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Fluorine in PDB 5ph0: Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09484A

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09484A, PDB code: 5ph0 was solved by N.M.Pearce, T.Krojer, R.Talon, A.R.Bradley, M.Fairhead, R.Sethi, N.Wright, E.Maclean, P.Collins, J.Brandao-Neto, A.Douangamath, Z.Renjie, A.Dias, M.Vollmar, J.Ng, A.Szykowska, N.Burgess-Brown, P.E.Brennan, O.Cox, U.Oppermann, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.41 / 1.34
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.467, 71.467, 150.264, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 16.2

Other elements in 5ph0:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09484A also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09484A (pdb code 5ph0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09484A, PDB code: 5ph0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5ph0

Go back to Fluorine Binding Sites List in 5ph0
Fluorine binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09484A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09484A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F417

b:15.2
occ:0.22
 F3 A:71N417 0.0 15.2 0.2
NH2 A:ARG299 0.9 15.8 0.7
C1 A:71N417 1.3 16.2 0.2
CZ A:ARG299 1.8 15.1 0.7
F1 A:71N417 2.1 17.0 0.2
F2 A:71N417 2.1 17.7 0.2
OE2 A:GLU39 2.1 13.1 0.6
NE A:ARG299 2.3 15.4 0.7
C4 A:71N417 2.4 16.6 0.2
N6 A:71N417 2.8 16.6 0.2
CD A:GLU39 3.0 14.5 0.6
NH1 A:ARG299 3.0 16.0 0.7
OH A:TYR199 3.1 12.1 1.0
CD A:GLU39 3.2 11.6 0.4
OE1 A:GLU39 3.2 12.6 0.4
OE2 A:GLU39 3.3 12.1 0.4
CB A:HIS44 3.4 11.2 1.0
OE1 A:GLU39 3.6 18.0 0.6
CD2 A:PHE275 3.6 10.8 1.0
N5 A:71N417 3.6 17.3 0.2
O A:HOH703 3.6 14.5 0.8
CZ A:TYR199 3.7 10.6 1.0
CD A:ARG299 3.8 17.3 0.7
CG A:HIS44 3.8 11.8 1.0
CG A:GLU39 3.9 11.2 0.4
CE2 A:TYR199 3.9 10.4 1.0
CD A:PRO276 3.9 10.1 1.0
CG A:GLU39 4.0 13.5 0.6
C12 A:71N417 4.1 17.0 0.2
CD2 A:HIS44 4.2 12.7 1.0
O A:HOH703 4.3 14.5 0.2
CB A:PHE275 4.4 10.1 1.0
CE2 A:PHE275 4.4 11.6 1.0
CG A:PHE275 4.4 9.3 1.0
C7 A:71N417 4.5 17.1 0.2
CG A:ARG299 4.6 16.6 0.7
CG A:PRO276 4.6 10.6 1.0
ND1 A:HIS44 4.6 12.3 1.0
CB A:ARG299 4.7 12.6 0.3
CE1 A:TYR199 4.7 11.0 1.0
CA A:HIS44 4.8 10.3 1.0
CB A:ARG299 4.8 15.8 0.7
O A:HOH767 4.9 23.0 0.8
CB A:GLU39 4.9 13.2 0.6
CB A:GLU39 5.0 11.6 0.4
N A:PRO276 5.0 9.6 1.0

Fluorine binding site 2 out of 3 in 5ph0

Go back to Fluorine Binding Sites List in 5ph0
Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09484A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09484A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F417

