Fluorine in PDB 5po9: Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B

The structure of Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B, PDB code: 5po9 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, J.Ng, P.E.Brennan, O.Cox, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Vondelft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.84 / 2.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.778, 56.410, 100.661, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 25.3

The structure of Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B (pdb code 5po9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B, PDB code: 5po9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B


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 BRD1 in Complex with N07950B within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:34.8 occ:0.95 F1 A:8T7201 0.0 34.8 0.9 C11 A:8T7201 1.3 33.9 0.9 F3 A:8T7201 2.2 34.0 0.9 F2 A:8T7201 2.2 30.5 0.9 C10 A:8T7201 2.3 33.6 0.9 C3 A:8T7201 3.0 31.1 0.9 C4 A:8T7201 3.2 24.9 0.9 C9 A:8T7201 3.3 39.0 0.9 N2 A:8T7201 3.4 29.5 0.9 CG1 A:VAL59 3.6 27.6 1.0 CG2 A:VAL64 3.6 36.3 1.0 CE1 A:TYR67 3.9 27.6 1.0 CD1 A:TYR67 4.0 28.5 1.0 C5 A:8T7201 4.0 44.0 0.9 CD2 A:TYR109 4.1 33.3 1.0 CG1 A:VAL64 4.1 27.3 1.0 CE2 A:TYR109 4.1 31.9 1.0 C2 A:8T7201 4.2 39.5 0.9 CG2 A:VAL59 4.2 33.3 1.0 C8 A:8T7201 4.3 31.0 0.9 CB A:VAL64 4.3 36.7 1.0 N1 A:8T7201 4.4 39.0 0.9 CB A:VAL59 4.6 37.6 1.0 CG A:TYR109 4.6 37.9 1.0 CZ A:TYR109 4.7 37.8 1.0 CZ A:TYR67 4.8 32.2 1.0 C6 A:8T7201 4.8 44.6 0.9 O A:HOH311 4.9 26.3 1.0 C7 A:8T7201 4.9 34.6 0.9 CG A:TYR67 4.9 36.2 1.0

Fluorine binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B


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 BRD1 in Complex with N07950B within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:30.5 occ:0.95 F2 A:8T7201 0.0 30.5 0.9 C11 A:8T7201 1.3 33.9 0.9 F1 A:8T7201 2.2 34.8 0.9 F3 A:8T7201 2.2 34.0 0.9 C10 A:8T7201 2.3 33.6 0.9 N2 A:8T7201 2.6 29.5 0.9 CD2 A:TYR109 3.3 33.3 1.0 OD1 A:ASN110 3.4 34.2 1.0 O A:HOH311 3.5 26.3 1.0 CE1 A:TYR67 3.5 27.6 1.0 C3 A:8T7201 3.6 31.1 0.9 CG A:TYR109 3.6 37.9 1.0 CB A:TYR109 3.7 24.8 1.0 ND2 A:ASN110 3.9 30.4 1.0 N1 A:8T7201 4.0 39.0 0.9 CG A:ASN110 4.0 31.5 1.0 CE2 A:TYR109 4.1 31.9 1.0 CD1 A:TYR67 4.2 28.5 1.0 CZ A:TYR67 4.4 32.2 1.0 C2 A:8T7201 4.4 39.5 0.9 OH A:TYR67 4.4 29.7 1.0 C4 A:8T7201 4.5 24.9 0.9 CD1 A:TYR109 4.6 33.1 1.0 CG2 A:VAL59 4.7 33.3 1.0 C9 A:8T7201 4.7 39.0 0.9 CZ A:TYR109 5.0 37.8 1.0

Fluorine binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B


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 BRD1 in Complex with N07950B within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:34.0 occ:0.95 F3 A:8T7201 0.0 34.0 0.9 C11 A:8T7201 1.3 33.9 0.9 F1 A:8T7201 2.2 34.8 0.9 F2 A:8T7201 2.2 30.5 0.9 C10 A:8T7201 2.3 33.6 0.9 C9 A:8T7201 3.1 39.0 0.9 C3 A:8T7201 3.2 31.1 0.9 ND2 A:ASN110 3.2 30.4 1.0 N2 A:8T7201 3.3 29.5 0.9 C4 A:8T7201 3.5 24.9 0.9 OD1 A:ASN110 3.6 34.2 1.0 CD2 A:TYR109 3.8 33.3 1.0 CG A:ASN110 3.8 31.5 1.0 CE2 A:TYR109 4.0 31.9 1.0 C8 A:8T7201 4.2 31.0 0.9 C2 A:8T7201 4.3 39.5 0.9 N1 A:8T7201 4.4 39.0 0.9 O A:HOH313 4.6 35.1 1.0 CD1 A:PHE116 4.6 31.1 1.0 CG A:PHE116 4.6 33.7 1.0 CG A:TYR109 4.7 37.9 1.0 C5 A:8T7201 4.8 44.0 0.9 CE1 A:PHE116 4.8 41.1 1.0 CD2 A:PHE116 4.9 51.4 1.0

