Iron 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:

Fluorine (F) 6 atoms
Bromine (Br) 6 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6e41

Go back to Iron Binding Sites List in 6e41
Iron binding site 1 out of 4 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 Iron with other atoms in the Fe 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:Fe501

b:42.3
occ:1.00
 FE A:HEM501 0.0 42.3 1.0
O04 A:HQS502 1.8 47.4 1.0
NA A:HEM501 1.9 40.2 1.0
NB A:HEM501 2.1 37.5 1.0
NC A:HEM501 2.1 42.7 1.0
ND A:HEM501 2.1 48.5 1.0
NE2 A:HIS346 2.2 46.3 1.0
N03 A:HQS502 2.7 46.6 1.0
C4A A:HEM501 2.9 44.2 1.0
C1B A:HEM501 3.0 41.6 1.0
C1A A:HEM501 3.0 45.9 1.0
CE1 A:HIS346 3.0 41.1 1.0
C4C A:HEM501 3.1 43.3 1.0
C4D A:HEM501 3.1 44.4 1.0
C1D A:HEM501 3.1 42.2 1.0
C1C A:HEM501 3.2 43.3 1.0
C4B A:HEM501 3.2 37.5 1.0
CD2 A:HIS346 3.2 42.9 1.0
CHB A:HEM501 3.3 41.2 1.0
CHA A:HEM501 3.4 41.7 1.0
CHD A:HEM501 3.5 46.9 1.0
CHC A:HEM501 3.6 41.6 1.0
C02 A:HQS502 3.6 44.7 1.0
N01 A:HQS502 4.0 46.0 1.0
C3A A:HEM501 4.1 41.0 1.0
C2A A:HEM501 4.2 41.0 1.0
ND1 A:HIS346 4.2 43.9 1.0
C2B A:HEM501 4.2 42.9 1.0
CG A:HIS346 4.3 46.8 1.0
C3C A:HEM501 4.3 41.1 1.0
C3D A:HEM501 4.3 45.4 1.0
C2C A:HEM501 4.3 45.7 1.0
C2D A:HEM501 4.3 44.5 1.0
C3B A:HEM501 4.4 41.3 1.0
CB A:ALA264 4.5 46.4 1.0
N A:ALA264 4.6 48.1 1.0
C05 A:HQS502 4.9 50.5 1.0

Iron binding site 2 out of 4 in 6e41

Go back to Iron Binding Sites List in 6e41
Iron binding site 2 out of 4 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 Iron with other atoms in the Fe 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
B:Fe501

b:40.8
occ:1.00
 FE B:HEM501 0.0 40.8 1.0
O04 B:HQS502 1.8 45.5 1.0
NB B:HEM501 2.0 40.6 1.0
NA B:HEM501 2.0 48.4 1.0
NE2 B:HIS346 2.0 43.4 1.0
ND B:HEM501 2.1 42.4 1.0
NC B:HEM501 2.1 42.4 1.0
N03 B:HQS502 2.7 45.6 1.0
CE1 B:HIS346 2.9 42.2 1.0
C4B B:HEM501 3.0 43.4 1.0
C1B B:HEM501 3.0 42.6 1.0
C1A B:HEM501 3.0 45.6 1.0
C4A B:HEM501 3.0 46.6 1.0
C4D B:HEM501 3.1 41.8 1.0
C1C B:HEM501 3.1 40.2 1.0
C4C B:HEM501 3.1 44.5 1.0
C1D B:HEM501 3.1 42.9 1.0
CD2 B:HIS346 3.1 42.0 1.0
CHB B:HEM501 3.4 42.6 1.0
CHA B:HEM501 3.4 38.8 1.0
CHC B:HEM501 3.4 40.8 1.0
CHD B:HEM501 3.5 43.8 1.0
C02 B:HQS502 3.6 42.3 1.0
N01 B:HQS502 4.0 45.9 1.0
ND1 B:HIS346 4.1 46.3 1.0
CG B:HIS346 4.2 36.5 1.0
C3B B:HEM501 4.2 43.2 1.0
C2B B:HEM501 4.2 41.5 1.0
C3A B:HEM501 4.3 46.1 1.0
C2A B:HEM501 4.3 48.9 1.0
C2C B:HEM501 4.3 42.7 1.0
C3D B:HEM501 4.3 42.9 1.0
C3C B:HEM501 4.3 41.7 1.0
C2D B:HEM501 4.3 41.0 1.0
CB B:ALA264 4.3 46.8 1.0
N B:ALA264 4.8 46.7 1.0
C05 B:HQS502 5.0 45.1 1.0