b:17.0
occ:0.22
 F1 A:71N417 0.0 17.0 0.2
C1 A:71N417 1.3 16.2 0.2
CZ A:ARG299 1.7 15.1 0.7
NH2 A:ARG299 1.9 15.8 0.7
NE A:ARG299 2.0 15.4 0.7
F3 A:71N417 2.1 15.2 0.2
F2 A:71N417 2.1 17.7 0.2
C4 A:71N417 2.3 16.6 0.2
NH1 A:ARG299 2.6 16.0 0.7
OH A:TYR199 2.9 12.1 1.0
CD A:ARG299 3.1 17.3 0.7
CG A:ARG299 3.1 16.6 0.7
N6 A:71N417 3.2 16.6 0.2
N5 A:71N417 3.2 17.3 0.2
CB A:ARG299 3.2 12.6 0.3
CB A:ARG299 3.3 15.8 0.7
OE2 A:GLU39 3.6 13.1 0.6
CZ A:TYR199 3.6 10.6 1.0
CG A:PRO276 3.7 10.6 1.0
CD A:PRO276 3.8 10.1 1.0
O A:ARG299 3.9 13.6 0.3
C A:ARG299 3.9 12.7 0.3
C A:ARG299 3.9 13.9 0.7
O A:HOH703 3.9 14.5 0.8
O A:ARG299 4.0 16.1 0.7
OE1 A:GLU39 4.0 12.6 0.4
CE1 A:TYR303 4.1 17.8 1.0
CE1 A:TYR199 4.1 11.0 1.0
CA A:ARG299 4.2 12.1 0.3
CA A:ARG299 4.2 13.4 0.7
N A:TRP300 4.3 12.9 1.0
CD A:GLU39 4.3 14.5 0.6
C12 A:71N417 4.3 17.0 0.2
OE1 A:GLU39 4.3 18.0 0.6
CG A:ARG299 4.3 11.5 0.3
OE2 A:GLU39 4.3 12.1 0.4
C7 A:71N417 4.3 17.1 0.2
CD A:GLU39 4.4 11.6 0.4
CB A:PRO276 4.4 10.5 1.0
CE2 A:TYR199 4.5 10.4 1.0
CD1 A:TYR303 4.5 15.3 1.0
OG1 A:THR297 4.7 13.9 1.0
CA A:TRP300 4.7 12.1 1.0
O A:HOH703 4.7 14.5 0.2
O A:HOH750 4.8 36.1 0.8
CZ A:TYR303 4.9 19.6 1.0
NE A:ARG299 4.9 9.1 0.3

Fluorine binding site 3 out of 3 in 5ph0

Go back to Fluorine Binding Sites List in 5ph0
Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09484A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09484A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F417

b:17.7
occ:0.22
 F2 A:71N417 0.0 17.7 0.2
NH2 A:ARG299 1.3 15.8 0.7
C1 A:71N417 1.3 16.2 0.2
CZ A:ARG299 1.7 15.1 0.7
O A:HOH703 1.9 14.5 0.8
NH1 A:ARG299 1.9 16.0 0.7
F1 A:71N417 2.1 17.0 0.2
F3 A:71N417 2.1 15.2 0.2
C4 A:71N417 2.4 16.6 0.2
O A:HOH703 2.6 14.5 0.2
N5 A:71N417 2.9 17.3 0.2
NE A:ARG299 3.0 15.4 0.7
CD A:PRO276 3.4 10.1 1.0
N6 A:71N417 3.5 16.6 0.2
CG A:PRO276 3.7 10.6 1.0
CE1 A:TYR303 3.7 17.8 1.0
O A:HOH767 3.8 23.0 0.8
OH A:TYR303 3.8 24.4 1.0
CB A:PRO276 3.9 10.5 1.0
CZ A:TYR303 3.9 19.6 1.0
N A:PRO276 4.1 9.6 1.0
CB A:HIS44 4.1 11.2 1.0
CD A:ARG299 4.1 17.3 0.7
C7 A:71N417 4.2 17.1 0.2
OE2 A:GLU39 4.3 13.1 0.6
CD2 A:HIS44 4.3 12.7 1.0
CB A:PHE275 4.4 10.1 1.0
O A:PRO276 4.4 10.3 1.0
CD1 A:TYR303 4.5 15.3 1.0
CG A:HIS44 4.5 11.8 1.0
C12 A:71N417 4.5 17.0 0.2
OH A:TYR199 4.5 12.1 1.0
CA A:PRO276 4.6 9.3 1.0
CG A:ARG299 4.6 16.6 0.7
CE2 A:TYR303 4.7 18.0 1.0
O A:HOH750 4.8 36.1 0.8
CD2 A:PHE275 4.8 10.8 1.0
O A:HOH767 4.8 16.1 0.2
CZ A:TYR199 4.8 10.6 1.0
C A:PHE275 4.9 9.6 1.0
C A:PRO276 5.0 9.8 1.0

Reference:

N.M.Pearce, T.Krojer, A.R.Bradley, P.Collins, R.P.Nowak, R.Talon, B.D.Marsden, S.Kelm, J.Shi, C.M.Deane, F.Von Delft. A Multi-Crystal Method For Extracting Obscured Crystallographic States From Conventionally Uninterpretable Electron Density. Nat Commun V. 8 15123 2017.
ISSN: ESSN 2041-1723
PubMed: 28436492
DOI: 10.1038/NCOMMS15123
Page generated: Tue Jul 15 06:02:32 2025

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