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Sodium 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
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium where determined in the Tungsten-Containing Formylmethanofuran Dehydrogenase From Methanothermobacter Wolfeii, Orthorhombic Form at 1.9 A, PDB code: 5t5i:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5t5i

Go back to Sodium Binding Sites List in 5t5i
Sodium binding site 1 out of 5 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 Sodium with other atoms in the Na 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:Na606

b:21.6
occ:1.00
 O A:HOH809 2.4 36.1 1.0
O A:HOH705 3.2 20.1 1.0
N A:GLY144 3.2 21.1 1.0
N A:VAL180 3.3 18.3 1.0
ND2 A:ASN145 3.5 19.8 1.0
O A:VAL180 3.6 19.0 1.0
CA A:GLY144 3.6 20.2 1.0
N A:ASN145 3.8 19.0 1.0
CB A:LEU142 3.9 18.5 1.0
CD2 A:LEU142 3.9 22.8 1.0
CB A:VAL180 3.9 21.0 1.0
CA A:VAL180 4.0 18.6 1.0
C A:GLY144 4.0 22.3 1.0
N A:PHE143 4.0 19.5 1.0
C A:VAL180 4.2 21.2 1.0
O A:KCX178 4.2 23.2 1.0
C A:ILE179 4.3 22.3 1.0
C A:PHE143 4.3 23.0 1.0
CA A:ILE179 4.3 18.9 1.0
CA A:LEU142 4.4 18.7 1.0
C A:LEU142 4.4 22.9 1.0
CG2 A:VAL180 4.5 21.6 1.0
CG A:LEU142 4.5 22.1 1.0
CG A:ASN145 4.5 28.0 1.0
CB A:ASN145 4.5 18.5 1.0
OG1 A:THR344 4.6 29.7 1.0
CA A:PHE143 4.7 19.7 1.0
CA A:ASN145 4.8 18.6 1.0
C A:KCX178 4.9 23.5 1.0
O A:GLY144 4.9 20.9 1.0
N A:ILE179 5.0 19.1 1.0

Sodium binding site 2 out of 5 in 5t5i

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Sodium binding site 2 out of 5 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 Sodium with other atoms in the Na 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
A:Na610

b:25.8
occ:1.00
 O A:HOH958 2.3 50.5 1.0
O A:HOH974 2.5 45.2 1.0
O A:GLY414 2.7 36.6 1.0
O A:LEU416 2.7 27.3 1.0
O A:ILE412 2.9 30.9 1.0
C A:GLY414 3.7 36.1 1.0
C A:GLU413 3.7 36.2 1.0
O A:GLU413 3.8 38.7 1.0
C A:LEU416 3.9 29.7 1.0
N A:GLY414 3.9 31.5 1.0
C A:ILE412 4.0 32.1 1.0
O A:HOH927 4.1 32.1 1.0
CA A:GLU413 4.1 29.9 1.0
N A:LEU416 4.3 28.2 1.0
CA A:GLY414 4.3 31.9 1.0
N A:GLU413 4.5 29.9 1.0
NE2 A:GLN421 4.5 35.7 1.0
C A:GLU415 4.5 34.2 1.0
CA A:LEU416 4.6 27.2 1.0
N A:GLU415 4.7 32.9 1.0
O A:LEU411 4.8 30.9 1.0
N A:LYS418 4.8 28.6 1.0
O A:HOH710 4.8 37.8 1.0
C A:HIS417 4.8 30.6 1.0
CD A:LYS418 4.9 74.4 1.0
N A:HIS417 4.9 26.8 1.0
CG A:LYS418 5.0 58.6 1.0
O A:GLU415 5.0 32.9 1.0

