Sodium in PDB 7yqs: Neutron Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex

The structure of Neutron Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex, PDB code: 7yqs was solved by N.Yano, T.Kondo, K.Kusaka, T.Yamada, T.Arakawa, T.Sakamoto, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.78, 65.8, 108.95, 90, 90, 90
R / Rfree (%)	16.2 / 19.1

The structure of Neutron Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Neutron Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex (pdb code 7yqs). 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 Neutron Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex, PDB code: 7yqs:

Sodium binding site 1 out of 1 in the Neutron Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Neutron Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:35.1 occ:1.00 O A:GLU221 2.4 31.0 1.0 O A:HOH970 2.5 48.6 1.0 O A:ASP198 2.5 31.4 1.0 O A:GLY171 2.6 32.0 1.0 O A:HOH963 2.6 53.9 1.0 O A:HOH828 2.8 48.9 1.0 D2 A:HOH828 3.3 37.6 0.3 C A:ASP198 3.4 29.4 1.0 HB3 A:ASP198 3.5 43.0 1.0 HA A:ASN199 3.5 26.3 1.0 D1 A:HOH828 3.6 37.1 0.5 C A:GLY171 3.6 32.2 1.0 HA3 A:GLY171 3.6 31.8 1.0 C A:GLU221 3.6 27.9 1.0 HA A:THR222 3.7 32.4 1.0 HG23 A:THR222 3.7 37.9 1.0 HA2 A:GLY171 3.8 34.5 1.0 CA A:GLY171 3.9 33.2 1.0 HA A:ASP198 4.1 30.7 1.0 N A:ASN199 4.1 27.8 1.0 HB2 A:SER172 4.1 31.6 1.0 HA A:GLU221 4.2 31.3 1.0 CA A:ASP198 4.2 30.6 1.0 CA A:ASN199 4.3 25.9 1.0 CB A:ASP198 4.3 37.4 1.0 HB3 A:ASN199 4.3 27.3 1.0 CA A:GLU221 4.5 28.7 1.0 HB3 A:GLU221 4.5 33.1 1.0 N A:THR222 4.5 28.6 1.0 CA A:THR222 4.6 29.7 1.0 O A:HOH756 4.6 51.3 1.0 CG2 A:THR222 4.7 34.7 1.0 N A:SER172 4.8 30.1 1.0 HB2 A:ASP198 4.9 38.1 1.0 CB A:ASN199 4.9 27.8 1.0 HD3 A:PRO223 4.9 37.9 1.0 OE1 A:GLU221 4.9 35.0 1.0

N.Yano, T.Kondo, K.Kusaka, T.Yamada, T.Arakawa, T.Sakamoto, S.Fushinobu. Charge Neutralization and Beta-Elimination Cleavage Mechanism of Family 42 L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase Revealed By Neutron Crystallography To Be Published.