Magnesium in PDB 8s8a: Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone Without Phosphate

Enzymatic activity of Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone Without Phosphate

All present enzymatic activity of Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone Without Phosphate:
3.1.3.16; 3.1.3.74;

Protein crystallography data

The structure of Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone Without Phosphate, PDB code: 8s8a was solved by M.Brenner, A.Gohla, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.17 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 54.037, 54.037, 212.493, 90, 90, 90
R / Rfree (%) 18.2 / 20.5

Other elements in 8s8a:

The structure of Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone Without Phosphate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone Without Phosphate (pdb code 8s8a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone Without Phosphate, PDB code: 8s8a:

Magnesium binding site 1 out of 1 in 8s8a

Go back to Magnesium Binding Sites List in 8s8a
Magnesium binding site 1 out of 1 in the Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone Without Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone Without Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:26.5
occ:1.00
 O A:HOH426 1.6 32.3 0.5
OD2 A:ASP25 2.0 39.5 1.0
OD1 A:ASP238 2.2 28.7 1.0
O A:ASP27 2.3 26.9 1.0
O A:HOH419 2.3 37.5 1.0
O A:HOH426 2.6 33.1 0.5
H7 A:UK9301 2.6 36.1 0.8
O3 A:UK9301 2.7 30.1 0.8
CG A:ASP25 3.1 35.6 1.0
CG A:ASP238 3.1 26.0 1.0
OD2 A:ASP238 3.4 25.9 1.0
C A:ASP27 3.4 27.1 1.0
HB2 A:ASP27 3.4 36.8 1.0
C11 A:UK9301 3.5 31.2 0.8
OD1 A:ASP25 3.6 33.3 1.0
HE A:ARG239 3.7 34.6 0.5
HG3 A:ARG239 3.7 31.6 0.5
HG23 A:VAL29 3.7 31.9 1.0
HD2 A:ARG239 3.8 34.5 0.5
H A:ASP238 4.0 28.3 1.0
HA3 A:GLY28 4.0 30.2 1.0
C10 A:UK9301 4.1 33.2 0.8
O2 A:UK9301 4.2 34.2 0.8
CB A:ASP27 4.2 30.7 1.0
CA A:ASP27 4.2 26.3 1.0
C12 A:UK9301 4.3 29.7 0.8
H A:ASP27 4.3 32.6 1.0
OD2 A:ASP243 4.3 29.2 1.0
HB3 A:ASP25 4.3 34.1 1.0
HB2 A:ARG239 4.3 31.0 0.5
O A:HOH515 4.3 33.6 1.0
NE A:ARG239 4.3 28.9 0.5
N A:ASP27 4.3 27.1 1.0
H8 A:UK9301 4.3 35.6 0.8
CD A:ARG239 4.3 28.7 0.5
CB A:ASP25 4.4 28.4 1.0
O A:HOH418 4.4 36.0 1.0
N A:GLY28 4.4 25.8 1.0
O A:HOH436 4.5 36.2 1.0
CG A:ARG239 4.5 26.4 0.5
CB A:ASP238 4.5 25.0 1.0
HB3 A:ASP27 4.5 36.8 1.0
O A:HOH542 4.6 38.8 1.0
HB3 A:ASP238 4.6 30.0 1.0
CG2 A:VAL29 4.6 26.6 1.0
CA A:GLY28 4.6 25.1 1.0
H A:CYS26 4.7 34.0 1.0
HG21 A:VAL29 4.7 31.9 1.0
N A:ASP238 4.8 23.6 1.0
H6 A:UK9301 4.8 41.1 0.8
HB2 A:ASP25 4.8 34.1 1.0
HB2 A:ARG239 4.9 31.6 0.5
HD2 A:ARG239 4.9 35.2 0.5
C A:CYS26 5.0 27.0 1.0

Reference:

M.Brenner, C.Zink, L.Witzinger, A.Keller, K.Hadamek, S.Bothe, M.Neuenschwander, C.Villmann, J.P.Von Kries, H.Schindelin, E.Jeanclos, A.Gohla. 7,8-Dihydroxyflavone Is A Direct Inhibitor of Pyridoxal Phosphatase Elife V.3094 2024.
ISSN: ESSN 2050-084X
DOI: 10.1101/2023.10.04.560852
Page generated: Fri Oct 4 18:04:19 2024

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