Sodium in PDB 6hxi: Structure of Atp Citrate Lyase From Methanothrix Soehngenii in Complex with Citrate and Coenzyme A

All present enzymatic activity of Structure of Atp Citrate Lyase From Methanothrix Soehngenii in Complex with Citrate and Coenzyme A:
2.3.3.8; 6.2.1.5;

The structure of Structure of Atp Citrate Lyase From Methanothrix Soehngenii in Complex with Citrate and Coenzyme A, PDB code: 6hxi was solved by K.Verstraete, K.Verschueren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.75 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	118.451, 275.020, 72.722, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.8

The binding sites of Sodium atom in the Structure of Atp Citrate Lyase From Methanothrix Soehngenii in Complex with Citrate and Coenzyme A (pdb code 6hxi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Atp Citrate Lyase From Methanothrix Soehngenii in Complex with Citrate and Coenzyme A, PDB code: 6hxi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Atp Citrate Lyase From Methanothrix Soehngenii in Complex with Citrate and Coenzyme A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Atp Citrate Lyase From Methanothrix Soehngenii in Complex with Citrate and Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:46.1 occ:1.00 O A:ASP255 2.4 65.8 1.0 O A:THR258 2.5 56.3 1.0 O A:ALA260 2.6 55.1 1.0 O A:HOH662 2.7 64.4 1.0 OD1 A:ASP255 3.2 73.8 1.0 C A:ASP255 3.5 67.3 1.0 CG A:ASP255 3.6 73.4 1.0 C A:THR258 3.6 55.8 1.0 O D:HOH906 3.8 52.3 1.0 C A:ALA260 3.8 56.3 1.0 OD2 A:ASP255 3.9 76.6 1.0 C A:GLY259 4.1 54.9 1.0 CA A:ASP255 4.1 62.2 1.0 O A:HOH635 4.2 60.1 1.0 O A:GLY259 4.2 52.6 1.0 CG2 A:THR258 4.3 48.6 1.0 N A:ALA260 4.4 53.4 1.0 N A:GLY259 4.4 51.3 1.0 CA A:GLY259 4.4 50.6 1.0 CB A:ASP255 4.5 64.1 1.0 CA A:THR258 4.6 52.8 1.0 CA A:SER261 4.6 55.9 1.0 N A:SER261 4.6 54.9 1.0 N A:SER256 4.6 65.3 1.0 N A:THR258 4.7 55.4 1.0 CA A:ALA260 4.7 53.5 1.0 CB A:THR258 5.0 53.4 1.0 CA A:SER256 5.0 64.8 1.0

Sodium binding site 2 out of 2 in the Structure of Atp Citrate Lyase From Methanothrix Soehngenii in Complex with Citrate and Coenzyme A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Atp Citrate Lyase From Methanothrix Soehngenii in Complex with Citrate and Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:41.3 occ:1.00 O C:ASP255 2.4 54.2 1.0 O C:THR258 2.5 46.0 1.0 O C:ALA260 2.6 42.1 1.0 OD1 C:ASP255 3.1 65.6 1.0 C C:ASP255 3.5 55.4 1.0 CG C:ASP255 3.5 65.0 1.0 C C:THR258 3.7 46.2 1.0 OD2 C:ASP255 3.8 76.5 1.0 C C:ALA260 3.8 45.1 1.0 CA C:ASP255 4.1 52.1 1.0 C C:GLY259 4.2 46.6 1.0 O C:GLY259 4.3 48.6 1.0 CG2 C:THR258 4.3 43.8 1.0 CB C:ASP255 4.4 53.6 1.0 N C:ALA260 4.4 43.2 1.0 N C:GLY259 4.5 41.0 1.0 CA C:GLY259 4.5 41.2 1.0 CA C:SER261 4.6 45.4 1.0 N C:SER256 4.6 53.4 1.0 N C:SER261 4.6 44.0 1.0 CA C:THR258 4.6 43.3 1.0 N C:THR258 4.7 45.3 1.0 CA C:ALA260 4.8 42.3 1.0 CA C:SER256 5.0 53.3 1.0

K.H.G.Verschueren, C.Blanchet, J.Felix, A.Dansercoer, D.De Vos, Y.Bloch, J.Van Beeumen, D.Svergun, I.Gutsche, S.N.Savvides, K.Verstraete. Structure of Atp Citrate Lyase and the Origin of Citrate Synthase in the Krebs Cycle. Nature V. 568 571 2019.
ISSN: ESSN 1476-4687
PubMed: 30944476
DOI: 10.1038/S41586-019-1095-5