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Fluorine in PDB 2skc: Pyridoxal Phosphorylase B in Complex with Fluorophosphate, Glucose and Inosine-5'-Monophosphate

Enzymatic activity of Pyridoxal Phosphorylase B in Complex with Fluorophosphate, Glucose and Inosine-5'-Monophosphate

All present enzymatic activity of Pyridoxal Phosphorylase B in Complex with Fluorophosphate, Glucose and Inosine-5'-Monophosphate:
2.4.1.1;

Protein crystallography data

The structure of Pyridoxal Phosphorylase B in Complex with Fluorophosphate, Glucose and Inosine-5'-Monophosphate, PDB code: 2skc was solved by N.G.Oikonomakos, S.E.Zographos, K.E.Tsitsanou, L.N.Johnson, K.R.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.84 / 2.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.500, 128.500, 116.300, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 21.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pyridoxal Phosphorylase B in Complex with Fluorophosphate, Glucose and Inosine-5'-Monophosphate (pdb code 2skc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Pyridoxal Phosphorylase B in Complex with Fluorophosphate, Glucose and Inosine-5'-Monophosphate, PDB code: 2skc:

Fluorine binding site 1 out of 1 in 2skc

Go back to Fluorine Binding Sites List in 2skc
Fluorine binding site 1 out of 1 in the Pyridoxal Phosphorylase B in Complex with Fluorophosphate, Glucose and Inosine-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pyridoxal Phosphorylase B in Complex with Fluorophosphate, Glucose and Inosine-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F997

b:22.2
occ:1.00
 F A:FPO997 0.0 22.2 1.0
P A:FPO997 1.6 21.9 1.0
O2 A:FPO997 2.4 24.4 1.0
O3 A:FPO997 2.4 28.8 1.0
O A:HOH1161 2.4 6.3 1.0
O1 A:FPO997 2.4 23.8 1.0
O4P A:PLP999 3.1 12.6 1.0
C5A A:PLP999 3.2 9.2 1.0
CA A:GLY675 3.6 11.4 1.0
N A:THR676 3.6 10.3 1.0
O A:HOH1081 4.0 7.5 1.0
C A:GLY675 4.1 9.6 1.0
OG1 A:THR676 4.1 6.3 1.0
O4 A:GLC998 4.2 6.1 1.0
NZ A:LYS574 4.2 22.3 1.0
C3 A:GLC998 4.2 8.7 1.0
O A:HOH1093 4.3 26.6 1.0
O A:HOH1075 4.3 16.3 1.0
CA A:GLY135 4.4 14.4 1.0
N A:GLY677 4.4 7.8 1.0
N A:GLY675 4.6 13.2 1.0
O3 A:GLC998 4.6 9.1 1.0
C4 A:GLC998 4.7 10.4 1.0
C5 A:PLP999 4.7 5.9 1.0
CA A:THR676 4.7 6.5 1.0
OE1 A:GLU672 4.7 11.2 1.0
N A:GLY135 4.8 12.6 1.0
CD A:GLU672 4.9 11.2 1.0
O1 A:GLC998 4.9 16.1 1.0
OE2 A:GLU672 4.9 8.1 1.0

Reference:

N.G.Oikonomakos, S.E.Zographos, K.E.Tsitsanou, L.N.Johnson, K.R.Acharya. Activator Anion Binding Site in Pyridoxal Phosphorylase B: the Binding of Phosphite, Phosphate, and Fluorophosphate in the Crystal. Protein Sci. V. 5 2416 1996.
ISSN: ISSN 0961-8368
PubMed: 8976550
Page generated: Mon Jul 14 14:20:21 2025

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