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Iron in PDB 5ti9: Crystal Structure of Human Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161

Enzymatic activity of Crystal Structure of Human Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161

All present enzymatic activity of Crystal Structure of Human Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161:
1.13.11.11;

Protein crystallography data

The structure of Crystal Structure of Human Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161, PDB code: 5ti9 was solved by F.Forouhar, A.Lewis-Ballester, S.Lew, S.Karkashon, J.Seetharaman, S.R.Yeh, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.93 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 143.601, 154.009, 87.801, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 23

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161 (pdb code 5ti9). 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 Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161, PDB code: 5ti9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5ti9

Go back to Iron Binding Sites List in 5ti9
Iron binding site 1 out of 4 in the Crystal Structure of Human Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161


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 Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:41.9
occ:1.00
 FE A:HEM402 0.0 41.9 1.0
O2 A:OXY401 1.8 73.7 1.0
NC A:HEM402 2.0 41.2 1.0
NB A:HEM402 2.0 43.1 1.0
ND A:HEM402 2.1 40.6 1.0
NA A:HEM402 2.1 44.5 1.0
NE2 A:HIS328 2.3 42.0 1.0
O1 A:OXY401 2.9 76.4 1.0
C4C A:HEM402 3.0 36.1 1.0
C1C A:HEM402 3.0 42.6 1.0
C1B A:HEM402 3.0 44.8 1.0
C4B A:HEM402 3.1 47.2 1.0
C1D A:HEM402 3.1 42.0 1.0
CE1 A:HIS328 3.1 42.1 1.0
C4A A:HEM402 3.1 45.2 1.0
C4D A:HEM402 3.1 42.2 1.0
C1A A:HEM402 3.2 44.5 1.0
CHD A:HEM402 3.4 35.9 1.0
CHC A:HEM402 3.4 49.4 1.0
CD2 A:HIS328 3.4 38.7 1.0
CHB A:HEM402 3.4 44.6 1.0
CHA A:HEM402 3.6 40.8 1.0
C2C A:HEM402 4.2 41.4 1.0
C3C A:HEM402 4.2 37.3 1.0
ND1 A:HIS328 4.3 44.6 1.0
C2B A:HEM402 4.3 49.2 1.0
C3B A:HEM402 4.3 47.6 1.0
C2D A:HEM402 4.3 36.6 1.0
CD1 A:TRP403 4.3 74.1 1.0
C3D A:HEM402 4.4 45.2 1.0
C3A A:HEM402 4.4 46.8 1.0
C2A A:HEM402 4.4 43.8 1.0
NE1 A:TRP403 4.4 71.4 1.0
CG A:HIS328 4.5 43.3 1.0
CG2 A:VAL332 4.7 52.2 1.0
CA A:GLY152 4.8 52.6 1.0
NE2 A:HIS76 4.9 46.4 1.0
N A:GLY152 4.9 51.1 1.0

Iron binding site 2 out of 4 in 5ti9

Go back to Iron Binding Sites List in 5ti9
Iron binding site 2 out of 4 in the Crystal Structure of Human Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161


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 Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:42.3
occ:1.00
 FE B:HEM402 0.0 42.3 1.0
O2 B:OXY401 1.8 54.6 1.0
NA B:HEM402 2.0 53.0 1.0
NB B:HEM402 2.0 38.6 1.0
ND B:HEM402 2.1 42.1 1.0
NC B:HEM402 2.1 46.7 1.0
NE2 B:HIS328 2.3 47.7 1.0
O1 B:OXY401 2.9 56.9 1.0
C1B B:HEM402 3.0 45.6 1.0
C1A B:HEM402 3.0 51.5 1.0
C4A B:HEM402 3.0 47.5 1.0
C4D B:HEM402 3.1 44.8 1.0
C4B B:HEM402 3.1 34.5 1.0
C1D B:HEM402 3.1 48.6 1.0
C1C B:HEM402 3.1 41.0 1.0
C4C B:HEM402 3.2 47.0 1.0
CE1 B:HIS328 3.2 40.5 1.0
CD2 B:HIS328 3.3 50.4 1.0
CHB B:HEM402 3.4 42.2 1.0
CHA B:HEM402 3.4 47.9 1.0
CHC B:HEM402 3.5 31.8 1.0
CHD B:HEM402 3.5 49.5 1.0
C2B B:HEM402 4.2 35.6 1.0
C3A B:HEM402 4.3 50.7 1.0
CD1 B:TRP403 4.3 54.9 1.0
C2A B:HEM402 4.3 50.0 1.0
C3B B:HEM402 4.3 39.9 1.0
C3D B:HEM402 4.3 52.8 1.0
NE1 B:TRP403 4.3 54.6 1.0
ND1 B:HIS328 4.3 46.9 1.0
C2D B:HEM402 4.3 46.8 1.0
C2C B:HEM402 4.4 40.3 1.0
C3C B:HEM402 4.4 43.4 1.0
CG B:HIS328 4.4 44.7 1.0
CG2 B:VAL332 4.7 50.4 1.0

Iron binding site 3 out of 4 in 5ti9

Go back to Iron Binding Sites List in 5ti9
Iron binding site 3 out of 4 in the Crystal Structure of Human Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161


