Bromine 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
Sodium	(Na)	1 atom

The binding sites of Bromine 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 Bromine atom.
In total 2 binding sites of Bromine 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 Bromine binding site number: 1; 2;

Bromine 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 Bromine with other atoms in the Br 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:Br305 b:22.9 occ:0.77 HG2 A:PRO232 3.1 23.3 1.0 HE1 A:PHE210 3.2 23.9 1.0 O A:HOH460 3.2 26.8 1.0 HD2 A:PRO232 3.2 25.6 1.0 HG21 A:VAL182 3.2 29.4 1.0 HG11 A:VAL182 3.3 26.8 1.0 O A:HOH745 3.4 40.6 1.0 HA2 A:GLY212 3.4 24.5 1.0 O A:HOH723 3.6 33.0 1.0 HA3 A:GLY212 3.6 24.5 1.0 HZ A:PHE210 3.7 26.6 1.0 CD A:PRO232 3.8 21.3 1.0 CG A:PRO232 3.9 19.4 1.0 HB A:VAL182 3.9 28.7 1.0 CE1 A:PHE210 3.9 19.9 1.0 HD3 A:PRO232 3.9 25.6 1.0 CA A:GLY212 4.0 20.4 1.0 HB2 A:ALA235 4.0 23.9 1.0 CG2 A:VAL182 4.1 24.5 1.0 CG1 A:VAL182 4.1 22.3 1.0 CZ A:PHE210 4.2 22.2 1.0 HB1 A:ALA235 4.2 23.9 1.0 HB3 A:ALA235 4.3 23.9 1.0 CB A:VAL182 4.3 23.9 1.0 O A:HOH606 4.3 30.1 1.0 CB A:ALA235 4.4 19.9 1.0 HG3 A:PRO232 4.4 23.3 1.0 HG23 A:VAL182 4.5 29.4 1.0 HG12 A:VAL182 4.6 26.8 1.0 HB1 A:ALA231 4.6 25.2 1.0 HB2 A:PRO232 4.7 23.7 1.0 HG22 A:VAL182 4.8 29.4 1.0 HG13 A:VAL182 4.8 26.8 1.0 O A:GLY212 4.8 23.2 1.0 CB A:PRO232 4.9 19.7 1.0 N A:GLY212 4.9 22.5 1.0 C A:GLY212 5.0 20.4 1.0

Bromine 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 Bromine with other atoms in the Br 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:Br306 b:27.5 occ:0.51 O A:HOH648 2.8 45.0 1.0 O A:HOH540 2.8 28.2 1.0 HG2 A:ARG242 3.1 40.2 0.6 HG2 A:ARG242 3.1 38.8 0.4 HH11 A:ARG242 3.2 35.5 0.4 HH12 A:ARG242 3.4 35.5 0.4 NH1 A:ARG242 3.4 29.6 0.4 HG21 A:ILE245 3.7 32.6 1.0 HA A:ARG242 3.7 26.9 0.4 HA A:ARG242 3.7 27.1 0.6 O A:HOH645 3.8 44.5 1.0 HD13 A:ILE245 3.9 27.0 1.0 HD12 A:ILE245 3.9 27.0 1.0 CG A:ARG242 4.0 33.5 0.6 CG A:ARG242 4.0 32.3 0.4 HB A:ILE245 4.1 25.3 1.0 HG3 A:ARG242 4.2 40.2 0.6 CZ A:ARG242 4.3 30.5 0.4 CD1 A:ILE245 4.3 22.5 1.0 CG2 A:ILE245 4.4 27.1 1.0 HG22 A:ILE245 4.4 32.6 1.0 HG3 A:ARG242 4.5 38.8 0.4 O A:HOH669 4.5 30.4 1.0 HD3 A:ARG242 4.6 43.0 0.4 CA A:ARG242 4.6 22.4 0.4 CA A:ARG242 4.6 22.6 0.6 CB A:ILE245 4.7 21.1 1.0 CB A:ARG242 4.7 24.7 0.4 CB A:ARG242 4.7 23.2 0.6 CD A:ARG242 4.7 35.8 0.4 HB3 A:ARG242 4.7 29.6 0.4 HD3 A:ARG242 4.8 42.2 0.6 HE A:ARG242 4.8 47.2 0.6 HB3 A:ARG242 4.8 27.8 0.6 NE A:ARG242 4.8 38.6 0.4 CD A:ARG242 4.9 35.2 0.6 O A:ARG242 4.9 23.1 0.4 O A:ARG242 4.9 23.6 0.6

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