Magnesium in PDB 5t5m: Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.

Enzymatic activity of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.

All present enzymatic activity of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.:
1.2.99.5;

Protein crystallography data

The structure of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A., PDB code: 5t5m 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) 48.22 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.543, 105.543, 340.549, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 18.2

Other elements in 5t5m:

The structure of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. also contains other interesting chemical elements:

Tungsten (W) 1 atom
Potassium (K) 1 atom
Zinc (Zn) 2 atoms
Iron (Fe) 44 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. (pdb code 5t5m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A., PDB code: 5t5m:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5t5m

Go back to Magnesium Binding Sites List in 5t5m
Magnesium binding site 1 out of 3 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 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, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:65.6
occ:1.00
 O A:HOH738 2.5 58.4 1.0
OE2 B:GLU138 2.7 61.3 1.0
O A:THR344 2.7 58.3 1.0
O A:HOH729 3.1 53.8 1.0
O A:VAL340 3.1 52.8 1.0
C A:THR344 3.5 56.7 1.0
N A:THR344 3.8 53.8 1.0
CD B:GLU138 3.9 62.2 1.0
N A:VAL340 3.9 49.3 1.0
NH1 B:ARG142 4.0 51.5 1.0
C A:VAL340 4.0 52.3 1.0
CA A:THR344 4.1 56.4 1.0
CB A:ASP339 4.4 50.4 1.0
OD1 A:ASP339 4.4 53.0 1.0
N A:GLY345 4.4 56.4 1.0
C A:ASP339 4.5 48.9 1.0
CA A:ASP339 4.5 49.9 1.0
OE1 A:GLU186 4.5 46.5 1.0
N A:GLU343 4.6 55.2 1.0
CA A:VAL340 4.6 49.6 1.0
C A:GLU343 4.6 53.5 1.0
OE1 B:GLU138 4.7 64.7 1.0
N A:LEU342 4.7 53.7 1.0
O A:THR185 4.8 50.0 1.0
CA A:GLY345 4.8 57.2 1.0
CG B:GLU138 4.9 60.2 1.0
N A:GLU341 4.9 53.1 1.0
CG A:ASP339 4.9 50.0 1.0
CZ B:ARG142 5.0 51.9 1.0

Magnesium binding site 2 out of 3 in 5t5m

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Magnesium binding site 2 out of 3 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 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, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:42.6
occ:1.00
 OG A:SER76 2.3 48.1 1.0
O A:ARG69 2.4 52.1 1.0
O A:HOH726 2.5 53.0 1.0
O B:GLY305 2.6 46.5 1.0
O A:HOH757 2.8 49.1 1.0
O A:ARG72 3.3 49.2 1.0
C A:ARG69 3.3 52.8 1.0
CB A:SER76 3.5 51.1 1.0
CA A:ARG69 3.6 51.6 1.0
C B:GLY305 3.7 51.4 1.0
O A:HOH771 3.7 56.6 1.0
CA B:GLY305 4.0 54.0 1.0
C A:ARG72 4.0 51.0 1.0
CB A:ARG69 4.1 54.2 1.0
N A:SER76 4.2 51.0 1.0
CA A:SER76 4.3 52.6 1.0
N A:MET70 4.5 53.6 1.0
CA A:PRO73 4.6 54.7 1.0
N A:PRO73 4.6 53.2 1.0
O A:GLY68 4.7 55.1 1.0
O A:VAL94 4.7 53.4 1.0
OG A:SER90 4.8 52.5 1.0
N B:TYR306 4.9 52.1 1.0
N A:ARG69 4.9 51.1 1.0
OD2 A:ASP75 4.9 57.5 1.0
CG A:ARG69 4.9 56.4 1.0
CA A:ARG72 4.9 51.3 1.0

Magnesium binding site 3 out of 3 in 5t5m

Go back to Magnesium Binding Sites List in 5t5m
Magnesium binding site 3 out of 3 in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Trigonal Form at 2.5 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:63.0
occ:1.00
 O C:ASP143 2.3 49.6 1.0
O B:HOH654 2.4 66.9 1.0
OG C:SER139 2.4 52.9 1.0
O B:HOH609 2.5 55.2 1.0
O C:TYR140 2.5 47.1 1.0
C C:ASP143 3.3 48.5 1.0
N C:ASP143 3.4 47.2 1.0
C C:TYR140 3.5 45.7 1.0
CB C:SER139 3.5 52.6 1.0
OD1 B:ASP128 3.6 58.3 1.0
N C:GLY142 3.6 51.4 1.0
CD2 C:TYR165 3.7 48.1 1.0
CA C:ASP143 3.8 49.2 1.0
C C:GLY142 3.9 49.1 1.0
CE2 C:TYR165 4.0 48.3 1.0
OE1 C:GLU164 4.0 62.2 1.0
C C:ARG141 4.0 50.3 1.0
CA C:ARG141 4.2 48.9 1.0
N C:TYR140 4.2 46.1 1.0
N C:ARG141 4.2 47.0 1.0
CG B:ASP128 4.3 56.2 1.0
CA C:GLY142 4.3 52.5 1.0
N C:TRP144 4.4 47.0 1.0
CG C:TYR165 4.4 48.0 1.0
C C:SER139 4.4 48.5 1.0
CB C:ASP143 4.4 53.0 1.0
OD2 B:ASP128 4.4 56.2 1.0
CD C:GLU164 4.5 61.4 1.0
CA C:TYR140 4.5 44.2 1.0
OE2 C:GLU164 4.5 65.9 1.0
CA C:SER139 4.6 52.3 1.0
O C:GLY142 4.7 47.7 1.0
CA C:TRP144 4.8 47.0 1.0
O C:ARG141 4.8 51.0 1.0
CB C:TYR165 4.8 49.8 1.0
CZ C:TYR165 4.8 49.7 1.0
O C:SER139 4.9 47.4 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 21:11:23 2020

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