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 Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:51.9
occ:1.00
 FE C:HEM401 0.0 51.9 1.0
OAB C:NFK402 1.7 60.8 1.0
NC C:HEM401 2.0 46.4 1.0
NB C:HEM401 2.1 49.7 1.0
NA C:HEM401 2.1 62.8 1.0
ND C:HEM401 2.1 45.2 1.0
NE2 C:HIS328 2.3 44.1 1.0
CAF C:NFK402 2.9 71.8 1.0
C4C C:HEM401 3.0 46.5 1.0
C1D C:HEM401 3.1 51.6 1.0
C1B C:HEM401 3.1 49.8 1.0
C1C C:HEM401 3.1 46.6 1.0
C4A C:HEM401 3.1 59.0 1.0
C4B C:HEM401 3.1 45.4 1.0
C1A C:HEM401 3.1 56.8 1.0
C4D C:HEM401 3.1 49.2 1.0
CE1 C:HIS328 3.1 47.5 1.0
CHD C:HEM401 3.4 44.1 1.0
CD2 C:HIS328 3.4 40.6 1.0
CHB C:HEM401 3.4 49.5 1.0
CHC C:HEM401 3.5 49.2 1.0
CHA C:HEM401 3.5 48.5 1.0
NAL C:NFK402 3.7 76.5 1.0
C3C C:HEM401 4.3 44.2 1.0
C2C C:HEM401 4.3 47.4 1.0
C2B C:HEM401 4.3 50.7 1.0
C3B C:HEM401 4.3 42.3 1.0
C3A C:HEM401 4.3 63.9 1.0
C2A C:HEM401 4.3 60.0 1.0
C2D C:HEM401 4.3 51.6 1.0
ND1 C:HIS328 4.3 50.1 1.0
C3D C:HEM401 4.3 45.9 1.0
CG C:HIS328 4.5 45.6 1.0
OD1 C:NFK402 4.7 0.0 1.0
CA C:GLY152 4.8 53.7 1.0
N C:GLY152 4.8 54.0 1.0
CG2 C:VAL332 4.9 55.8 1.0
NE2 C:HIS76 5.0 41.7 1.0

Iron binding site 4 out of 4 in 5ti9

Go back to Iron Binding Sites List in 5ti9
Iron binding site 4 out of 4 in the Crystal Structure of Human Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161


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 Tdo in Complex with Trp and Dioxygen, Northeast Structural Genomics Consortium Target HR6161 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:44.4
occ:1.00
 FE D:HEM401 0.0 44.4 1.0
OAB D:NFK402 1.7 47.2 1.0
NB D:HEM401 1.9 47.0 1.0
NC D:HEM401 2.1 46.6 1.0
ND D:HEM401 2.1 33.8 1.0
NA D:HEM401 2.1 47.1 1.0
NE2 D:HIS328 2.3 42.1 1.0
CAF D:NFK402 2.9 50.5 1.0
C4B D:HEM401 2.9 53.7 1.0
C1B D:HEM401 3.0 54.9 1.0
C1D D:HEM401 3.0 49.8 1.0
C1C D:HEM401 3.1 46.3 1.0
C4C D:HEM401 3.1 39.5 1.0
C4A D:HEM401 3.1 44.5 1.0
C4D D:HEM401 3.1 45.4 1.0
C1A D:HEM401 3.2 49.2 1.0
CD2 D:HIS328 3.2 52.2 1.0
CE1 D:HIS328 3.3 53.9 1.0
CHC D:HEM401 3.4 47.6 1.0
CHD D:HEM401 3.4 42.8 1.0
CHB D:HEM401 3.4 43.2 1.0
CHA D:HEM401 3.6 48.2 1.0
NAL D:NFK402 3.6 56.9 1.0
C3B D:HEM401 4.2 48.0 1.0
C2B D:HEM401 4.2 54.0 1.0
C2C D:HEM401 4.3 51.1 1.0
C3C D:HEM401 4.3 45.1 1.0
C2D D:HEM401 4.3 47.8 1.0
C3D D:HEM401 4.3 35.9 1.0
C3A D:HEM401 4.3 52.7 1.0
CG D:HIS328 4.4 56.2 1.0
C2A D:HEM401 4.4 54.7 1.0
ND1 D:HIS328 4.4 62.7 1.0
CA D:GLY152 4.7 45.0 1.0
N D:GLY152 4.8 46.6 1.0
NE2 D:HIS76 4.9 38.0 1.0
CAO D:NFK402 5.0 71.6 1.0
CG2 D:VAL332 5.0 47.0 1.0

Reference:

A.Lewis-Ballester, F.Forouhar, S.M.Kim, S.Lew, Y.Wang, S.Karkashon, J.Seetharaman, D.Batabyal, B.Y.Chiang, M.Hussain, M.A.Correia, S.R.Yeh, L.Tong. Molecular Basis For Catalysis and Substrate-Mediated Cellular Stabilization of Human Tryptophan 2,3-Dioxygenase. Sci Rep V. 6 35169 2016.
ISSN: ESSN 2045-2322
PubMed: 27762317
DOI: 10.1038/SREP35169
Page generated: Tue Aug 6 09:00:25 2024

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