Sodium in PDB 6rx8: Edds Lyase Variant D290M/Y320M with Bound Fumarate

The structure of Edds Lyase Variant D290M/Y320M with Bound Fumarate, PDB code: 6rx8 was solved by E.Grandi, G.J.Poelarends, A.M.W.H.Thunnissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.84 / 1.92
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.160, 144.230, 144.451, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.1

The binding sites of Sodium atom in the Edds Lyase Variant D290M/Y320M with Bound Fumarate (pdb code 6rx8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Edds Lyase Variant D290M/Y320M with Bound Fumarate, PDB code: 6rx8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Edds Lyase Variant D290M/Y320M with Bound Fumarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Edds Lyase Variant D290M/Y320M with Bound Fumarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:19.9 occ:0.50 OE1 A:GLU188 2.3 19.7 1.0 O A:HOH710 2.3 15.5 1.0 HH22 A:ARG192 2.8 22.3 1.0 HB2 A:GLU188 3.1 21.0 1.0 HB3 A:GLU188 3.1 21.0 1.0 CD A:GLU188 3.4 19.5 1.0 HH21 A:ARG192 3.5 22.3 1.0 NH2 A:ARG192 3.5 18.6 1.0 CB A:GLU188 3.5 17.5 1.0 HA A:ARG185 3.7 20.7 1.0 OE2 A:GLU240 3.8 20.5 1.0 O A:HOH941 3.9 20.4 1.0 CG A:GLU188 4.1 17.8 1.0 HG2 A:ARG185 4.4 21.7 1.0 OE2 A:GLU188 4.4 19.1 1.0 HG2 A:GLU188 4.5 21.4 1.0 O A:ARG185 4.6 19.1 1.0 CA A:ARG185 4.7 17.2 1.0 CZ A:ARG192 4.7 16.9 1.0 HH12 A:ARG192 4.8 22.7 1.0 HG3 A:GLU188 4.9 21.4 1.0 CA A:GLU188 4.9 17.6 1.0 H A:LEU189 5.0 21.6 1.0 CD A:GLU240 5.0 19.0 1.0 HB3 A:ARG185 5.0 20.0 1.0

Sodium binding site 2 out of 2 in the Edds Lyase Variant D290M/Y320M with Bound Fumarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Edds Lyase Variant D290M/Y320M with Bound Fumarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:12.5 occ:1.00 HH22 A:ARG185 2.2 21.8 1.0 HZ2 A:LYS181 2.8 34.3 1.0 HD2 A:LYS181 2.8 26.0 1.0 NH2 A:ARG185 3.0 18.2 1.0 HH21 A:ARG185 3.2 21.8 1.0 HE3 A:LYS181 3.4 28.6 1.0 O A:HOH938 3.5 35.8 1.0 NZ A:LYS181 3.5 28.6 1.0 CD A:LYS181 3.6 21.6 1.0 CE A:LYS181 3.7 23.8 1.0 HH12 A:ARG185 3.8 21.4 1.0 HZ1 A:LYS181 3.8 34.3 1.0 HB3 A:LYS181 4.0 20.6 1.0 CZ A:ARG185 4.0 18.4 1.0 HD3 A:LYS181 4.1 26.0 1.0 HZ3 A:LYS181 4.2 34.3 1.0 NH1 A:ARG185 4.3 17.8 1.0 HB2 A:LYS181 4.5 20.6 1.0 CB A:LYS181 4.6 17.2 1.0 HE2 A:LYS181 4.7 28.6 1.0 CG A:LYS181 4.7 19.1 1.0

J.Zhang, E.Grandi, H.Fu, T.Saravanan, L.Bothof, P.G.Tepper, A.W.H.Thunnissen, G.J.Poelarends. Engineered C-N Lyase: Enantioselective Synthesis of Chiral Synthons For Artificial Dipeptide Sweeteners. Angew.Chem.Int.Ed.Engl. 2019.
ISSN: ESSN 1521-3773
PubMed: 31625664
DOI: 10.1002/ANIE.201910704