Sodium in PDB 6g3e: Crystal Structure of Edds Lyase in Complex with Formate

The structure of Crystal Structure of Edds Lyase in Complex with Formate, PDB code: 6g3e was solved by H.Poddar, A.M.W.H.Thunnissem, G.J.Poelarends, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 1.90
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.440, 144.330, 145.810, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 16.6

The binding sites of Sodium atom in the Crystal Structure of Edds Lyase in Complex with Formate (pdb code 6g3e). 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 Crystal Structure of Edds Lyase in Complex with Formate, PDB code: 6g3e:

Sodium binding site 1 out of 1 in the Crystal Structure of Edds Lyase in Complex with Formate


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 Edds Lyase in Complex with Formate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:30.0 occ:1.00 O A:HOH1051 2.2 30.5 1.0 O A:HOH896 2.3 24.9 1.0 O A:HOH962 2.4 43.5 1.0 OD2 A:ASP184 2.4 17.2 1.0 O A:HOH893 2.5 28.5 1.0 O A:HOH1054 2.6 34.1 1.0 CG A:ASP184 3.2 17.2 1.0 OD1 A:ASP184 3.3 17.5 1.0 O A:ALA180 4.2 8.7 1.0 O A:HOH929 4.3 37.5 1.0 O A:HOH749 4.3 11.8 1.0 O A:HOH763 4.4 29.2 1.0 O A:HOH761 4.4 22.4 1.0 O A:HOH1123 4.6 19.0 1.0 CB A:ASP184 4.6 9.4 1.0 C A:ALA180 4.7 9.3 1.0 NH2 A:ARG187 4.7 17.6 1.0 CB A:ALA180 4.7 13.5 1.0 O A:HOH983 4.9 31.9 1.0 OE2 A:GLU464 4.9 28.1 1.0 OE1 A:GLU464 4.9 23.9 1.0

H.Poddar, J.De Villiers, J.Zhang, V.Puthan Veetil, H.Raj, A.W.H.Thunnissen, G.J.Poelarends. Structural Basis For the Catalytic Mechanism of Ethylenediamine- N, N'-Disuccinic Acid Lyase, A Carbon-Nitrogen Bond-Forming Enzyme with A Broad Substrate Scope. Biochemistry V. 57 3752 2018.
ISSN: ISSN 1520-4995
PubMed: 29741885
DOI: 10.1021/ACS.BIOCHEM.8B00406