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Fluorine in PDB 5rxd: INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692

Enzymatic activity of INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692

All present enzymatic activity of INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692:
3.1.3.36; 3.1.3.56; 3.1.3.86;

Protein crystallography data

The structure of INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692, PDB code: 5rxd was solved by W.J.Bradshaw, J.A.Newman, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.21 / 1.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.415, 79.183, 89.185, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.1

Other elements in 5rxd:

The structure of INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692 (pdb code 5rxd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692, PDB code: 5rxd:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5rxd

Go back to Fluorine Binding Sites List in 5rxd
Fluorine binding site 1 out of 3 in the INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:39.0
occ:0.66
 F01 A:WNP901 0.0 39.0 0.7
C02 A:WNP901 1.4 37.3 0.7
F03 A:WNP901 2.2 38.7 0.7
F04 A:WNP901 2.2 38.3 0.7
C05 A:WNP901 2.4 34.9 0.7
O06 A:WNP901 2.9 37.7 0.7
N07 A:WNP901 3.5 31.0 0.7
O A:VAL479 3.7 11.2 1.0
O A:HOH1314 3.9 16.0 1.0
O A:HOH1381 4.3 33.1 1.0
C A:VAL479 4.4 10.6 1.0
O A:THR478 4.5 15.1 1.0
CA A:ALA480 4.7 9.8 1.0
C08 A:WNP901 4.8 27.8 0.7
N A:ALA480 4.9 9.9 1.0

Fluorine binding site 2 out of 3 in 5rxd

Go back to Fluorine Binding Sites List in 5rxd
Fluorine binding site 2 out of 3 in the INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:38.7
occ:0.66
 F03 A:WNP901 0.0 38.7 0.7
C02 A:WNP901 1.4 37.3 0.7
F04 A:WNP901 2.2 38.3 0.7
F01 A:WNP901 2.2 39.0 0.7
C05 A:WNP901 2.4 34.9 0.7
N07 A:WNP901 2.7 31.0 0.7
O A:THR478 2.8 15.1 1.0
O06 A:WNP901 3.5 37.7 0.7
C A:THR478 3.8 12.2 1.0
CB A:THR478 4.0 12.8 1.0
CG2 A:THR478 4.1 12.3 1.0
O A:VAL479 4.1 11.2 1.0
C08 A:WNP901 4.2 27.8 0.7
C A:VAL479 4.3 10.6 1.0
CA A:THR478 4.5 12.1 1.0
N A:VAL479 4.6 10.3 1.0
CA A:VAL479 4.8 10.3 1.0
C14 A:WNP901 4.8 25.8 0.7
N A:ALA480 4.9 9.9 1.0

Fluorine binding site 3 out of 3 in 5rxd

Go back to Fluorine Binding Sites List in 5rxd
Fluorine binding site 3 out of 3 in the INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of INPP5D Pandda Analysis Group Deposition -- Crystal Structure of the Phosphatase and C2 Domains of SHIP1 in Complex with Z111810692 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:38.3
occ:0.66
 F04 A:WNP901 0.0 38.3 0.7
C02 A:WNP901 1.4 37.3 0.7
F03 A:WNP901 2.2 38.7 0.7
F01 A:WNP901 2.2 39.0 0.7
C05 A:WNP901 2.3 34.9 0.7
O06 A:WNP901 2.8 37.7 0.7
N07 A:WNP901 3.4 31.0 0.7
C08 A:WNP901 4.7 27.8 0.7
O A:THR478 4.8 15.1 1.0

Reference:

W.J.Bradshaw, J.A.Newman, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, O.Gileadi. INPP5D Pandda Analysis Group Deposition To Be Published.
Page generated: Tue Jul 15 07:00:04 2025

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