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Fluorine in PDB 6e41: Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog

Enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog

All present enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog:
1.13.11.52;

Protein crystallography data

The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog, PDB code: 6e41 was solved by S.Luo, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.25 / 2.29
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.916, 201.722, 114.893, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 25.1

Other elements in 6e41:

The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog also contains other interesting chemical elements:

Bromine (Br) 6 atoms
Iron (Fe) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog (pdb code 6e41). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog, PDB code: 6e41:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6e41

Go back to Fluorine Binding Sites List in 6e41
Fluorine binding site 1 out of 6 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:56.6
occ:1.00
F25 A:HQS502 0.0 56.6 1.0
C21 A:HQS502 1.4 54.6 1.0
C20 A:HQS502 2.4 46.5 1.0
C22 A:HQS502 2.4 54.5 1.0
BR A:HQS502 3.1 57.8 1.0
CE1 A:PHE164 3.3 36.0 1.0
CD1 A:PHE164 3.3 35.0 1.0
SG A:CYS129 3.4 38.7 1.0
C19 A:HQS502 3.7 50.2 1.0
C23 A:HQS502 3.7 45.6 1.0
CB A:VAL130 4.0 40.0 1.0
CG1 A:VAL130 4.2 47.0 1.0
C18 A:HQS502 4.2 50.9 1.0
CD1 A:TYR126 4.2 47.6 1.0
CE2 A:PHE163 4.2 38.9 1.0
N A:VAL130 4.3 38.0 1.0
C A:CYS129 4.5 37.1 1.0
CZ A:PHE164 4.5 30.2 1.0
CB A:CYS129 4.6 33.7 1.0
CG A:PHE164 4.6 34.1 1.0
CD2 A:PHE163 4.6 34.6 1.0
CA A:VAL130 4.7 38.4 1.0
CA A:TYR126 4.7 37.9 1.0
CE1 A:TYR126 4.7 39.5 1.0
O A:CYS129 4.8 37.1 1.0
O A:TYR126 5.0 34.0 1.0

Fluorine binding site 2 out of 6 in 6e41

Go back to Fluorine Binding Sites List in 6e41
Fluorine binding site 2 out of 6 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:49.6
occ:1.00
F25 A:HQS503 0.0 49.6 1.0
C21 A:HQS503 1.4 50.4 1.0
C22 A:HQS503 2.4 46.0 1.0
C20 A:HQS503 2.4 43.9 1.0
BR A:HQS503 3.1 77.9 1.0
C23 A:HQS503 3.7 46.5 1.0
C19 A:HQS503 3.7 46.2 1.0
CB A:ASN222 4.0 41.4 1.0
C18 A:HQS503 4.2 47.9 1.0
CG A:ASN222 4.3 42.6 1.0
ND2 A:ASN222 4.7 50.2 1.0
OD1 A:ASN222 4.8 51.2 1.0
CA A:ASN222 5.0 40.3 1.0

Fluorine binding site 3 out of 6 in 6e41

Go back to Fluorine Binding Sites List in 6e41
Fluorine binding site 3 out of 6 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:53.1
occ:1.00
F25 B:HQS502 0.0 53.1 1.0
C21 B:HQS502 1.4 49.3 1.0
C22 B:HQS502 2.4 44.7 1.0
C20 B:HQS502 2.4 45.3 1.0
CG2 B:VAL130 2.9 34.7 1.0
BR B:HQS502 3.0 52.9 1.0
CD1 B:PHE164 3.2 35.5 1.0
CE1 B:PHE164 3.3 35.9 1.0
SG B:CYS129 3.5 39.5 1.0
C23 B:HQS502 3.6 40.7 1.0
C19 B:HQS502 3.6 44.0 1.0
CE2 B:PHE163 4.0 46.0 1.0
C18 B:HQS502 4.1 45.0 1.0
CD2 B:PHE163 4.3 44.8 1.0
CB B:VAL130 4.3 40.7 1.0
CD1 B:TYR126 4.5 34.7 1.0
CG B:PHE164 4.5 37.0 1.0
CZ B:PHE164 4.6 30.5 1.0
N B:VAL130 4.6 36.8 1.0
C B:CYS129 4.7 35.7 1.0
CB B:CYS129 4.8 34.5 1.0
O B:CYS129 4.8 39.3 1.0
CA B:PHE164 4.9 32.2 1.0
CE1 B:TYR126 4.9 36.9 1.0
CA B:VAL130 4.9 33.7 1.0
CZ B:PHE163 4.9 46.0 1.0
CD1 B:LEU234 5.0 41.5 1.0

