Manganese in PDB 7uf3: Ribb From Vibrio Cholera Bound with L-Xylulose-5-Phosphate (L-XY5P) and Manganese

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

The structure of Ribb From Vibrio Cholera Bound with L-Xylulose-5-Phosphate (L-XY5P) and Manganese, PDB code: 7uf3 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)	39.51 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	60.369, 79.016, 91.349, 90, 90, 90
R / Rfree (%)	16.1 / 21.4

The binding sites of Manganese atom in the Ribb From Vibrio Cholera Bound with L-Xylulose-5-Phosphate (L-XY5P) and Manganese (pdb code 7uf3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Ribb From Vibrio Cholera Bound with L-Xylulose-5-Phosphate (L-XY5P) and Manganese, PDB code: 7uf3:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Ribb From Vibrio Cholera Bound with L-Xylulose-5-Phosphate (L-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 L-Xylulose-5-Phosphate (L-XY5P) and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:19.8 occ:1.00 OE1 A:GLU39 2.1 22.3 1.0 O14 A:N3U301 2.1 20.0 1.0 ND1 A:HIS154 2.1 18.7 1.0 O A:HOH430 2.2 23.5 1.0 O05 A:N3U301 2.3 20.0 1.0 O08 A:N3U301 2.3 20.0 1.0 H081 A:N3U301 2.9 20.0 1.0 CE1 A:HIS154 2.9 20.1 1.0 HE1 A:HIS154 3.0 24.1 1.0 C04 A:N3U301 3.1 20.0 1.0 HB2 A:HIS154 3.1 20.3 1.0 CD A:GLU39 3.2 22.1 1.0 HH12 A:ARG38 3.2 27.1 1.0 C03 A:N3U301 3.2 20.0 1.0 CG A:HIS154 3.2 17.5 1.0 P11 A:N3U301 3.3 20.0 1.0 H A:HIS154 3.5 19.9 1.0 H012 A:N3U301 3.6 20.0 1.0 O10 A:N3U301 3.6 20.0 1.0 OE2 A:GLU39 3.7 21.1 1.0 CB A:HIS154 3.7 16.9 1.0 OD2 A:ASP43 3.9 21.8 1.0 C01 A:N3U301 4.0 20.0 1.0 O12 A:N3U301 4.0 20.0 1.0 MN A:MN303 4.0 22.1 1.0 H031 A:N3U301 4.0 20.0 1.0 NH1 A:ARG38 4.0 22.6 1.0 OD1 A:ASP43 4.1 19.6 1.0 NE2 A:HIS154 4.1 19.2 1.0 C02 A:N3U301 4.2 20.0 1.0 CD2 A:HIS154 4.3 16.5 1.0 CG A:ASP43 4.3 23.1 1.0 HG3 A:GLU175 4.3 22.4 1.0 N A:HIS154 4.3 16.6 1.0 HH11 A:ARG38 4.4 27.1 1.0 HB3 A:HIS154 4.4 20.3 1.0 CG A:GLU39 4.5 21.6 1.0 OE1 A:GLU41 4.5 19.6 1.0 O A:HOH432 4.5 22.3 1.0 O13 A:N3U301 4.5 20.0 1.0 HB2 A:GLU41 4.5 24.5 1.0 HH22 A:ARG38 4.5 23.8 1.0 C06 A:N3U301 4.5 20.0 1.0 HG2 A:GLU175 4.5 22.4 1.0 HG3 A:GLU39 4.6 25.9 1.0 HB2 A:GLU39 4.6 24.5 1.0 O A:HOH436 4.6 17.0 1.0 CA A:HIS154 4.7 20.1 1.0 H021 A:N3U301 4.8 20.0 1.0 H071 A:N3U301 4.8 20.0 1.0 HE2 A:HIS154 4.8 23.1 1.0 CG A:GLU175 4.9 18.7 1.0 H062 A:N3U301 4.9 20.0 1.0 CB A:GLU39 5.0 20.4 1.0 HB3 A:ASP34 5.0 23.3 1.0

Manganese binding site 2 out of 3 in the Ribb From Vibrio Cholera Bound with L-Xylulose-5-Phosphate (L-XY5P) and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ribb From Vibrio Cholera Bound with L-Xylulose-5-Phosphate (L-XY5P) and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:22.1 occ:1.00 H071 A:N3U301 1.8 20.0 1.0 OE2 A:GLU39 2.0 21.1 1.0 O A:HOH436 2.2 17.0 1.0 O07 A:N3U301 2.2 20.0 1.0 O A:HOH432 2.3 22.3 1.0 O05 A:N3U301 2.3 20.0 1.0 C04 A:N3U301 3.0 20.0 1.0 C06 A:N3U301 3.1 20.0 1.0 CD A:GLU39 3.1 22.1 1.0 HD22 A:ASN92 3.1 36.0 1.0 OE1 A:GLU39 3.5 22.3 1.0 H062 A:N3U301 3.7 20.0 1.0 ND2 A:ASN92 3.8 30.0 1.0 H061 A:N3U301 3.9 20.0 1.0 O A:HOH410 3.9 30.5 1.0 HD21 A:ASN92 4.0 36.0 1.0 MN A:MN302 4.0 19.8 1.0 HG1 A:THR94 4.0 29.0 1.0 OE1 A:GLU41 4.1 19.6 1.0 OE2 A:GLU175 4.2 20.8 1.0 HG2 A:GLU39 4.3 25.9 1.0 O A:HOH430 4.3 23.5 1.0 CG A:GLU39 4.3 21.6 1.0 O12 A:N3U301 4.5 20.0 1.0 C03 A:N3U301 4.5 20.0 1.0 HG2 A:GLU175 4.6 22.4 1.0 OG1 A:THR94 4.7 24.2 1.0 HB2 A:ASN92 4.7 43.3 1.0 O14 A:N3U301 4.8 20.0 1.0 O10 A:N3U301 4.8 20.0 1.0 O08 A:N3U301 4.8 20.0 1.0 HB3 A:GLU39 4.9 24.5 1.0 H031 A:N3U301 4.9 20.0 1.0 HG3 A:GLU39 4.9 25.9 1.0 P11 A:N3U301 5.0 20.0 1.0

Manganese binding site 3 out of 3 in the Ribb From Vibrio Cholera Bound with L-Xylulose-5-Phosphate (L-XY5P) and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ribb From Vibrio Cholera Bound with L-Xylulose-5-Phosphate (L-XY5P) and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn304 b:64.0 occ:0.50 HA A:ASP214 3.7 69.8 1.0 HD13 A:LEU149 3.8 36.6 1.0 HA A:ILE211 3.9 39.3 1.0 HD11 A:LEU149 4.1 36.6 1.0 H A:LEU215 4.2 66.3 1.0 HD12 A:LEU149 4.2 36.6 1.0 CD1 A:LEU149 4.3 30.5 1.0 O A:LEU215 4.4 53.5 1.0 N A:LEU215 4.5 55.3 1.0 O A:ARG210 4.5 29.7 1.0 HB2 A:LYS216 4.5 83.2 1.0 CA A:ASP214 4.6 58.2 1.0 HG12 A:ILE211 4.6 27.1 1.0 C A:ASP214 4.7 57.1 1.0 C A:LEU215 4.8 61.9 1.0 CA A:ILE211 4.8 32.8 1.0 O A:ILE211 5.0 54.0 1.0 HA A:LYS216 5.0 66.1 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