Iron in PDB 2nw7: Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferric Heme. Northeast Structural Genomics Target XCR13

The structure of Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferric Heme. Northeast Structural Genomics Target XCR13, PDB code: 2nw7 was solved by F.Forouhar, J.L.R.Anderson, C.G.Mowat, A.Hussain, C.Bruckmann, S.J.Thackray, J.Seetharaman, T.Tucker, C.K.Ho, L.C.Ma, K.Cunningham, H.Janjua, L.Zhao, R.Xiao, J.Liu, M.C.Baran, T.B.Acton, B.Rost, G.T.Montelione, S.K.Chapman, L.Tong, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.43 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.939, 109.359, 125.513, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 26.3

The binding sites of Iron atom in the Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferric Heme. Northeast Structural Genomics Target XCR13 (pdb code 2nw7). 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 Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferric Heme. Northeast Structural Genomics Target XCR13, PDB code: 2nw7:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferric Heme. Northeast Structural Genomics Target XCR13


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 Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferric Heme. Northeast Structural Genomics Target XCR13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:32.0 occ:1.00 FE A:HEM401 0.0 32.0 1.0 ND A:HEM401 2.0 42.2 1.0 NC A:HEM401 2.1 40.3 1.0 NB A:HEM401 2.1 41.9 1.0 NA A:HEM401 2.2 43.3 1.0 NE2 A:HIS240 2.5 29.7 1.0 C1D A:HEM401 2.9 41.6 1.0 C4D A:HEM401 3.0 42.8 1.0 C4C A:HEM401 3.0 40.5 1.0 C1C A:HEM401 3.1 39.4 1.0 C1B A:HEM401 3.1 42.5 1.0 C1A A:HEM401 3.1 43.1 1.0 C4B A:HEM401 3.1 41.3 1.0 C4A A:HEM401 3.1 43.0 1.0 CE1 A:HIS240 3.2 30.2 1.0 CHD A:HEM401 3.3 41.3 1.0 CHA A:HEM401 3.4 42.8 1.0 CHB A:HEM401 3.5 42.5 1.0 CHC A:HEM401 3.5 39.6 1.0 CD2 A:HIS240 3.6 30.4 1.0 C2D A:HEM401 4.2 42.4 1.0 C3D A:HEM401 4.2 42.9 1.0 C3C A:HEM401 4.3 40.5 1.0 C2C A:HEM401 4.3 40.0 1.0 C2B A:HEM401 4.3 43.5 1.0 ND1 A:HIS240 4.4 33.0 1.0 C2A A:HEM401 4.4 44.0 1.0 C3A A:HEM401 4.4 43.1 1.0 C3B A:HEM401 4.4 42.2 1.0 CG A:HIS240 4.6 32.1 1.0 N A:GLY125 4.7 56.1 1.0 CG2 A:VAL244 4.8 32.6 1.0 CA A:GLY125 5.0 55.9 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferric Heme. Northeast Structural Genomics Target XCR13


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 Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferric Heme. Northeast Structural Genomics Target XCR13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:25.3 occ:1.00 FE B:HEM401 0.0 25.3 1.0 ND B:HEM401 2.0 34.6 1.0 NC B:HEM401 2.0 31.1 1.0 NB B:HEM401 2.1 35.3 1.0 NA B:HEM401 2.2 36.3 1.0 NE2 B:HIS240 2.4 31.9 1.0 C1D B:HEM401 2.9 32.2 1.0 C4D B:HEM401 3.0 34.8 1.0 C4C B:HEM401 3.0 30.9 1.0 CE1 B:HIS240 3.1 33.3 1.0 C1C B:HEM401 3.1 31.0 1.0 C1B B:HEM401 3.1 36.2 1.0 C1A B:HEM401 3.1 36.5 1.0 C4B B:HEM401 3.1 35.4 1.0 C4A B:HEM401 3.1 37.5 1.0 CHD B:HEM401 3.3 29.8 1.0 CHA B:HEM401 3.4 35.6 1.0 CHB B:HEM401 3.5 36.2 1.0 CHC B:HEM401 3.5 32.8 1.0 CD2 B:HIS240 3.5 31.4 1.0 C2D B:HEM401 4.2 33.0 1.0 C3D B:HEM401 4.2 34.6 1.0 ND1 B:HIS240 4.3 34.3 1.0 C3C B:HEM401 4.3 31.0 1.0 C2C B:HEM401 4.3 31.2 1.0 C2B B:HEM401 4.3 37.5 1.0 C2A B:HEM401 4.4 38.3 1.0 C3A B:HEM401 4.4 37.4 1.0 C3B B:HEM401 4.4 37.7 1.0 CG B:HIS240 4.5 32.0 1.0 N B:GLY125 4.6 37.5 1.0 CG2 B:VAL244 4.9 30.3 1.0 CA B:GLY125 5.0 38.0 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferric Heme. Northeast Structural Genomics Target XCR13


