:GLU138 3.8 38.6 1.0
NH2 J:ARG142 3.9 24.7 1.0
N I:VAL340 3.9 20.2 1.0
CA I:THR344 4.1 18.0 1.0
N I:GLU343 4.1 17.1 1.0
OE1 I:GLU186 4.3 19.7 1.0
C I:GLU343 4.4 22.1 1.0
CA I:VAL340 4.5 19.2 1.0
OE1 J:GLU138 4.5 25.6 1.0
N I:LEU342 4.5 19.4 1.0
C I:ASP339 4.5 21.0 1.0
N I:GLU341 4.6 17.3 1.0
CB I:ASP339 4.6 20.2 1.0
N I:GLY345 4.6 20.9 1.0
CA I:ASP339 4.7 18.4 1.0
CA I:GLU343 4.8 17.4 1.0
CA I:GLU341 4.8 17.0 1.0
C I:GLU341 4.9 21.3 1.0
CG J:GLU138 4.9 24.5 1.0
OD1 I:ASP339 4.9 28.9 1.0
C I:LEU342 5.0 21.9 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: Mon Dec 14 21:11:22 2020

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