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Iron in PDB 6pz1: Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site

Enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site

All present enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site:
1.13.11.52;

Protein crystallography data

The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site, PDB code: 6pz1 was solved by K.N.Pham, A.Lewis-Ballester, S.R.Yeh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.479, 97.858, 131.966, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 27

Other elements in 6pz1:

The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site (pdb code 6pz1). 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 Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site, PDB code: 6pz1:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6pz1

Go back to Iron Binding Sites List in 6pz1
Iron binding site 1 out of 2 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site


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 in Complex with Pf-06840003 in Active Site and Si Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:74.3
occ:1.00
 FE A:HEM501 0.0 74.3 1.0
ND A:HEM501 1.9 75.1 1.0
NA A:HEM501 2.0 74.8 1.0
NC A:HEM501 2.1 74.7 1.0
NB A:HEM501 2.1 75.4 1.0
NE2 A:HIS346 2.1 67.9 1.0
C4D A:HEM501 2.9 74.5 1.0
C1D A:HEM501 2.9 74.9 1.0
C1A A:HEM501 3.0 74.8 1.0
C4C A:HEM501 3.0 75.0 1.0
C4A A:HEM501 3.1 74.6 1.0
CE1 A:HIS346 3.1 68.2 1.0
C1B A:HEM501 3.1 75.6 1.0
C4B A:HEM501 3.1 75.7 1.0
CD2 A:HIS346 3.1 68.1 1.0
C1C A:HEM501 3.1 74.9 1.0
CHA A:HEM501 3.3 74.7 1.0
CHD A:HEM501 3.4 75.0 1.0
CHB A:HEM501 3.5 75.3 1.0
CHC A:HEM501 3.5 75.6 1.0
C1 A:AOJ502 3.7 0.1 1.0
C5 A:AOJ502 4.0 0.8 1.0
C3D A:HEM501 4.1 74.1 1.0
C2D A:HEM501 4.2 74.2 1.0
C2A A:HEM501 4.2 74.8 1.0
ND1 A:HIS346 4.2 67.9 1.0
C4 A:AOJ502 4.2 0.1 1.0
C3A A:HEM501 4.2 74.1 1.0
O2 A:AOJ502 4.2 0.7 1.0
CG A:HIS346 4.2 68.6 1.0
CB A:ALA264 4.2 85.0 1.0
C3C A:HEM501 4.3 75.7 1.0
C12 A:AOJ502 4.3 0.7 1.0
C2C A:HEM501 4.3 75.0 1.0
C2B A:HEM501 4.3 75.6 1.0
C3B A:HEM501 4.4 75.6 1.0
C2 A:AOJ502 4.8 0.6 1.0

Iron binding site 2 out of 2 in 6pz1

Go back to Iron Binding Sites List in 6pz1
Iron binding site 2 out of 2 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site


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 in Complex with Pf-06840003 in Active Site and Si Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:77.1
occ:1.00
 FE B:HEM501 0.0 77.1 1.0
ND B:HEM501 1.9 77.4 1.0
NA B:HEM501 2.0 77.5 1.0
NC B:HEM501 2.1 76.0 1.0
NB B:HEM501 2.1 76.6 1.0
NE2 B:HIS346 2.2 86.6 1.0
C1D B:HEM501 2.9 77.1 1.0
C4D B:HEM501 2.9 77.6 1.0
C1A B:HEM501 3.0 78.1 1.0
C4C B:HEM501 3.0 75.9 1.0
C4A B:HEM501 3.0 77.7 1.0
C1B B:HEM501 3.1 76.2 1.0
C4B B:HEM501 3.1 76.1 1.0
C1C B:HEM501 3.2 75.8 1.0
CE1 B:HIS346 3.2 86.9 1.0
CD2 B:HIS346 3.2 87.7 1.0
CHA B:HEM501 3.3 77.8 1.0
CHD B:HEM501 3.3 76.7 1.0
CHB B:HEM501 3.5 76.6 1.0
CHC B:HEM501 3.5 75.8 1.0
C1 B:AOJ502 3.7 72.8 1.0
C4 B:AOJ502 3.9 73.9 1.0
O2 B:AOJ502 4.0 74.7 1.0
C5 B:AOJ502 4.1 71.4 1.0
C2D B:HEM501 4.2 77.2 1.0
C3D B:HEM501 4.2 77.6 1.0
C2A B:HEM501 4.2 78.3 1.0
C3A B:HEM501 4.2 78.4 1.0
C3C B:HEM501 4.3 75.6 1.0
ND1 B:HIS346 4.3 87.5 1.0
C2C B:HEM501 4.3 76.0 1.0
C2B B:HEM501 4.3 76.2 1.0
CG B:HIS346 4.3 88.5 1.0
C12 B:AOJ502 4.4 71.7 1.0
C3B B:HEM501 4.4 76.2 1.0
CB B:ALA264 4.5 76.4 1.0
C2 B:AOJ502 4.7 73.1 1.0
N1 B:AOJ502 4.7 74.2 1.0

Reference:

K.N.Pham, A.Lewis-Ballester, S.R.Yeh. Structural Basis of Inhibitor Selectivity in Human Indoleamine 2,3-Dioxygenase 1 and Tryptophan Dioxygenase. J.Am.Chem.Soc. V. 141 18771 2019.
ISSN: ESSN 1520-5126
PubMed: 31682426
DOI: 10.1021/JACS.9B08871
Page generated: Wed Aug 7 06:44:54 2024

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