Manganese in PDB 7uf4: Ribb From Vibrio Cholera Bound with Intermediate 1 of the Reaction Cycle and D-Ribulose-5-Phosphate (D-RU5P)

All present enzymatic activity of Ribb From Vibrio Cholera Bound with Intermediate 1 of the Reaction Cycle and D-Ribulose-5-Phosphate (D-RU5P):
4.1.99.12;

The structure of Ribb From Vibrio Cholera Bound with Intermediate 1 of the Reaction Cycle and D-Ribulose-5-Phosphate (D-RU5P), PDB code: 7uf4 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)	39.28 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	60.337, 78.558, 90.535, 90, 90, 90
R / Rfree (%)	16.9 / 22.4

The binding sites of Manganese atom in the Ribb From Vibrio Cholera Bound with Intermediate 1 of the Reaction Cycle and D-Ribulose-5-Phosphate (D-RU5P) (pdb code 7uf4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Ribb From Vibrio Cholera Bound with Intermediate 1 of the Reaction Cycle and D-Ribulose-5-Phosphate (D-RU5P), PDB code: 7uf4:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Ribb From Vibrio Cholera Bound with Intermediate 1 of the Reaction Cycle and D-Ribulose-5-Phosphate (D-RU5P)


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 Intermediate 1 of the Reaction Cycle and D-Ribulose-5-Phosphate (D-RU5P) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:72.6 occ:1.00 H14 A:5RP302 1.7 39.1 0.8 H051 A:N46301 1.8 39.5 0.2 OE1 A:GLU39 2.0 35.8 1.0 O14 A:5RP302 2.0 32.6 0.8 O05 A:N46301 2.2 32.9 0.2 ND1 A:HIS154 2.3 33.8 1.0 O A:HOH420 2.4 31.1 1.0 O13 A:5RP302 2.6 35.3 0.8 O10 A:N46301 2.8 34.1 0.2 O12 A:5RP302 2.8 34.2 0.8 C6 A:5RP302 2.9 36.5 0.8 CD A:GLU39 2.9 42.7 1.0 H062 A:N46301 3.0 44.2 0.2 CE1 A:HIS154 3.0 27.1 1.0 H71 A:5RP302 3.0 44.3 0.8 HE1 A:HIS154 3.0 32.5 1.0 O12 A:N46301 3.1 39.1 0.2 C04 A:N46301 3.1 36.3 0.2 C5 A:5RP302 3.1 36.8 0.8 OE2 A:GLU39 3.3 39.1 1.0 HB2 A:HIS154 3.3 34.1 1.0 C7 A:5RP302 3.4 36.9 0.8 H5 A:5RP302 3.4 44.2 0.8 CG A:HIS154 3.4 24.6 1.0 C06 A:N46301 3.4 36.8 0.2 C03 A:N46301 3.4 36.7 0.2 H13 A:5RP302 3.4 42.4 0.8 HH12 A:ARG38 3.6 38.7 1.0 OD2 A:ASP43 3.7 27.1 1.0 O07 A:N46301 3.8 34.0 0.2 O8 A:5RP302 3.8 33.8 0.8 H6 A:5RP302 3.8 43.8 0.8 P9 A:5RP302 3.8 27.1 0.8 P08 A:N46301 3.8 27.6 0.2 CB A:HIS154 3.9 28.4 1.0 H A:HIS154 4.0 40.6 1.0 H041 A:N46301 4.0 43.6 0.2 NE2 A:HIS154 4.1 34.6 1.0 OD1 A:ASP43 4.1 26.6 1.0 HB2 A:GLU39 4.2 47.5 1.0 CG A:GLU39 4.2 40.8 1.0 HB2 A:GLU41 4.3 25.6 1.0 CG A:ASP43 4.3 25.9 1.0 NH1 A:ARG38 4.3 32.3 1.0 O A:HOH402 4.3 27.5 1.0 CD2 A:HIS154 4.3 29.3 1.0 H72 A:5RP302 4.4 44.3 0.8 H061 A:N46301 4.4 44.2 0.2 HH11 A:ARG38 4.5 38.7 1.0 HG3 A:GLU39 4.5 49.0 1.0 HB3 A:HIS154 4.5 34.1 1.0 O09 A:N46301 4.5 37.0 0.2 C3 A:5RP302 4.5 33.7 0.8 HB3 A:GLU39 4.6 47.5 1.0 O11 A:5RP302 4.6 37.1 0.8 OE1 A:GLU41 4.6 29.1 1.0 CB A:GLU39 4.6 39.6 1.0 HG3 A:GLU175 4.7 35.7 1.0 HG2 A:GLU175 4.7 35.7 1.0 N A:HIS154 4.8 33.8 1.0 C02 A:N46301 4.8 34.3 0.2 HE2 A:HIS154 4.8 41.5 1.0 HB3 A:ASP34 4.9 37.4 1.0 OD2 A:ASP34 4.9 38.1 1.0 HG2 A:GLU39 4.9 49.0 1.0 O4 A:5RP302 5.0 34.8 0.8 CA A:HIS154 5.0 28.0 1.0