Fluorine binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B within 5.0Å range: probe atom residue distance (Å) B Occ B:F203 b:38.2 occ:0.87 F1 B:8T7203 0.0 38.2 0.9 C11 B:8T7203 1.3 31.8 0.9 F2 B:8T7203 2.2 39.2 0.9 F3 B:8T7203 2.2 34.4 0.9 C10 B:8T7203 2.3 23.5 0.9 C3 B:8T7203 2.9 32.1 0.9 C9 B:8T7203 3.0 41.9 0.9 C4 B:8T7203 3.1 32.3 0.9 N2 B:8T7203 3.4 33.0 0.9 CE2 B:TYR109 3.8 27.6 1.0 CD2 B:TYR109 3.8 35.3 1.0 CG2 B:VAL64 3.8 31.6 1.0 CE1 B:TYR67 3.8 26.4 1.0 CG1 B:VAL59 3.8 28.4 1.0 CD1 B:TYR67 3.8 32.1 1.0 CG1 B:VAL64 3.9 27.1 1.0 C8 B:8T7203 4.0 48.1 0.9 C2 B:8T7203 4.2 31.7 0.9 C5 B:8T7203 4.2 33.3 0.9 CG2 B:VAL59 4.2 33.0 1.0 CB B:VAL64 4.3 29.6 1.0 N1 B:8T7203 4.4 32.2 0.9 CZ B:TYR109 4.5 31.4 1.0 CG B:TYR109 4.6 31.2 1.0 CB B:VAL59 4.7 35.7 1.0 ND2 B:ASN110 4.8 32.8 1.0 CZ B:TYR67 4.8 29.5 1.0 O B:HOH312 4.8 23.9 1.0 CG B:TYR67 4.8 33.7 1.0 C7 B:8T7203 4.9 43.7 0.9 C6 B:8T7203 4.9 40.3 0.9

Fluorine binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B within 5.0Å range: probe atom residue distance (Å) B Occ B:F203 b:39.2 occ:0.87 F2 B:8T7203 0.0 39.2 0.9 C11 B:8T7203 1.3 31.8 0.9 F1 B:8T7203 2.2 38.2 0.9 F3 B:8T7203 2.2 34.4 0.9 C10 B:8T7203 2.2 23.5 0.9 N2 B:8T7203 2.6 33.0 0.9 CD2 B:TYR109 3.1 35.3 1.0 OD1 B:ASN110 3.3 35.0 1.0 O B:HOH312 3.3 23.9 1.0 CE1 B:TYR67 3.4 26.4 1.0 CG B:TYR109 3.5 31.2 1.0 C3 B:8T7203 3.6 32.1 0.9 CB B:TYR109 3.6 28.9 1.0 CE2 B:TYR109 3.8 27.6 1.0 ND2 B:ASN110 3.9 32.8 1.0 CG B:ASN110 3.9 38.6 1.0 N1 B:8T7203 3.9 32.2 0.9 CD1 B:TYR67 4.1 32.1 1.0 CZ B:TYR67 4.3 29.5 1.0 OH B:TYR67 4.4 28.7 1.0 C2 B:8T7203 4.4 31.7 0.9 C4 B:8T7203 4.5 32.3 0.9 C9 B:8T7203 4.5 41.9 0.9 CD1 B:TYR109 4.6 26.6 1.0 CG2 B:VAL59 4.7 33.0 1.0 CZ B:TYR109 4.8 31.4 1.0 CA B:CYS106 4.9 29.1 1.0 CA B:TYR109 5.0 31.1 1.0 N B:ASN110 5.0 29.2 1.0 C1 B:8T7203 5.0 26.2 0.9

Fluorine binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of BRD1 in Complex with N07950B within 5.0Å range: probe atom residue distance (Å) B Occ B:F203 b:34.4 occ:0.87 F3 B:8T7203 0.0 34.4 0.9 C11 B:8T7203 1.3 31.8 0.9 F1 B:8T7203 2.2 38.2 0.9 F2 B:8T7203 2.2 39.2 0.9 C10 B:8T7203 2.3 23.5 0.9 ND2 B:ASN110 2.7 32.8 1.0 C9 B:8T7203 3.0 41.9 0.9 C3 B:8T7203 3.2 32.1 0.9 N2 B:8T7203 3.3 33.0 0.9 CD2 B:TYR109 3.4 35.3 1.0 OD1 B:ASN110 3.4 35.0 1.0 CG B:ASN110 3.4 38.6 1.0 C4 B:8T7203 3.6 32.3 0.9 CE2 B:TYR109 3.7 27.6 1.0 C8 B:8T7203 4.1 48.1 0.9 CD2 B:PHE116 4.3 37.0 1.0 C2 B:8T7203 4.4 31.7 0.9 N1 B:8T7203 4.4 32.2 0.9 O B:HOH387 4.4 45.5 1.0 CG B:TYR109 4.5 31.2 1.0 CB B:ASN110 4.9 25.6 1.0 CZ B:TYR109 4.9 31.4 1.0 CE2 B:PHE116 4.9 26.5 1.0 C5 B:8T7203 4.9 33.3 0.9

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