Iron in PDB 6ubp: Crystal Structure of A Photochemical Intermediate of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Carbon Monoxide and Tryptophan

Enzymatic activity of Crystal Structure of A Photochemical Intermediate of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Carbon Monoxide and Tryptophan

All present enzymatic activity of Crystal Structure of A Photochemical Intermediate of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Carbon Monoxide and Tryptophan:
1.13.11.52;

Protein crystallography data

The structure of Crystal Structure of A Photochemical Intermediate of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Carbon Monoxide and Tryptophan, PDB code: 6ubp was solved by K.N.Pham, S.R.Yeh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.34 / 2.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.944, 97.727, 130.628, 90, 90, 90
R / Rfree (%) 21.5 / 26.4

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Photochemical Intermediate of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Carbon Monoxide and Tryptophan (pdb code 6ubp). 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 A Photochemical Intermediate of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Carbon Monoxide and Tryptophan, PDB code: 6ubp:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6ubp

Go back to Iron Binding Sites List in 6ubp
Iron binding site 1 out of 2 in the Crystal Structure of A Photochemical Intermediate of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Carbon Monoxide and Tryptophan


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 A Photochemical Intermediate of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Carbon Monoxide and Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:98.2
occ:1.00
 FE A:HEM501 0.0 98.2 1.0
ND A:HEM501 1.9 99.3 1.0
NA A:HEM501 2.0 98.6 1.0
NC A:HEM501 2.1 98.9 1.0
NB A:HEM501 2.1 98.9 1.0
NE2 A:HIS346 2.2 81.1 1.0
C4D A:HEM501 2.9 99.1 1.0
C1D A:HEM501 2.9 99.2 1.0
C1A A:HEM501 3.0 99.1 1.0
C4A A:HEM501 3.0 98.8 1.0
C4C A:HEM501 3.1 98.6 1.0
C1B A:HEM501 3.1 99.0 1.0
CE1 A:HIS346 3.1 81.6 1.0
C4B A:HEM501 3.1 98.6 1.0
C1C A:HEM501 3.1 99.2 1.0
CD2 A:HIS346 3.2 81.8 1.0
CHA A:HEM501 3.3 99.1 1.0
CHD A:HEM501 3.4 98.9 1.0
CHB A:HEM501 3.5 99.2 1.0
CHC A:HEM501 3.5 99.0 1.0
CB A:ALA264 3.9 107.7 1.0
C2D A:HEM501 4.1 99.0 1.0
C3D A:HEM501 4.1 98.5 1.0
C2A A:HEM501 4.2 99.2 1.0
C3A A:HEM501 4.2 98.5 1.0
ND1 A:HIS346 4.2 81.8 1.0
C3C A:HEM501 4.3 98.8 1.0
C2C A:HEM501 4.3 98.9 1.0
CG A:HIS346 4.3 82.6 1.0
C2B A:HEM501 4.3 98.7 1.0
C3B A:HEM501 4.4 98.2 1.0
CA A:ALA264 4.8 107.7 1.0
C A:ALA264 4.8 106.5 1.0
N A:GLY265 4.9 105.0 1.0

Iron binding site 2 out of 2 in 6ubp

Go back to Iron Binding Sites List in 6ubp
Iron binding site 2 out of 2 in the Crystal Structure of A Photochemical Intermediate of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Carbon Monoxide and Tryptophan


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 A Photochemical Intermediate of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Carbon Monoxide and Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:96.3
occ:1.00
 FE B:HEM501 0.0 96.3 1.0
ND B:HEM501 1.9 97.1 1.0
NA B:HEM501 2.0 98.1 1.0
NC B:HEM501 2.1 95.5 1.0
NB B:HEM501 2.1 96.5 1.0
NE2 B:HIS346 2.3 103.2 1.0
C1D B:HEM501 2.9 96.2 1.0
C4D B:HEM501 2.9 97.1 1.0
C1A B:HEM501 3.0 99.1 1.0
C4A B:HEM501 3.0 98.7 1.0
C4C B:HEM501 3.0 95.2 1.0
C1B B:HEM501 3.1 97.1 1.0
C4B B:HEM501 3.1 96.0 1.0
CE1 B:HIS346 3.1 103.1 1.0
C1C B:HEM501 3.1 94.9 1.0
CD2 B:HIS346 3.3 103.3 1.0
CHA B:HEM501 3.3 97.8 1.0
CHD B:HEM501 3.3 95.7 1.0
CHB B:HEM501 3.4 97.6 1.0
CHC B:HEM501 3.5 95.1 1.0
CB B:ALA264 3.9 117.0 1.0
C3D B:HEM501 4.1 97.1 1.0
C2D B:HEM501 4.1 96.3 1.0
O B:HOH607 4.2 138.0 1.0
C2A B:HEM501 4.2 100.9 1.0
C3A B:HEM501 4.2 100.1 1.0
C3C B:HEM501 4.3 95.3 1.0
ND1 B:HIS346 4.3 103.2 1.0
C2C B:HEM501 4.3 94.8 1.0
C2B B:HEM501 4.3 96.7 1.0
C3B B:HEM501 4.4 96.2 1.0
CG B:HIS346 4.4 103.9 1.0
C B:ALA264 4.7 114.5 1.0
N B:GLY265 4.8 112.9 1.0
CA B:ALA264 4.8 116.3 1.0

Reference:

K.N.Pham, A.Lewis-Ballester, S.R.Yeh. Conformational Plasticity in Human Heme-Based Dioxygenases. J.Am.Chem.Soc. 2020.
ISSN: ESSN 1520-5126
PubMed: 33373218
DOI: 10.1021/JACS.0C09970
Page generated: Wed Mar 3 13:56:24 2021

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