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Sodium in PDB 6fp4: Thioredoxin Glutathione Reductase From Schistosoma Mansoni in Complex with 1,8-Naphthyridine-2-Carboxylic Acid

Enzymatic activity of Thioredoxin Glutathione Reductase From Schistosoma Mansoni in Complex with 1,8-Naphthyridine-2-Carboxylic Acid

All present enzymatic activity of Thioredoxin Glutathione Reductase From Schistosoma Mansoni in Complex with 1,8-Naphthyridine-2-Carboxylic Acid:
1.8.1.9;

Protein crystallography data

The structure of Thioredoxin Glutathione Reductase From Schistosoma Mansoni in Complex with 1,8-Naphthyridine-2-Carboxylic Acid, PDB code: 6fp4 was solved by I.Silvestri, F.Fata, A.E.Miele, G.Boumis, D.L.Williams, F.Angelucci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.68 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.316, 101.584, 58.783, 90.00, 112.78, 90.00
R / Rfree (%) 19.5 / 22.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Thioredoxin Glutathione Reductase From Schistosoma Mansoni in Complex with 1,8-Naphthyridine-2-Carboxylic Acid (pdb code 6fp4). 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 Thioredoxin Glutathione Reductase From Schistosoma Mansoni in Complex with 1,8-Naphthyridine-2-Carboxylic Acid, PDB code: 6fp4:

Sodium binding site 1 out of 1 in 6fp4

Go back to Sodium Binding Sites List in 6fp4
Sodium binding site 1 out of 1 in the Thioredoxin Glutathione Reductase From Schistosoma Mansoni in Complex with 1,8-Naphthyridine-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thioredoxin Glutathione Reductase From Schistosoma Mansoni in Complex with 1,8-Naphthyridine-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:40.0
occ:1.00
 H A:GLU259 2.2 47.4 1.0
HH21 A:ARG393 2.5 42.3 1.0
OD2 A:ASP433 2.6 43.5 1.0
O1A A:FAD601 2.7 36.1 1.0
HA3 A:GLY258 2.9 46.6 1.0
N A:GLU259 3.0 39.5 1.0
HG1 A:THR153 3.1 50.5 1.0
OG1 A:THR153 3.1 42.0 1.0
H5'1 A:FAD601 3.2 47.0 1.0
HA2 A:GLY258 3.3 46.6 1.0
NH2 A:ARG393 3.3 35.2 1.0
O3P A:FAD601 3.4 35.6 1.0
CA A:GLY258 3.5 38.8 1.0
HB A:THR153 3.5 48.5 1.0
HB2 A:ASP433 3.5 52.4 1.0
CG A:ASP433 3.6 42.0 1.0
HB2 A:GLU259 3.6 51.4 1.0
H3' A:FAD601 3.6 43.2 1.0
PA A:FAD601 3.6 37.1 1.0
HH22 A:ARG393 3.6 42.3 1.0
C A:GLY258 3.7 39.0 1.0
O A:HOH713 3.8 35.0 1.0
CB A:THR153 3.8 40.4 1.0
O A:GLU259 3.9 36.8 1.0
HG21 A:THR153 3.9 48.5 1.0
CA A:GLU259 4.0 40.8 1.0
CB A:ASP433 4.0 43.7 1.0
HE A:ARG393 4.0 41.0 1.0
C5' A:FAD601 4.1 39.1 1.0
O4' A:FAD601 4.2 37.2 1.0
CB A:GLU259 4.2 42.9 1.0
HG3 A:GLU259 4.2 52.6 1.0
C A:GLU259 4.3 40.4 1.0
HB3 A:ASP433 4.3 52.4 1.0
O2A A:FAD601 4.3 38.6 1.0
CZ A:ARG393 4.4 34.5 1.0
CG2 A:THR153 4.4 40.4 1.0
C3' A:FAD601 4.4 36.0 1.0
C4' A:FAD601 4.5 37.4 1.0
OD1 A:ASP433 4.6 39.0 1.0
NE A:ARG393 4.6 34.1 1.0
P A:FAD601 4.6 35.7 1.0
H A:THR153 4.6 48.2 1.0
H52A A:FAD601 4.7 52.3 1.0
H5'2 A:FAD601 4.7 47.0 1.0
CG A:GLU259 4.8 43.8 1.0
O5' A:FAD601 4.8 38.8 1.0
N A:GLY258 4.8 40.0 1.0
HA A:GLU259 4.8 49.0 1.0
O2P A:FAD601 4.9 40.1 1.0
H A:ASP433 4.9 51.3 1.0
HO4' A:FAD601 4.9 44.6 1.0
O A:GLY258 4.9 41.1 1.0
HO3' A:FAD601 5.0 44.9 1.0
HG23 A:THR153 5.0 48.5 1.0

Reference:

I.Silvestri, H.Lyu, F.Fata, G.Boumis, A.E.Miele, M.Ardini, R.Ippoliti, A.Bellelli, A.Jadhav, W.A.Lea, A.Simeonov, Q.Cheng, E.S.J.Arner, G.R.J.Thatcher, P.A.Petukhov, D.L.Williams, F.Angelucci. Fragment-Based Discovery of A Regulatory Site in Thioredoxin Glutathione Reductase Acting As "Doorstop" For Nadph Entry. Acs Chem. Biol. V. 13 2190 2018.
ISSN: ESSN 1554-8937
PubMed: 29800515
DOI: 10.1021/ACSCHEMBIO.8B00349
Page generated: Tue Oct 8 08:49:11 2024

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