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 Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferric Heme. Northeast Structural Genomics Target XCR13 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:45.8 occ:1.00 FE C:HEM401 0.0 45.8 1.0 NC C:HEM401 2.0 50.8 1.0 ND C:HEM401 2.0 52.6 1.0 NB C:HEM401 2.1 52.2 1.0 NA C:HEM401 2.3 53.5 1.0 NE2 C:HIS240 2.3 26.0 1.0 C4C C:HEM401 3.0 51.3 1.0 C1D C:HEM401 3.0 52.3 1.0 C1C C:HEM401 3.0 50.6 1.0 C4B C:HEM401 3.1 51.5 1.0 C1B C:HEM401 3.1 52.8 1.0 C4D C:HEM401 3.1 53.3 1.0 CE1 C:HIS240 3.2 26.7 1.0 C4A C:HEM401 3.2 53.7 1.0 C1A C:HEM401 3.3 53.1 1.0 CHD C:HEM401 3.3 51.8 1.0 CD2 C:HIS240 3.3 27.0 1.0 CHC C:HEM401 3.4 50.1 1.0 CHB C:HEM401 3.5 53.4 1.0 CHA C:HEM401 3.6 52.1 1.0 C2D C:HEM401 4.2 52.4 1.0 C3C C:HEM401 4.2 51.2 1.0 C2C C:HEM401 4.2 51.2 1.0 C2B C:HEM401 4.3 53.2 1.0 C3D C:HEM401 4.3 53.5 1.0 C3B C:HEM401 4.3 52.5 1.0 ND1 C:HIS240 4.3 27.9 1.0 CG C:HIS240 4.4 27.9 1.0 C3A C:HEM401 4.5 54.0 1.0 C2A C:HEM401 4.5 55.2 1.0 CG2 C:VAL244 4.7 21.9 1.0 N C:GLY125 4.8 53.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferric Heme. Northeast Structural Genomics Target XCR13


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 Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferric Heme. Northeast Structural Genomics Target XCR13 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:30.6 occ:1.00 FE D:HEM401 0.0 30.6 1.0 ND D:HEM401 2.0 38.8 1.0 NC D:HEM401 2.0 35.1 1.0 NB D:HEM401 2.0 39.4 1.0 NA D:HEM401 2.2 41.0 1.0 NE2 D:HIS240 2.5 26.1 1.0 C1D D:HEM401 3.0 37.1 1.0 C4C D:HEM401 3.0 35.3 1.0 C1C D:HEM401 3.1 35.5 1.0 C1B D:HEM401 3.1 40.5 1.0 C4D D:HEM401 3.1 39.4 1.0 C4B D:HEM401 3.1 38.3 1.0 C4A D:HEM401 3.1 41.9 1.0 C1A D:HEM401 3.2 41.5 1.0 CE1 D:HIS240 3.3 27.6 1.0 CHD D:HEM401 3.4 34.9 1.0 CHC D:HEM401 3.4 36.2 1.0 CHB D:HEM401 3.4 41.0 1.0 CHA D:HEM401 3.5 39.8 1.0 CD2 D:HIS240 3.6 27.1 1.0 C2D D:HEM401 4.2 37.9 1.0 C2B D:HEM401 4.3 41.1 1.0 C3D D:HEM401 4.3 39.5 1.0 C3C D:HEM401 4.3 34.8 1.0 C2C D:HEM401 4.3 35.0 1.0 C3B D:HEM401 4.3 40.0 1.0 C3A D:HEM401 4.4 42.4 1.0 C2A D:HEM401 4.4 44.4 1.0 ND1 D:HIS240 4.5 28.8 1.0 CG D:HIS240 4.6 28.6 1.0 N D:GLY125 4.7 38.6 1.0 CG2 D:VAL244 4.8 26.7 1.0 CA D:GLY125 4.9 37.9 1.0

F.Forouhar, J.L.Anderson, C.G.Mowat, S.M.Vorobiev, A.Hussain, M.Abashidze, C.Bruckmann, S.J.Thackray, J.Seetharaman, T.Tucker, R.Xiao, L.C.Ma, L.Zhao, T.B.Acton, G.T.Montelione, S.K.Chapman, L.Tong. Molecular Insights Into Substrate Recognition and Catalysis By Tryptophan 2,3-Dioxygenase. Proc.Natl.Acad.Sci.Usa V. 104 473 2007.
ISSN: ISSN 0027-8424
PubMed: 17197414
DOI: 10.1073/PNAS.0610007104