Manganese in PDB 7uf5: Ribb From Vibrio Cholera Bound with Intermediate 2 in the Reaction Cycle and the Products Dhbp and Formate

Enzymatic activity of Ribb From Vibrio Cholera Bound with Intermediate 2 in the Reaction Cycle and the Products Dhbp and Formate

All present enzymatic activity of Ribb From Vibrio Cholera Bound with Intermediate 2 in the Reaction Cycle and the Products Dhbp and Formate:
4.1.99.12;

Protein crystallography data

The structure of Ribb From Vibrio Cholera Bound with Intermediate 2 in the Reaction Cycle and the Products Dhbp and Formate, PDB code: 7uf5 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) 39.49 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 60.912, 78.99, 90.367, 90, 90, 90
R / Rfree (%) 20.6 / 23.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Ribb From Vibrio Cholera Bound with Intermediate 2 in the Reaction Cycle and the Products Dhbp and Formate (pdb code 7uf5). 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 Intermediate 2 in the Reaction Cycle and the Products Dhbp and Formate, PDB code: 7uf5:

Manganese binding site 1 out of 1 in 7uf5

Go back to Manganese Binding Sites List in 7uf5
Manganese binding site 1 out of 1 in the Ribb From Vibrio Cholera Bound with Intermediate 2 in the Reaction Cycle and the Products Dhbp and Formate


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 2 in the Reaction Cycle and the Products Dhbp and Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn304

b:29.6
occ:1.00
H101 A:N52301 1.7 26.8 0.6
O10 A:N52301 1.8 22.4 0.6
O08 A:N52301 2.2 27.9 0.6
O09 A:N4O302 2.2 27.9 0.4
H031 A:N4O302 2.3 37.8 0.4
O A:HOH424 2.4 25.5 1.0
OE1 A:GLU39 2.4 29.9 1.0
O14 A:N52301 2.4 31.0 0.6
ND1 A:HIS154 2.5 25.0 1.0
H A:FMT303 2.6 16.4 0.4
O11 A:N4O302 2.6 18.4 0.4
C03 A:N52301 3.0 34.0 0.6
HB2 A:HIS154 3.1 33.1 1.0
C03 A:N4O302 3.1 31.5 0.4
C02 A:N52301 3.1 29.2 0.6
HH12 A:ARG38 3.1 46.0 1.0
C02 A:N4O302 3.1 30.3 0.4
P06 A:N52301 3.3 30.9 0.6
CE1 A:HIS154 3.3 35.4 1.0
O05 A:N52301 3.3 24.5 0.6
CD A:GLU39 3.4 35.1 1.0
HE1 A:HIS154 3.4 42.5 1.0
C A:FMT303 3.4 13.7 0.4
CG A:HIS154 3.5 30.3 1.0
P07 A:N4O302 3.5 29.6 0.4
OE2 A:GLU39 3.6 27.6 1.0
H A:HIS154 3.6 30.0 1.0
O1 A:FMT303 3.7 26.5 0.4
O12 A:N52301 3.8 7.3 0.6
CB A:HIS154 3.8 27.6 1.0
C04 A:N52301 3.9 40.0 0.6
O06 A:N4O302 3.9 34.6 0.4
NH1 A:ARG38 3.9 38.3 1.0
OD2 A:ASP43 3.9 27.9 1.0
O07 A:N52301 4.0 30.0 0.6
O04 A:N4O302 4.1 33.0 0.4
C05 A:N4O302 4.1 28.8 0.4
C11 A:N52301 4.2 41.5 0.6
O10 A:N4O302 4.2 32.2 0.4
HH11 A:ARG38 4.2 46.0 1.0
OD1 A:ASP43 4.3 28.2 1.0
H041 A:N4O302 4.4 39.6 0.4
N A:HIS154 4.4 25.0 1.0
HG3 A:GLU175 4.4 28.8 1.0
HB3 A:HIS154 4.4 33.1 1.0
HH22 A:ARG38 4.4 38.7 1.0
H111 A:N52301 4.4 49.8 0.6
O09 A:N52301 4.5 23.6 0.6
H041 A:N52301 4.5 48.0 0.6
H121 A:N52301 4.5 8.7 0.6
O A:HOH401 4.5 26.3 1.0
CG A:ASP43 4.5 27.2 1.0
NE2 A:HIS154 4.5 30.1 1.0
C01 A:N4O302 4.5 39.4 0.4
O2 A:FMT303 4.5 23.1 0.4
HB2 A:GLU39 4.5 48.2 1.0
HG2 A:GLU175 4.5 28.8 1.0
O08 A:N4O302 4.6 27.8 0.4
CD2 A:HIS154 4.6 24.9 1.0
OE1 A:GLU41 4.6 30.8 1.0
C01 A:N52301 4.6 44.0 0.6
HB2 A:GLU41 4.6 36.0 1.0
H042 A:N52301 4.7 48.0 0.6
CG A:GLU39 4.7 34.1 1.0
H011 A:N4O302 4.7 47.3 0.4
CA A:HIS154 4.7 22.6 1.0
H052 A:N4O302 4.8 34.5 0.4
H051 A:N4O302 4.8 34.5 0.4
H012 A:N4O302 4.8 47.3 0.4
H013 A:N52301 4.9 52.8 0.6
HB3 A:ASP34 4.9 33.6 1.0
CG A:GLU175 5.0 24.0 1.0
CZ A:ARG38 5.0 42.5 1.0

Reference:

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
Page generated: Fri Apr 7 12:45:12 2023

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