Manganese in PDB 7uf2: Ribb From Vibrio Cholera Bound with D-Xylulose-5-Phosphate (D-XY5P) and Manganese

All present enzymatic activity of Ribb From Vibrio Cholera Bound with D-Xylulose-5-Phosphate (D-XY5P) and Manganese:
4.1.99.12;

The structure of Ribb From Vibrio Cholera Bound with D-Xylulose-5-Phosphate (D-XY5P) and Manganese, PDB code: 7uf2 was solved by N.Kenjic, K.M.Meneely, A.L.Lamb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.55 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	61.029, 79.106, 91.34, 90, 90, 90
R / Rfree (%)	16.4 / 22

The binding sites of Manganese atom in the Ribb From Vibrio Cholera Bound with D-Xylulose-5-Phosphate (D-XY5P) and Manganese (pdb code 7uf2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Ribb From Vibrio Cholera Bound with D-Xylulose-5-Phosphate (D-XY5P) and Manganese, PDB code: 7uf2:

Manganese binding site 1 out of 1 in the Ribb From Vibrio Cholera Bound with D-Xylulose-5-Phosphate (D-XY5P) and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ribb From Vibrio Cholera Bound with D-Xylulose-5-Phosphate (D-XY5P) and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:63.6 occ:1.00 H7A A:5SP301 1.3 57.6 1.0 HD1 A:HIS154 1.9 22.6 1.0 OE1 A:GLU39 2.1 21.7 0.5 OE1 A:GLU39 2.2 27.7 0.5 C7 A:5SP301 2.3 48.0 1.0 O A:HOH435 2.4 19.7 1.0 ND1 A:HIS154 2.4 18.9 1.0 O14 A:5SP301 2.7 31.5 1.0 H7 A:5SP301 2.8 57.6 1.0 O10 A:5SP301 2.8 22.8 1.0 CE1 A:HIS154 2.9 21.4 1.0 HE1 A:HIS154 2.9 25.6 1.0 C6 A:5SP301 3.0 51.8 1.0 CD A:GLU39 3.1 32.4 0.5 CD A:GLU39 3.2 31.0 0.5 HO14 A:5SP301 3.2 37.8 1.0 O8 A:5SP301 3.2 39.8 1.0 OE2 A:GLU39 3.4 30.1 0.5 P9 A:5SP301 3.4 23.1 1.0 CG A:HIS154 3.5 21.1 1.0 HB2 A:HIS154 3.5 23.2 1.0 OE2 A:GLU39 3.5 28.2 0.5 HH12 A:ARG38 3.6 32.7 1.0 O13 A:5SP301 3.7 60.9 1.0 OD2 A:ASP43 3.8 22.9 1.0 H6 A:5SP301 3.8 62.1 1.0 C5 A:5SP301 3.9 57.4 1.0 CB A:HIS154 4.0 19.3 1.0 NE2 A:HIS154 4.0 20.1 1.0 H A:HIS154 4.0 29.1 1.0 O A:HOH403 4.1 37.0 1.0 O11 A:5SP301 4.1 27.5 1.0 HO13 A:5SP301 4.1 73.0 1.0 HB2 A:GLU39 4.2 33.0 0.5 HB2 A:GLU39 4.2 33.0 0.5 CD2 A:HIS154 4.3 21.1 1.0 OD1 A:ASP43 4.3 19.2 1.0 HB2 A:GLU41 4.3 19.9 1.0 NH1 A:ARG38 4.4 27.3 1.0 OE1 A:GLU41 4.4 22.0 1.0 CG A:GLU39 4.4 27.1 0.5 CG A:GLU39 4.4 27.1 0.5 CG A:ASP43 4.5 23.2 1.0 O A:HOH411 4.5 29.7 1.0 H5 A:5SP301 4.6 68.9 1.0 HG3 A:GLU175 4.6 18.1 1.0 HH11 A:ARG38 4.6 32.7 1.0 HG3 A:GLU39 4.6 32.5 0.5 HB3 A:HIS154 4.6 23.2 1.0 HB3 A:GLU39 4.6 33.0 0.5 HG2 A:GLU175 4.6 18.1 1.0 CB A:GLU39 4.7 27.5 0.5 HE2 A:HIS154 4.7 24.1 1.0 CB A:GLU39 4.7 27.5 0.5 O12 A:5SP301 4.7 17.2 1.0 HB3 A:GLU39 4.7 33.0 0.5 N A:HIS154 4.8 24.3 1.0 HG2 A:GLU39 4.9 32.5 0.5 C3 A:5SP301 4.9 43.9 1.0 HG3 A:GLU39 4.9 32.5 0.5 HB3 A:ASP34 5.0 21.5 1.0 HH22 A:ARG38 5.0 31.0 1.0 HD22 A:LEU173 5.0 20.3 1.0

N.Kenjic, K.M.Meneely, D.J.Wherritt, M.C.Denler, T.A.Jackson, G.R.Moran, A.L.Lamb. Evidence For the Chemical Mechanism of Ribb (3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase) of Riboflavin Biosynthesis. J.Am.Chem.Soc. V. 144 12769 2022.
ISSN: ESSN 1520-5126
PubMed: 35802469
DOI: 10.1021/JACS.2C03376