Fluorine binding site 4 out of 6 in 6e41

Go back to Fluorine Binding Sites List in 6e41
Fluorine binding site 4 out of 6 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:58.7
occ:1.00
F25 C:HQS502 0.0 58.7 1.0
C21 C:HQS502 1.4 52.1 1.0
C22 C:HQS502 2.4 50.1 1.0
C20 C:HQS502 2.4 50.5 1.0
CG2 C:VAL130 2.8 42.9 1.0
BR C:HQS502 3.1 57.7 1.0
SG C:CYS129 3.3 36.3 1.0
CE1 C:PHE164 3.4 38.7 1.0
CD1 C:PHE164 3.5 36.1 1.0
C23 C:HQS502 3.7 44.9 1.0
C19 C:HQS502 3.7 49.8 1.0
CE2 C:PHE163 4.1 43.5 1.0
C18 C:HQS502 4.2 47.5 1.0
CB C:VAL130 4.2 45.9 1.0
CD1 C:TYR126 4.2 43.2 1.0
N C:VAL130 4.4 39.5 1.0
CD2 C:PHE163 4.5 39.9 1.0
C C:CYS129 4.5 41.6 1.0
CB C:CYS129 4.6 31.7 1.0
CZ C:PHE164 4.6 32.4 1.0
CE1 C:TYR126 4.7 44.5 1.0
CG C:PHE164 4.7 37.0 1.0
CA C:VAL130 4.7 39.9 1.0
O C:CYS129 4.7 37.8 1.0
CA C:TYR126 4.8 36.3 1.0
CD1 C:LEU234 4.8 39.9 1.0

Fluorine binding site 5 out of 6 in 6e41

Go back to Fluorine Binding Sites List in 6e41
Fluorine binding site 5 out of 6 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F503

b:54.0
occ:1.00
F25 C:HQS503 0.0 54.0 1.0
C21 C:HQS503 1.4 52.6 1.0
C22 C:HQS503 2.4 49.5 1.0
C20 C:HQS503 2.4 49.5 1.0
BR C:HQS503 3.1 69.2 1.0
C23 C:HQS503 3.7 45.7 1.0
C19 C:HQS503 3.7 50.1 1.0
CB C:ASN222 4.0 47.5 1.0
C18 C:HQS503 4.2 53.0 1.0
ND2 C:ASN222 4.4 54.2 1.0
CG C:ASN222 4.5 52.2 1.0

Fluorine binding site 6 out of 6 in 6e41

Go back to Fluorine Binding Sites List in 6e41
Fluorine binding site 6 out of 6 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and An Epacadostat Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:52.1
occ:1.00
F25 D:HQS502 0.0 52.1 1.0
C21 D:HQS502 1.4 53.3 1.0
C22 D:HQS502 2.4 47.9 1.0
C20 D:HQS502 2.4 49.1 1.0
CG2 D:VAL130 2.8 39.4 1.0
BR D:HQS502 3.1 52.5 1.0
CD1 D:PHE164 3.1 37.5 1.0
CE1 D:PHE164 3.1 36.8 1.0
SG D:CYS129 3.5 40.8 1.0
C23 D:HQS502 3.7 38.8 1.0
C19 D:HQS502 3.7 43.6 1.0
CE2 D:PHE163 4.1 43.8 1.0
C18 D:HQS502 4.2 44.4 1.0
CB D:VAL130 4.2 43.7 1.0
CD2 D:PHE163 4.4 44.0 1.0
CG D:PHE164 4.4 36.9 1.0
CZ D:PHE164 4.5 36.9 1.0
CD1 D:TYR126 4.5 38.7 1.0
N D:VAL130 4.5 35.4 1.0
C D:CYS129 4.6 37.4 1.0
CB D:CYS129 4.7 33.4 1.0
O D:CYS129 4.7 40.0 1.0
CA D:VAL130 4.8 38.0 1.0
CE1 D:TYR126 4.9 41.2 1.0
CA D:TYR126 4.9 32.6 1.0
CA D:PHE164 5.0 33.5 1.0
CD1 D:LEU234 5.0 36.7 1.0
CZ D:PHE163 5.0 42.7 1.0
OG D:SER167 5.0 35.1 1.0

Reference:

S.Luo, K.Xu, S.Xiang, J.Chen, C.Chen, C.Guo, Y.Tong, L.Tong. High-Resolution Structures of Inhibitor Complexes of Human Indoleamine 2,3-Dioxygenase 1 in A New Crystal Form. Acta Crystallogr F Struct V. 74 717 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30387777
DOI: 10.1107/S2053230X18012955
Page generated: Thu Aug 1 19:18:55 2024

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