Sodium binding site 3 out of 5 in 5t5i

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Sodium binding site 3 out of 5 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 Sodium with other atoms in the Na 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
I:Na606

b:20.1
occ:1.00
 O I:HOH819 2.8 33.6 1.0
N I:VAL180 3.2 16.8 1.0
O I:HOH721 3.2 17.7 1.0
N I:GLY144 3.2 18.4 1.0
O I:VAL180 3.5 18.4 1.0
ND2 I:ASN145 3.5 17.0 1.0
CA I:GLY144 3.5 17.9 1.0
N I:ASN145 3.8 16.6 1.0
CB I:VAL180 3.9 18.9 1.0
CD2 I:LEU142 3.9 20.6 1.0
CA I:VAL180 3.9 16.6 1.0
CB I:LEU142 3.9 16.9 1.0
C I:GLY144 4.0 21.0 1.0
N I:PHE143 4.0 16.8 1.0
C I:VAL180 4.1 19.6 1.0
O I:KCX178 4.1 19.4 1.0
C I:ILE179 4.2 21.4 1.0
CA I:ILE179 4.2 18.3 1.0
C I:PHE143 4.3 20.6 1.0
CG2 I:VAL180 4.4 18.3 1.0
CA I:LEU142 4.4 17.4 1.0
C I:LEU142 4.5 22.5 1.0
CG I:LEU142 4.5 20.4 1.0
CG I:ASN145 4.5 22.3 1.0
CB I:ASN145 4.6 18.0 1.0
OG1 I:THR344 4.7 30.9 1.0
CA I:PHE143 4.7 16.4 1.0
C I:KCX178 4.9 21.2 1.0
CA I:ASN145 4.9 15.8 1.0
N I:ILE179 4.9 19.0 1.0
O I:GLY144 4.9 18.9 1.0

Sodium binding site 4 out of 5 in 5t5i

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Sodium binding site 4 out of 5 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 Sodium with other atoms in the Na 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
I:Na610

b:28.1
occ:1.00
 O I:HOH1035 2.4 43.6 1.0
O I:LEU416 2.6 29.5 1.0
O I:GLY414 2.7 34.8 1.0
O I:ILE412 2.9 29.5 1.0
C I:GLY414 3.7 35.3 1.0
C I:GLU413 3.8 35.6 1.0
C I:LEU416 3.8 29.8 1.0
O I:GLU413 3.9 35.6 1.0
O I:HOH958 3.9 28.7 1.0
C I:ILE412 4.0 30.7 1.0
N I:GLY414 4.0 31.3 1.0
N I:LEU416 4.2 27.7 1.0
CA I:GLU413 4.2 30.4 1.0
CA I:GLY414 4.3 31.4 1.0
C I:GLU415 4.4 32.4 1.0
CA I:LEU416 4.4 26.3 1.0
NE2 I:GLN421 4.5 38.0 1.0
N I:GLU413 4.5 29.7 1.0
N I:GLU415 4.6 31.6 1.0
O I:HOH791 4.7 34.1 1.0
O I:LEU411 4.7 26.9 1.0
N I:HIS417 4.8 27.4 1.0
C I:HIS417 4.9 31.2 1.0
N I:LYS418 4.9 29.3 1.0
O I:GLU415 4.9 31.0 1.0
CB I:LEU416 4.9 26.1 1.0
CA I:GLU415 5.0 31.9 1.0

Sodium binding site 5 out of 5 in 5t5i

Go back to Sodium Binding Sites List in 5t5i
Sodium binding site 5 out of 5 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 Sodium with other atoms in the Na 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
L:Na201

b:22.2
occ:1.00
 O L:HOH398 2.9 46.9 1.0
O L:HOH303 3.1 38.7 1.0
ND2 L:ASN36 3.5 29.8 1.0
N L:GLY74 3.5 23.9 1.0
O L:HOH345 3.5 25.0 1.0
CA L:GLU73 3.7 25.5 1.0
CE L:MET39 3.8 26.0 1.0
CB L:ASN36 4.0 24.6 1.0
CB L:MET39 4.0 23.5 1.0
C L:GLU73 4.1 27.6 1.0
CG L:ASN36 4.2 33.1 1.0
CG L:GLU73 4.2 41.0 1.0
N L:MET39 4.4 24.4 1.0
O L:PRO72 4.4 25.3 1.0
CB L:GLU73 4.5 27.6 1.0
CA L:GLY74 4.5 23.3 1.0
CA L:MET39 4.7 23.1 1.0
N L:GLU73 4.7 24.0 1.0
CG L:MET39 4.7 26.2 1.0
C L:PRO72 4.9 27.0 1.0
CB L:GLU38 5.0 32.1 1.0
SD L:MET39 5.0 28.8 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: Tue Dec 15 11:35:49 2020

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