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Iron in PDB 6r63: Crystal Structure of Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and Mmg-0358

Enzymatic activity of Crystal Structure of Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and Mmg-0358

All present enzymatic activity of Crystal Structure of Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and Mmg-0358:
1.13.11.52;

Protein crystallography data

The structure of Crystal Structure of Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and Mmg-0358, PDB code: 6r63 was solved by U.F.Roehrig, A.Reynaud, F.Pojer, O.Michielin, V.Zoete, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.45 / 2.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.910, 97.870, 119.235, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 28.7

Other elements in 6r63:

The structure of Crystal Structure of Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and Mmg-0358 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and Mmg-0358 (pdb code 6r63). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and Mmg-0358, PDB code: 6r63:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6r63

Go back to Iron Binding Sites List in 6r63
Iron binding site 1 out of 2 in the Crystal Structure of Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and Mmg-0358


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 Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and Mmg-0358 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:61.6
occ:0.92
FE A:HEM501 0.0 61.6 0.9
ND A:HEM501 1.9 66.8 0.9
NE2 A:HIS346 2.0 61.1 1.0
NA A:HEM501 2.0 65.2 0.9
NB A:HEM501 2.1 60.2 0.9
N2 A:JTB502 2.1 61.9 0.8
NC A:HEM501 2.1 61.0 0.9
CE1 A:HIS346 2.7 63.1 1.0
C4D A:HEM501 2.9 62.4 0.9
C1D A:HEM501 2.9 61.1 0.9
C1A A:HEM501 3.0 66.6 0.9
C1 A:JTB502 3.0 58.8 0.8
C4A A:HEM501 3.0 61.1 0.9
C1B A:HEM501 3.1 61.1 0.9
C4C A:HEM501 3.1 54.7 0.9
C4B A:HEM501 3.1 60.2 0.9
CD2 A:HIS346 3.1 61.6 1.0
C1C A:HEM501 3.1 60.1 0.9
N1 A:JTB502 3.3 63.3 0.8
CHA A:HEM501 3.3 61.4 0.9
CHD A:HEM501 3.4 50.5 0.9
CHB A:HEM501 3.5 60.7 0.9
CHC A:HEM501 3.5 57.1 0.9
ND1 A:HIS346 3.9 71.0 1.0
CG A:HIS346 4.1 64.6 1.0
C2D A:HEM501 4.1 62.5 0.9
C3D A:HEM501 4.1 57.9 0.9
C2A A:HEM501 4.2 66.2 0.9
C3A A:HEM501 4.2 60.8 0.9
C2 A:JTB502 4.2 61.3 0.8
C2B A:HEM501 4.3 58.0 0.9
C3C A:HEM501 4.3 54.0 0.9
C2C A:HEM501 4.3 54.0 0.9
N3 A:JTB502 4.3 64.9 0.8
C3B A:HEM501 4.3 60.5 0.9
CB A:ALA264 4.5 60.2 1.0

Iron binding site 2 out of 2 in 6r63

Go back to Iron Binding Sites List in 6r63
Iron binding site 2 out of 2 in the Crystal Structure of Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and Mmg-0358


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 Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and Mmg-0358 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:60.8
occ:1.00
FE B:HEM501 0.0 60.8 1.0
ND B:HEM501 1.9 70.1 1.0
NA B:HEM501 2.0 62.0 1.0
NE2 B:HIS346 2.0 61.9 1.0
N2 B:JTB502 2.1 65.2 0.9
NC B:HEM501 2.1 64.3 1.0
NB B:HEM501 2.1 68.0 1.0
C1D B:HEM501 2.9 66.2 1.0
C4D B:HEM501 2.9 65.8 1.0
CE1 B:HIS346 2.9 61.4 1.0
C1A B:HEM501 3.0 64.6 1.0
C4C B:HEM501 3.0 64.5 1.0
CD2 B:HIS346 3.0 65.5 1.0
C4A B:HEM501 3.0 65.8 1.0
C1 B:JTB502 3.1 59.8 0.9
C4B B:HEM501 3.1 67.1 1.0
C1B B:HEM501 3.1 69.4 1.0
C1C B:HEM501 3.1 68.1 1.0
N1 B:JTB502 3.1 69.5 0.9
CHA B:HEM501 3.4 64.2 1.0
CHD B:HEM501 3.4 62.9 1.0
CHB B:HEM501 3.5 70.3 1.0
CHC B:HEM501 3.5 67.9 1.0
ND1 B:HIS346 4.0 59.2 1.0
CG B:HIS346 4.1 63.3 1.0
C2D B:HEM501 4.1 65.0 1.0
C3D B:HEM501 4.1 64.4 1.0
C2A B:HEM501 4.2 64.8 1.0
C3A B:HEM501 4.2 64.1 1.0
C3C B:HEM501 4.2 66.5 1.0
C2 B:JTB502 4.2 64.4 0.9
C2C B:HEM501 4.3 68.6 1.0
N3 B:JTB502 4.3 69.0 0.9
C2B B:HEM501 4.3 67.7 1.0
C3B B:HEM501 4.4 66.2 1.0
CB B:ALA264 4.8 60.5 1.0

Reference:

U.F.Rohrig, A.Reynaud, S.R.Majjigapu, P.Vogel, F.Pojer, V.Zoete. Inhibition Mechanisms of Indoleamine 2,3-Dioxygenase 1 (IDO1). J.Med.Chem. V. 62 8784 2019.
ISSN: ISSN 0022-2623
PubMed: 31525930
DOI: 10.1021/ACS.JMEDCHEM.9B00942
Page generated: Wed Aug 7 08:39:54 2024

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