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

Protein crystallography data

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

Other elements in 5po9:

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

Fluorine Binding Sites:

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 5po9

Go back to Fluorine Binding Sites List in 5po9
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 5po9

Go back to Fluorine Binding Sites List in 5po9
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 5po9

Go back to Fluorine Binding Sites List in 5po9
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 5po9

Go back to Fluorine Binding Sites List in 5po9
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 5po9

Go back to Fluorine Binding Sites List in 5po9
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 5po9

Go back to Fluorine Binding Sites List in 5po9
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

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: Sun Dec 13 12:30:56 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy