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Iron in PDB 6ud5: Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Carbon Monoxide and Tryptophan

Enzymatic activity of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Carbon Monoxide and Tryptophan

All present enzymatic activity of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Carbon Monoxide and Tryptophan:
1.13.11.11;

Protein crystallography data

The structure of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Carbon Monoxide and Tryptophan, PDB code: 6ud5 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) 19.97 / 2.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 144.725, 154.493, 88.306, 90, 90, 90
R / Rfree (%) 18.3 / 21.7

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Carbon Monoxide and Tryptophan (pdb code 6ud5). 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 Tryptophan 2,3-Dioxygenase in Complex with Carbon Monoxide and Tryptophan, PDB code: 6ud5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6ud5

Go back to Iron Binding Sites List in 6ud5
Iron binding site 1 out of 4 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase 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 Human Tryptophan 2,3-Dioxygenase in Complex with Carbon Monoxide and Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:32.2
occ:1.00
 FE A:HEM500 0.0 32.2 1.0
C A:CMO501 1.9 34.7 1.0
ND A:HEM500 1.9 33.7 1.0
NA A:HEM500 2.0 35.1 1.0
NE2 A:HIS328 2.1 30.0 1.0
NC A:HEM500 2.1 32.7 1.0
NB A:HEM500 2.1 33.8 1.0
C4D A:HEM500 2.9 32.6 1.0
C1D A:HEM500 2.9 32.1 1.0
CE1 A:HIS328 2.9 30.6 1.0
O A:CMO501 3.0 41.9 1.0
C1A A:HEM500 3.0 35.1 1.0
C4C A:HEM500 3.0 31.7 1.0
C4A A:HEM500 3.1 35.4 1.0
C4B A:HEM500 3.1 34.1 1.0
C1B A:HEM500 3.1 34.7 1.0
C1C A:HEM500 3.1 31.7 1.0
CD2 A:HIS328 3.2 29.0 1.0
CHA A:HEM500 3.4 33.3 1.0
CHD A:HEM500 3.4 31.6 1.0
CHB A:HEM500 3.5 35.7 1.0
CHC A:HEM500 3.5 32.1 1.0
O A:HOH691 4.0 48.3 1.0
ND1 A:HIS328 4.1 28.9 1.0
C3D A:HEM500 4.2 32.1 1.0
C2D A:HEM500 4.2 32.0 1.0
C2A A:HEM500 4.2 35.7 1.0
C3A A:HEM500 4.2 36.2 1.0
CG A:HIS328 4.2 29.1 1.0
C3C A:HEM500 4.3 30.5 1.0
C2C A:HEM500 4.3 31.0 1.0
C2B A:HEM500 4.3 34.0 1.0
C3B A:HEM500 4.4 34.2 1.0
CD1 A:TRP502 4.5 33.9 1.0
NE1 A:TRP502 4.5 33.7 1.0
CG2 A:VAL332 4.8 34.6 1.0
CA A:GLY152 4.9 40.4 1.0

Iron binding site 2 out of 4 in 6ud5

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Iron binding site 2 out of 4 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase 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 Human Tryptophan 2,3-Dioxygenase in Complex with Carbon Monoxide and Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:29.9
occ:1.00
 FE B:HEM500 0.0 29.9 1.0
ND B:HEM500 1.9 29.5 1.0
C B:CMO501 1.9 33.2 1.0
NA B:HEM500 2.0 29.2 1.0
NC B:HEM500 2.1 27.5 1.0
NE2 B:HIS328 2.1 31.0 1.0
NB B:HEM500 2.1 28.4 1.0
C4D B:HEM500 2.9 29.2 1.0
CE1 B:HIS328 2.9 30.5 1.0
O B:CMO501 2.9 35.9 1.0
C1D B:HEM500 2.9 28.5 1.0
C1A B:HEM500 3.0 28.6 1.0
C4C B:HEM500 3.1 27.8 1.0
C4A B:HEM500 3.1 28.2 1.0
C4B B:HEM500 3.1 26.9 1.0
C1B B:HEM500 3.1 28.3 1.0
C1C B:HEM500 3.1 27.3 1.0
CD2 B:HIS328 3.2 29.7 1.0
CHA B:HEM500 3.3 28.8 1.0
CHD B:HEM500 3.4 27.8 1.0
CHB B:HEM500 3.5 28.4 1.0
CHC B:HEM500 3.5 26.9 1.0
O B:HOH637 4.0 39.5 1.0
ND1 B:HIS328 4.1 29.9 1.0
C3D B:HEM500 4.1 28.9 1.0
C2D B:HEM500 4.1 28.4 1.0
C2A B:HEM500 4.2 29.0 1.0
C3A B:HEM500 4.2 28.6 1.0
CG B:HIS328 4.3 28.9 1.0
C3C B:HEM500 4.3 26.8 1.0
C2C B:HEM500 4.3 26.4 1.0
C2B B:HEM500 4.3 26.8 1.0
C3B B:HEM500 4.3 26.5 1.0
CD1 B:TRP502 4.5 30.4 1.0
NE1 B:TRP502 4.6 29.4 1.0
CG2 B:VAL332 4.9 28.1 1.0
CA B:GLY152 5.0 33.3 1.0

Iron binding site 3 out of 4 in 6ud5

Go back to Iron Binding Sites List in 6ud5
Iron binding site 3 out of 4 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase 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 3 of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Carbon Monoxide and Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:29.1
occ:1.00
 FE C:HEM500 0.0 29.1 1.0
C C:CMO501 1.9 31.7 1.0
ND C:HEM500 1.9 30.9 1.0
NA C:HEM500 2.0 30.6 1.0
NE2 C:HIS328 2.1 28.4 1.0
NC C:HEM500 2.1 28.7 1.0
NB C:HEM500 2.1 29.8 1.0
CE1 C:HIS328 2.9 28.9 1.0
C1D C:HEM500 2.9 30.2 1.0
C4D C:HEM500 2.9 31.0 1.0
O C:CMO501 2.9 36.0 1.0
C1A C:HEM500 3.0 31.3 1.0
C4C C:HEM500 3.0 29.2 1.0
C4A C:HEM500 3.1 31.5 1.0
C1B C:HEM500 3.1 30.3 1.0
C4B C:HEM500 3.1 29.3 1.0
C1C C:HEM500 3.1 29.0 1.0
CD2 C:HIS328 3.2 28.1 1.0
CHD C:HEM500 3.4 30.0 1.0
CHA C:HEM500 3.4 30.6 1.0
CHB C:HEM500 3.5 30.7 1.0
CHC C:HEM500 3.5 28.3 1.0
O C:HOH620 3.9 40.0 1.0
ND1 C:HIS328 4.0 29.3 1.0
C3D C:HEM500 4.2 30.6 1.0
C2D C:HEM500 4.2 30.6 1.0
CG C:HIS328 4.2 29.1 1.0
C2A C:HEM500 4.2 31.7 1.0
C3A C:HEM500 4.2 32.0 1.0
C3C C:HEM500 4.3 28.3 1.0
C2C C:HEM500 4.3 28.8 1.0
C2B C:HEM500 4.3 30.5 1.0
C3B C:HEM500 4.4 30.0 1.0
CD1 C:TRP502 4.5 35.9 1.0
NE1 C:TRP502 4.5 36.9 1.0
CG2 C:VAL332 4.9 32.8 1.0

Iron binding site 4 out of 4 in 6ud5

Go back to Iron Binding Sites List in 6ud5
Iron binding site 4 out of 4 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase 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 4 of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Carbon Monoxide and Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe500

b:27.8
occ:1.00
 FE D:HEM500 0.0 27.8 1.0
ND D:HEM500 1.9 28.7 1.0
NA D:HEM500 2.0 27.6 1.0
C D:CMO501 2.1 34.5 1.0
NC D:HEM500 2.1 27.4 1.0
NE2 D:HIS328 2.1 27.3 1.0
NB D:HEM500 2.1 28.4 1.0
C1D D:HEM500 2.9 28.3 1.0
C4D D:HEM500 2.9 29.0 1.0
CE1 D:HIS328 2.9 26.6 1.0
C1A D:HEM500 3.0 28.5 1.0
C4C D:HEM500 3.0 27.0 1.0
O D:CMO501 3.1 34.6 1.0
C4A D:HEM500 3.1 28.2 1.0
C4B D:HEM500 3.1 28.0 1.0
C1B D:HEM500 3.1 27.3 1.0
C1C D:HEM500 3.1 27.7 1.0
CD2 D:HIS328 3.2 26.5 1.0
CHD D:HEM500 3.3 27.9 1.0
CHA D:HEM500 3.4 28.1 1.0
CHB D:HEM500 3.5 28.1 1.0
CHC D:HEM500 3.5 27.6 1.0
ND1 D:HIS328 4.1 26.3 1.0
O D:HOH650 4.1 35.7 1.0
C2D D:HEM500 4.2 27.9 1.0
C3D D:HEM500 4.2 28.6 1.0
C2A D:HEM500 4.2 28.4 1.0
C3A D:HEM500 4.2 28.4 1.0
C3C D:HEM500 4.3 26.9 1.0
CG D:HIS328 4.3 26.6 1.0
C2C D:HEM500 4.3 26.6 1.0
C2B D:HEM500 4.3 28.3 1.0
C3B D:HEM500 4.3 27.5 1.0
CD1 D:TRP502 4.5 30.9 1.0
NE1 D:TRP502 4.6 30.7 1.0
CG2 D:VAL332 4.9 28.0 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 Aug 7 12:16:54 2024

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