Sodium in PDB 7p0x: Crystal Structure of Thioredoxin Reductase From Brugia Malayi

The structure of Crystal Structure of Thioredoxin Reductase From Brugia Malayi, PDB code: 7p0x was solved by F.Fata, M.Ardini, I.Silvestri, F.Gabriele, Q.Cheng, E.S.J.Arner, D.L.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.90 / 2.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	146.921, 258.985, 129.067, 90, 90, 90
R / Rfree (%)	19.7 / 23.8

The structure of Crystal Structure of Thioredoxin Reductase From Brugia Malayi also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Thioredoxin Reductase From Brugia Malayi (pdb code 7p0x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Thioredoxin Reductase From Brugia Malayi, PDB code: 7p0x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Thioredoxin Reductase From Brugia Malayi


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 Thioredoxin Reductase From Brugia Malayi within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:54.7 occ:0.61 O A:ALA255 2.5 69.2 1.0 O1P A:FAD601 2.5 58.9 1.0 N A:GLY118 2.6 59.3 1.0 CB A:ALA255 3.1 61.4 1.0 CA A:GLY118 3.4 60.8 1.0 N A:GLY115 3.4 59.1 1.0 N A:GLY117 3.4 60.4 1.0 C A:ALA255 3.5 60.7 1.0 C A:GLY115 3.5 57.8 1.0 CA A:GLY115 3.6 55.7 1.0 C A:GLY117 3.6 60.0 1.0 CA A:GLY117 3.7 61.9 1.0 O A:GLY115 3.7 57.4 1.0 P A:FAD601 3.8 56.4 1.0 CA A:ALA255 3.8 63.3 1.0 O A:GLY113 3.9 68.6 1.0 O5B A:FAD601 3.9 64.4 1.0 N A:SER116 4.0 56.2 1.0 C A:GLY113 4.1 68.0 1.0 O3P A:FAD601 4.1 54.7 1.0 C5B A:FAD601 4.3 70.6 1.0 C A:SER116 4.3 61.3 1.0 CA A:GLY113 4.4 69.1 1.0 O2P A:FAD601 4.5 66.0 1.0 N A:GLY114 4.6 66.6 1.0 C A:GLY118 4.6 61.9 1.0 C A:GLY114 4.7 61.5 1.0 PA A:FAD601 4.7 62.4 1.0 N A:VAL256 4.7 62.4 1.0 N A:LEU119 4.8 59.6 1.0 O A:GLY117 4.8 61.9 1.0 CA A:SER116 4.8 60.1 1.0 C4B A:FAD601 4.9 69.9 1.0 O5' A:FAD601 4.9 57.9 1.0 O1A A:FAD601 5.0 61.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Thioredoxin Reductase From Brugia Malayi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Thioredoxin Reductase From Brugia Malayi within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:67.0 occ:0.81 OD2 A:ASP136 2.4 75.6 1.0 O A:HOH732 2.4 65.7 1.0 OH A:TYR222 2.5 81.1 1.0 CG A:ASP136 3.4 71.9 1.0 CA A:LEU149 3.6 70.1 1.0 CB A:ASP136 3.6 71.2 1.0 CD1 A:LEU149 3.6 72.9 1.0 CZ A:TYR222 3.6 77.7 1.0 O A:ASP136 3.6 75.4 1.0 ND2 A:ASN224 3.7 76.2 1.0 N A:LEU149 3.8 69.9 1.0 CB A:LEU149 3.8 73.1 1.0 C A:ASP136 4.0 74.0 1.0 CE1 A:TYR222 4.0 76.8 1.0 C A:GLY148 4.1 69.0 1.0 O A:HOH709 4.3 66.3 1.0 CG A:LEU149 4.3 73.4 1.0 CA A:ASP136 4.4 74.7 1.0 CG A:ASN224 4.5 81.7 1.0 O A:GLY148 4.5 69.5 1.0 OD1 A:ASP136 4.6 65.3 1.0 N A:PHE137 4.6 72.1 1.0 CA A:GLY148 4.8 68.4 1.0 CE2 A:TYR222 4.8 76.0 1.0 CG2 A:VAL138 4.8 72.7 1.0 CA A:PHE137 4.9 74.0 1.0 C A:LEU149 4.9 66.9 1.0

F.Fata, R.Gencheva, Q.Cheng, R.Lullo, M.Ardini, I.Silvestri, F.Gabriele, R.Ippoliti, C.A.Bulman, J.A.Sakanari, D.L.Williams, E.S.J.Arner, F.Angelucci. Biochemical and Structural Characterizations of Thioredoxin Reductase Selenoproteins of the Parasitic Filarial Nematodes Brugia Malayi and Onchocerca Volvulus. Redox Biol V. 51 02278 2022.
ISSN: ISSN 2213-2317
PubMed: 35276442
DOI: 10.1016/J.REDOX.2022.102278