Potassium 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
Bromine	(Br)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of A Class II Pyruvate Aldolase From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate, PDB code: 6r62:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 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 Potassium with other atoms in the K 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:K307 b:21.6 occ:1.00 O A:ALA31 2.6 20.5 1.0 O A:LEU33 2.6 21.6 1.0 O A:HOH646 2.7 33.1 1.0 O A:TYR35 2.8 20.6 1.0 O A:GLY63 2.8 21.6 1.0 O A:HOH599 3.0 33.6 1.0 HB2 A:ALA64 3.4 24.5 1.0 H A:TYR35 3.5 23.1 1.0 C A:GLY63 3.6 22.2 1.0 C A:ALA31 3.8 16.9 1.0 C A:LEU33 3.9 20.8 1.0 C A:TYR35 3.9 19.4 1.0 HZ2 A:LYS3 3.9 76.4 1.0 HA A:ARG32 4.0 22.8 1.0 HA A:ASP34 4.0 23.2 1.0 HA A:ALA64 4.0 22.4 1.0 HZ3 A:LYS3 4.0 76.4 1.0 N A:TYR35 4.0 19.3 1.0 O A:HOH629 4.1 46.2 1.0 CB A:ALA64 4.2 20.4 1.0 HA3 A:GLY63 4.2 29.2 1.0 N A:ALA64 4.2 19.4 1.0 C A:ARG32 4.3 18.8 1.0 HB2 A:TYR35 4.3 20.8 1.0 CA A:ALA64 4.3 18.6 1.0 O A:HOH446 4.3 26.4 1.0 O A:HOH769 4.4 50.8 1.0 NZ A:LYS3 4.4 63.7 1.0 HE2 A:LYS3 4.4 63.5 1.0 CA A:ARG32 4.5 19.0 1.0 N A:LEU33 4.5 18.9 1.0 HA A:ALA31 4.5 21.0 1.0 CA A:GLY63 4.5 24.3 1.0 CA A:TYR35 4.5 17.9 1.0 O A:ARG32 4.6 23.5 1.0 N A:ARG32 4.6 18.2 1.0 CA A:ASP34 4.6 19.4 1.0 HA A:ASP36 4.7 21.8 1.0 O A:GLY62 4.7 25.1 1.0 HB1 A:ALA64 4.7 24.5 1.0 N A:ASP34 4.7 19.2 1.0 H A:LEU33 4.7 22.7 1.0 C A:ASP34 4.8 23.4 1.0 CA A:ALA31 4.8 17.5 1.0 CA A:LEU33 4.8 21.3 1.0 HB3 A:ALA64 4.9 24.5 1.0 H A:ALA64 4.9 23.3 1.0 CB A:TYR35 4.9 17.3 1.0 O A:HOH538 5.0 40.8 1.0 CE A:LYS3 5.0 52.9 1.0 N A:ASP36 5.0 19.7 1.0

Potassium binding site 2 out of 2 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 Potassium with other atoms in the K binding site number 2 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:K308 b:24.3 occ:0.62 O A:SER158 2.6 26.8 1.0 OD1 A:ASP160 2.9 38.4 1.0 O A:HOH411 3.1 42.9 1.0 OD2 A:ASP160 3.4 46.5 1.0 CG A:ASP160 3.5 40.5 1.0 HB2 A:SER158 3.7 33.1 1.0 C A:SER158 3.8 24.7 1.0 HH12 A:ARG97 3.9 56.3 0.5 O A:HOH794 4.1 28.7 0.6 HA A:SER158 4.2 31.5 1.0 OXT A:ACT303 4.3 30.7 1.0 N A:ASP160 4.4 25.6 0.4 CA A:SER158 4.4 26.2 1.0 CB A:SER158 4.4 27.6 1.0 HA A:VAL159 4.5 27.0 1.0 O A:HOH409 4.6 38.0 1.0 N A:ASP160 4.7 24.2 0.6 NH1 A:ARG97 4.7 46.9 0.5 CB A:ASP160 4.8 29.5 1.0 N A:VAL159 4.8 26.5 1.0 OG A:SER158 4.9 31.8 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