Iron binding site 3 out of 4 in 6e41

Go back to Iron Binding Sites List in 6e41
Iron binding site 3 out of 4 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 Iron with other atoms in the Fe 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
C:Fe501

b:45.4
occ:1.00
 FE C:HEM501 0.0 45.4 1.0
O04 C:HQS502 1.8 48.9 1.0
NA C:HEM501 2.0 43.9 1.0
NC C:HEM501 2.0 48.2 1.0
NB C:HEM501 2.1 43.9 1.0
NE2 C:HIS346 2.1 48.1 1.0
ND C:HEM501 2.2 50.4 1.0
N03 C:HQS502 2.7 52.2 1.0
C4A C:HEM501 3.0 48.5 1.0
CE1 C:HIS346 3.0 46.0 1.0
C1B C:HEM501 3.0 45.6 1.0
C4C C:HEM501 3.0 47.0 1.0
C1C C:HEM501 3.1 45.4 1.0
C1A C:HEM501 3.1 48.8 1.0
C4B C:HEM501 3.1 39.4 1.0
C1D C:HEM501 3.1 43.8 1.0
CD2 C:HIS346 3.2 45.0 1.0
C4D C:HEM501 3.2 46.2 1.0
CHB C:HEM501 3.3 44.5 1.0
CHD C:HEM501 3.4 46.2 1.0
CHC C:HEM501 3.5 41.8 1.0
CHA C:HEM501 3.5 45.6 1.0
C02 C:HQS502 3.6 47.2 1.0
N01 C:HQS502 3.9 46.8 1.0
ND1 C:HIS346 4.1 47.8 1.0
C3A C:HEM501 4.2 46.1 1.0
C3C C:HEM501 4.2 44.2 1.0
C2B C:HEM501 4.2 44.9 1.0
CG C:HIS346 4.2 48.2 1.0
C2C C:HEM501 4.3 48.0 1.0
C2A C:HEM501 4.3 45.5 1.0
C3B C:HEM501 4.3 44.1 1.0
C2D C:HEM501 4.4 46.9 1.0
C3D C:HEM501 4.4 47.6 1.0
CB C:ALA264 4.4 48.9 1.0
N C:ALA264 4.7 49.5 1.0
C05 C:HQS502 4.9 52.5 1.0

Iron binding site 4 out of 4 in 6e41

Go back to Iron Binding Sites List in 6e41
Iron binding site 4 out of 4 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 Iron with other atoms in the Fe 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
D:Fe501

b:37.6
occ:1.00
 FE D:HEM501 0.0 37.6 1.0
O04 D:HQS502 1.8 47.3 1.0
NA D:HEM501 1.9 41.2 1.0
ND D:HEM501 2.0 41.6 1.0
NB D:HEM501 2.1 37.3 1.0
NC D:HEM501 2.1 41.0 1.0
NE2 D:HIS346 2.1 45.0 1.0
N03 D:HQS502 2.7 44.4 1.0
C4A D:HEM501 3.0 42.5 1.0
C1A D:HEM501 3.0 42.8 1.0
CE1 D:HIS346 3.0 41.4 1.0
C4D D:HEM501 3.0 40.7 1.0
C1B D:HEM501 3.0 40.0 1.0
C1D D:HEM501 3.1 42.3 1.0
C4C D:HEM501 3.1 38.7 1.0
C4B D:HEM501 3.1 42.0 1.0
C1C D:HEM501 3.1 37.9 1.0
CD2 D:HIS346 3.2 41.8 1.0
CHA D:HEM501 3.4 38.6 1.0
CHB D:HEM501 3.4 42.5 1.0
CHD D:HEM501 3.4 40.8 1.0
CHC D:HEM501 3.5 38.6 1.0
C02 D:HQS502 3.7 41.3 1.0
N01 D:HQS502 4.0 45.0 1.0
ND1 D:HIS346 4.1 43.6 1.0
C3A D:HEM501 4.2 43.3 1.0
C2A D:HEM501 4.2 43.7 1.0
CG D:HIS346 4.3 34.4 1.0
CB D:ALA264 4.3 45.3 1.0
C3C D:HEM501 4.3 42.7 1.0
C2D D:HEM501 4.3 41.0 1.0
C2B D:HEM501 4.3 38.6 1.0
C3D D:HEM501 4.3 43.8 1.0
C3B D:HEM501 4.3 41.4 1.0
C2C D:HEM501 4.3 43.2 1.0
N D:ALA264 4.8 40.9 1.0
C05 D:HQS502 5.0 45.6 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: Sun Dec 13 16:24:48 2020

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