Manganese binding site 2 out of 2 in the Ribb From Vibrio Cholera Bound with Intermediate 1 of the Reaction Cycle and D-Ribulose-5-Phosphate (D-RU5P)


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 Intermediate 1 of the Reaction Cycle and D-Ribulose-5-Phosphate (D-RU5P) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn304 b:84.2 occ:1.00 O A:ALA123 3.2 30.1 1.0 HG3 A:GLN168 3.4 103.7 1.0 HD2 A:PRO169 3.4 37.2 1.0 O A:HOH421 3.6 26.0 1.0 HG2 A:GLN75 3.6 44.9 1.0 HG2 A:PRO169 3.7 32.3 1.0 HB2 A:ALA170 3.8 34.8 1.0 OE1 A:GLN75 3.8 38.3 1.0 HB2 A:GLN75 3.9 35.9 1.0 HG2 A:GLN168 3.9 103.7 1.0 CD A:GLN75 3.9 36.1 1.0 HG3 A:PRO125 4.0 47.6 1.0 HA A:PRO125 4.0 48.3 1.0 CG A:GLN168 4.1 86.4 1.0 HE21 A:GLN168 4.1 83.2 1.0 CG A:GLN75 4.2 37.4 1.0 CD A:PRO169 4.3 31.0 1.0 C A:ALA123 4.3 36.4 1.0 HA A:ALA123 4.3 42.9 1.0 HB3 A:ALA123 4.3 33.8 1.0 CG A:PRO169 4.4 26.9 1.0 CB A:GLN75 4.5 29.9 1.0 HB3 A:PRO125 4.5 44.0 1.0 NE2 A:GLN75 4.5 34.2 1.0 HB3 A:ALA170 4.5 34.8 1.0 CB A:ALA170 4.6 29.0 1.0 NE2 A:GLN168 4.6 69.3 1.0 CA A:PRO125 4.7 40.2 1.0 N A:PRO125 4.7 32.5 1.0 O A:PRO169 4.7 31.8 1.0 CG A:PRO125 4.7 39.7 1.0 HE22 A:GLN75 4.8 41.0 1.0 CD A:GLN168 4.8 73.0 1.0 CA A:ALA123 4.8 35.7 1.0 HB3 A:GLN75 4.8 35.9 1.0 N A:PRO169 4.8 34.8 1.0 HE21 A:GLN75 4.9 41.0 1.0 CB A:PRO125 4.9 36.6 1.0 C A:PRO169 4.9 30.8 1.0 HD3 A:PRO125 4.9 41.3 1.0 HD22 A:LEU71 5.0 36.0 1.0 HD3 A:PRO169 5.0 37.2 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