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Iron in PDB 2nw9: Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferrous Heme and 6-Fluoro-Tryptophan. Northeast Structural Genomics Target XCR13

Protein crystallography data

The structure of Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferrous Heme and 6-Fluoro-Tryptophan. Northeast Structural Genomics Target XCR13, PDB code: 2nw9 was solved by F.Forouhar, J.L.R.Anderson, C.G.Mowat, C.Bruckmann, S.J.Thackray, J.Seetharaman, 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.Champman, 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) 26.38 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.212, 114.212, 96.095, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 18.4

Other elements in 2nw9:

The structure of Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferrous Heme and 6-Fluoro-Tryptophan. Northeast Structural Genomics Target XCR13 also contains other interesting chemical elements:

Fluorine (F) 1 atom
Manganese (Mn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferrous Heme and 6-Fluoro-Tryptophan. Northeast Structural Genomics Target XCR13 (pdb code 2nw9). 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 Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferrous Heme and 6-Fluoro-Tryptophan. Northeast Structural Genomics Target XCR13, PDB code: 2nw9:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 2nw9

Go back to Iron Binding Sites List in 2nw9
Iron binding site 1 out of 2 in the Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferrous Heme and 6-Fluoro-Tryptophan. 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 Ferrous Heme and 6-Fluoro-Tryptophan. Northeast Structural Genomics Target XCR13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:20.1
occ:1.00
FE A:HEM401 0.0 20.1 1.0
NC A:HEM401 2.1 19.1 1.0
ND A:HEM401 2.2 21.7 1.0
NA A:HEM401 2.2 23.6 1.0
NB A:HEM401 2.2 21.1 1.0
NE2 A:HIS240 2.3 18.4 1.0
C1D A:HEM401 3.0 20.6 1.0
C4C A:HEM401 3.1 19.9 1.0
C1A A:HEM401 3.1 23.6 1.0
CE1 A:HIS240 3.2 19.4 1.0
C4A A:HEM401 3.2 23.5 1.0
C1C A:HEM401 3.2 19.7 1.0
C1B A:HEM401 3.2 22.2 1.0
C4D A:HEM401 3.2 21.7 1.0
C4B A:HEM401 3.3 21.3 1.0
CHD A:HEM401 3.3 20.1 1.0
CD2 A:HIS240 3.3 19.8 1.0
CHB A:HEM401 3.5 22.9 1.0
CHA A:HEM401 3.5 22.9 1.0
O A:HOH426 3.5 24.1 1.0
CHC A:HEM401 3.6 19.9 1.0
ND1 A:HIS240 4.3 17.4 1.0
C2D A:HEM401 4.3 20.4 1.0
C3C A:HEM401 4.3 20.6 1.0
C2C A:HEM401 4.4 19.2 1.0
C3A A:HEM401 4.4 23.5 1.0
C2A A:HEM401 4.4 24.5 1.0
CG A:HIS240 4.4 17.4 1.0
C2B A:HEM401 4.5 22.4 1.0
C3B A:HEM401 4.5 21.7 1.0
C3D A:HEM401 4.5 20.9 1.0
CD1 A:FT6307 4.5 24.2 1.0
CG2 A:VAL244 4.6 17.0 1.0
NE1 A:FT6307 4.6 24.5 1.0

Iron binding site 2 out of 2 in 2nw9

Go back to Iron Binding Sites List in 2nw9
Iron binding site 2 out of 2 in the Crystal Structure of Tryptophan 2,3-Dioxygenase (Tdo) From Xanthomonas Campestris in Complex with Ferrous Heme and 6-Fluoro-Tryptophan. 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 Ferrous Heme and 6-Fluoro-Tryptophan. Northeast Structural Genomics Target XCR13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:14.7
occ:1.00
FE B:HEM401 0.0 14.7 1.0
NA B:HEM401 2.2 13.9 1.0
NC B:HEM401 2.2 14.8 1.0
ND B:HEM401 2.2 13.8 1.0
NB B:HEM401 2.2 15.0 1.0
NE2 B:HIS240 2.3 13.0 1.0
CE1 B:HIS240 3.0 15.1 1.0
C1D B:HEM401 3.1 14.6 1.0
C4C B:HEM401 3.1 12.5 1.0
C1A B:HEM401 3.1 14.3 1.0
C4A B:HEM401 3.1 14.4 1.0
C1B B:HEM401 3.2 14.4 1.0
C1C B:HEM401 3.2 13.3 1.0
C4B B:HEM401 3.2 14.5 1.0
C4D B:HEM401 3.2 13.8 1.0
CHD B:HEM401 3.4 12.4 1.0
CD2 B:HIS240 3.4 13.7 1.0
CHB B:HEM401 3.5 14.1 1.0
CHA B:HEM401 3.5 13.7 1.0
O B:HOH419 3.5 18.0 1.0
CHC B:HEM401 3.6 15.1 1.0
ND1 B:HIS240 4.2 13.7 1.0
C2D B:HEM401 4.3 12.9 1.0
C3C B:HEM401 4.3 12.1 1.0
C3A B:HEM401 4.4 16.1 1.0
CG2 B:VAL244 4.4 12.8 1.0
C2C B:HEM401 4.4 12.2 1.0
C2A B:HEM401 4.4 14.4 1.0
CG B:HIS240 4.4 12.6 1.0
C2B B:HEM401 4.4 14.5 1.0
C3B B:HEM401 4.5 15.1 1.0
C3D B:HEM401 4.5 13.7 1.0
N B:GLY125 4.5 15.5 1.0
CB B:SER124 4.7 16.4 1.0
CH2 B:TRP102 5.0 12.6 1.0

Reference:

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
Page generated: Sun Aug 4 00:48:48 2024

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