Sodium in PDB 6r62: Crystal Structure of A Class II Pyruvate Aldolase From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate

The structure of Crystal Structure of A Class II Pyruvate Aldolase From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate, PDB code: 6r62 was solved by S.R.Marsden, L.Mestrom, P.L.Hagedoorn, I.Bento, D.G.G.Mcmillan, U.Hanefeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.30 / 1.55
Space group	P 42 3 2
Cell size a, b, c (Å), α, β, γ (°)	116.569, 116.569, 116.569, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 18.6

The structure of Crystal Structure of A Class II Pyruvate Aldolase From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Potassium	(K)	2 atoms
Bromine	(Br)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of A Class II Pyruvate Aldolase From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate (pdb code 6r62). 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 A Class II Pyruvate Aldolase From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate, PDB code: 6r62:

Sodium binding site 1 out of 1 in the Crystal Structure of A Class II Pyruvate Aldolase From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate


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 A Class II Pyruvate Aldolase From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:25.9 occ:0.30 O A:HOH523 2.4 26.8 1.0 O A:HOH438 2.6 29.3 1.0 O A:HOH576 3.7 26.3 1.0 O A:HOH750 3.8 56.3 0.5 O A:HOH463 4.1 32.1 1.0 OD1 A:ASP77 4.4 21.6 1.0 OD2 A:ASP77 4.5 21.5 1.0 O A:HOH614 4.7 44.2 1.0 CG A:ASP77 4.9 24.6 1.0

S.R.Marsden, L.Mestrom, I.Bento, P.L.Hagedoorn, D.G.G.Mcmillan, U.Hanefeld. Ch-Pi Interactions Promote the Conversion of Hydroxypyruvate in A Class II Pyruvate Aldolase Adv.Synth.Catal. 2019.
ISSN: ESSN 1615-4169
DOI: 10.1002/ADSC.201900205