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Sodium in PDB 5exe: Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct

Enzymatic activity of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct

All present enzymatic activity of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct:
1.2.7.10;

Protein crystallography data

The structure of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct, PDB code: 5exe was solved by M.I.Gibson, P.Y.-T.Chen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.70 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.653, 144.131, 161.715, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.3

Other elements in 5exe:

The structure of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Iron (Fe) 24 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct (pdb code 5exe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct, PDB code: 5exe:

Sodium binding site 1 out of 1 in 5exe

Go back to Sodium Binding Sites List in 5exe
Sodium binding site 1 out of 1 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Tpp Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na404

b:28.7
occ:1.00
O F:GLN213 2.3 26.3 1.0
OD2 F:ASP130 2.4 28.2 1.0
O F:LEU211 2.4 20.9 1.0
O F:HOH728 2.6 35.6 1.0
O F:HOH541 2.6 34.5 1.0
O F:HOH627 2.8 21.9 1.0
CG F:ASP130 3.3 30.4 1.0
C F:LEU211 3.4 22.5 1.0
C F:GLN213 3.5 29.0 1.0
OD1 F:ASP130 3.6 28.4 1.0
O F:HOH579 3.7 38.0 1.0
CA F:LEU211 3.9 20.4 1.0
O F:GLY210 4.1 19.4 1.0
O F:HOH713 4.1 52.1 1.0
O F:HOH527 4.2 21.2 1.0
N F:GLN213 4.2 23.8 1.0
O F:GLY215 4.4 21.7 1.0
C F:ASN212 4.4 23.9 1.0
N F:GLU214 4.4 24.2 1.0
CA F:GLU214 4.4 29.7 1.0
N F:ASN212 4.4 22.9 1.0
CA F:GLN213 4.4 26.9 1.0
N F:GLY215 4.5 24.5 1.0
CB F:ASP130 4.7 18.1 1.0
O F:ASN212 4.8 27.6 1.0
CA F:ASN212 4.8 22.1 1.0
C F:ASP130 4.9 20.8 1.0
CB F:LEU211 4.9 20.1 1.0
O F:ASP130 5.0 18.4 1.0
C F:GLY210 5.0 21.2 1.0
N F:LEU211 5.0 16.9 1.0

Reference:

M.I.Gibson, P.Y.Chen, A.C.Johnson, E.Pierce, M.Can, S.W.Ragsdale, C.L.Drennan. One-Carbon Chemistry of Oxalate Oxidoreductase Captured By X-Ray Crystallography. Proc.Natl.Acad.Sci.Usa V. 113 320 2016.
ISSN: ESSN 1091-6490
PubMed: 26712008
DOI: 10.1073/PNAS.1518537113
Page generated: Tue Dec 15 10:57:53 2020

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