Sodium in PDB 6rxa: Edds Lyase Variant D290M/Y320M with Bound Formate

The structure of Edds Lyase Variant D290M/Y320M with Bound Formate, PDB code: 6rxa 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)	51.27 / 1.44
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.892, 144.936, 146.130, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 18.2

The binding sites of Sodium atom in the Edds Lyase Variant D290M/Y320M with Bound Formate (pdb code 6rxa). 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 Formate, PDB code: 6rxa:
Jump to Sodium binding site number: 1; 2;

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


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 Formate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:15.0 occ:0.50 OE1 A:GLU188 2.3 13.7 1.0 O A:HOH713 2.4 14.2 1.0 HH22 A:ARG192 2.9 15.6 1.0 HB3 A:GLU188 3.1 15.9 1.0 HB2 A:GLU188 3.2 15.9 1.0 CD A:GLU188 3.4 13.6 1.0 HH21 A:ARG192 3.5 15.6 1.0 CB A:GLU188 3.5 13.2 1.0 NH2 A:ARG192 3.5 13.0 1.0 HA A:ARG185 3.8 14.0 1.0 O A:HOH907 4.0 16.8 1.0 OE2 A:GLU240 4.0 17.5 1.0 CG A:GLU188 4.0 12.9 1.0 HG2 A:GLU188 4.4 15.5 1.0 HG2 A:ARG185 4.4 16.0 1.0 OE2 A:GLU188 4.4 13.8 1.0 O A:ARG185 4.6 12.7 1.0 CA A:ARG185 4.7 11.7 1.0 CZ A:ARG192 4.8 12.5 1.0 HG3 A:GLU188 4.8 15.5 1.0 HH12 A:ARG192 4.9 15.2 1.0 CA A:GLU188 4.9 12.9 1.0

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


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 Formate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:14.0 occ:1.00 HH22 A:ARG185 2.3 16.1 1.0 HD2 A:LYS181 2.8 18.4 1.0 HZ1 A:LYS181 2.9 29.7 1.0 NH2 A:ARG185 3.1 13.3 1.0 HE3 A:LYS181 3.2 22.8 1.0 HH21 A:ARG185 3.4 16.1 1.0 CD A:LYS181 3.6 15.3 1.0 CE A:LYS181 3.6 19.0 1.0 NZ A:LYS181 3.6 24.7 1.0 HH12 A:ARG185 3.7 17.1 1.0 HB3 A:LYS181 4.0 15.8 1.0 HZ3 A:LYS181 4.1 29.7 1.0 CZ A:ARG185 4.1 13.5 1.0 HD3 A:LYS181 4.1 18.4 1.0 NH1 A:ARG185 4.3 14.2 1.0 HZ2 A:LYS181 4.3 29.7 1.0 HB2 A:LYS181 4.5 15.8 1.0 CB A:LYS181 4.5 13.1 1.0 HE2 A:LYS181 4.6 22.8 1.0 CG A:LYS181 4.7 14.1 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