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Calcium 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
Iron (Fe) 88 atoms
Sodium (Na) 5 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 5t5i

Go back to Calcium Binding Sites List in 5t5i
Calcium 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 Calcium with other atoms in the Ca 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:Ca508

b:25.9
occ:1.00
O C:ASP143 2.6 28.2 1.0
OG C:SER139 2.7 26.4 1.0
OD1 B:ASP128 2.8 26.5 1.0
O C:TYR140 2.9 23.7 1.0
O C:HOH420 3.0 36.1 1.0
OE2 C:GLU164 3.2 30.0 1.0
CG B:ASP128 3.5 27.4 1.0
CD2 C:TYR165 3.6 23.2 1.0
OD2 B:ASP128 3.6 30.8 1.0
N C:ASP143 3.7 21.0 1.0
C C:ASP143 3.7 26.5 1.0
N C:GLY142 3.7 22.3 1.0
CE2 C:TYR165 3.7 24.0 1.0
C C:TYR140 3.8 25.0 1.0
CB C:SER139 3.9 22.3 1.0
CD C:GLU164 4.0 35.1 1.0
OE1 C:GLU164 4.2 29.2 1.0
C C:GLY142 4.2 24.5 1.0
CA C:ASP143 4.2 21.3 1.0
C C:ARG141 4.2 24.9 1.0
CA C:ARG141 4.3 21.6 1.0
O B:HOH682 4.3 34.9 1.0
CA C:GLY142 4.4 22.2 1.0
N C:ARG141 4.4 22.0 1.0
CG C:TYR165 4.4 22.9 1.0
N C:TYR140 4.6 23.2 1.0
CZ C:TYR165 4.7 28.8 1.0
C C:SER139 4.8 24.7 1.0
CB B:ASP128 4.8 21.4 1.0
N C:TRP144 4.8 23.7 1.0
CB C:ASP143 4.9 23.2 1.0
CA C:TYR140 4.9 22.5 1.0
O C:GLY142 4.9 22.2 1.0
CA C:SER139 5.0 20.2 1.0
CB C:TYR165 5.0 21.9 1.0

Calcium binding site 2 out of 2 in 5t5i

Go back to Calcium Binding Sites List in 5t5i
Calcium 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 Calcium with other atoms in the Ca 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
J:Ca508

b:24.2
occ:1.00
O K:ASP143 2.7 25.1 1.0
OG K:SER139 2.7 22.6 1.0
O K:TYR140 2.9 22.0 1.0
OD1 J:ASP128 2.9 28.1 1.0
O K:HOH416 3.0 32.5 1.0
OE2 K:GLU164 3.2 25.8 1.0
CG J:ASP128 3.5 28.5 1.0
N K:ASP143 3.6 19.9 1.0
OD2 J:ASP128 3.7 27.6 1.0
CD2 K:TYR165 3.7 22.1 1.0
N K:GLY142 3.7 20.0 1.0
C K:ASP143 3.7 24.3 1.0
C K:TYR140 3.8 23.3 1.0
CE2 K:TYR165 3.8 22.9 1.0
CB K:SER139 3.9 21.4 1.0
CD K:GLU164 4.1 38.6 1.0
C K:GLY142 4.1 21.6 1.0
OE1 K:GLU164 4.2 26.9 1.0
C K:ARG141 4.2 21.9 1.0
CA K:ARG141 4.2 19.2 1.0
CA K:ASP143 4.2 20.1 1.0
O J:HOH708 4.3 31.9 1.0
N K:ARG141 4.3 20.3 1.0
CA K:GLY142 4.4 19.4 1.0
N K:TYR140 4.5 22.1 1.0
CG K:TYR165 4.5 21.8 1.0
C K:SER139 4.7 23.3 1.0
CB J:ASP128 4.8 18.7 1.0
CZ K:TYR165 4.8 24.8 1.0
CB K:ASP143 4.8 20.0 1.0
CA K:TYR140 4.8 20.3 1.0
N K:TRP144 4.9 22.1 1.0
O K:GLY142 4.9 20.8 1.0
CA K:SER139 4.9 19.2 1.0
O K:ARG141 5.0 18.8 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: Sat Dec 12 05:43:39 2020

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