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Iron in PDB 7p46: Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo)

Enzymatic activity of Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo)

All present enzymatic activity of Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo):
1.13.11.11;

Protein crystallography data

The structure of Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo), PDB code: 7p46 was solved by H.Kwon, J.Basran, E.S.Booth, L.P.Campbell, S.J.Thackray, P.C.E.Moody, C.G.Mowat, E.L.Raven, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 89.78 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.095, 117.752, 138.819, 90, 95.52, 90
R / Rfree (%) 14.9 / 18.5

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo) (pdb code 7p46). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo), PDB code: 7p46:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 7p46

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Iron binding site 1 out of 8 in the Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo)


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 Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:10.8
occ:1.00
FE A:HEM301 0.0 10.8 1.0
C A:CYN302 1.7 8.2 1.0
ND A:HEM301 2.0 10.5 1.0
NA A:HEM301 2.0 9.3 1.0
NC A:HEM301 2.0 9.8 1.0
NB A:HEM301 2.0 10.6 1.0
NE2 A:HIS240 2.0 11.3 1.0
C4D A:HEM301 3.0 10.2 1.0
N A:CYN302 3.0 9.4 1.0
C1D A:HEM301 3.0 9.3 1.0
C1A A:HEM301 3.0 10.9 1.0
C1B A:HEM301 3.0 10.6 1.0
CE1 A:HIS240 3.0 11.5 1.0
C1C A:HEM301 3.0 11.6 1.0
C4A A:HEM301 3.0 10.4 1.0
C4C A:HEM301 3.0 10.7 1.0
C4B A:HEM301 3.0 11.0 1.0
CD2 A:HIS240 3.1 12.3 1.0
CHB A:HEM301 3.4 11.1 1.0
CHA A:HEM301 3.4 10.6 1.0
CHC A:HEM301 3.4 12.4 1.0
CHD A:HEM301 3.5 11.0 1.0
ND1 A:HIS240 4.2 11.9 1.0
C2C A:HEM301 4.2 10.6 1.0
CG A:HIS240 4.2 11.6 1.0
C3D A:HEM301 4.2 9.8 1.0
C3A A:HEM301 4.2 11.2 1.0
C2A A:HEM301 4.3 10.7 1.0
C2D A:HEM301 4.3 10.7 1.0
C3C A:HEM301 4.3 11.4 1.0
C2B A:HEM301 4.3 12.6 1.0
C3B A:HEM301 4.3 12.3 1.0
O2 A:KYN303 4.4 11.7 1.0
N A:KYN303 4.7 11.8 1.0
CG2 A:VAL244 4.8 12.5 1.0
N1 A:KYN303 4.8 12.4 1.0

Iron binding site 2 out of 8 in 7p46

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Iron binding site 2 out of 8 in the Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo)


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 Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:9.4
occ:1.00
FE B:HEM301 0.0 9.4 1.0
C B:CYN302 1.8 6.1 1.0
ND B:HEM301 1.9 8.8 1.0
NA B:HEM301 2.0 7.8 1.0
NC B:HEM301 2.0 8.5 1.0
NE2 B:HIS240 2.0 8.6 1.0
NB B:HEM301 2.0 8.9 1.0
C1D B:HEM301 2.9 8.4 1.0
CE1 B:HIS240 3.0 10.6 1.0
C4D B:HEM301 3.0 8.5 1.0
C1A B:HEM301 3.0 9.2 1.0
C4A B:HEM301 3.0 9.3 1.0
C1C B:HEM301 3.0 9.4 1.0
C4B B:HEM301 3.0 8.4 1.0
C1B B:HEM301 3.0 8.5 1.0
C4C B:HEM301 3.0 9.5 1.0
N B:CYN302 3.1 8.9 1.0
CD2 B:HIS240 3.2 9.8 1.0
CHD B:HEM301 3.4 8.6 1.0
CHB B:HEM301 3.4 9.2 1.0
CHA B:HEM301 3.4 9.0 1.0
CHC B:HEM301 3.5 8.8 1.0
ND1 B:HIS240 4.1 10.8 1.0
C3A B:HEM301 4.2 9.2 1.0
C2C B:HEM301 4.2 8.9 1.0
C3C B:HEM301 4.2 9.3 1.0
C2A B:HEM301 4.2 9.1 1.0
C2D B:HEM301 4.2 8.8 1.0
C2B B:HEM301 4.2 8.6 1.0
CG B:HIS240 4.3 10.0 1.0
C3D B:HEM301 4.3 8.8 1.0
C3B B:HEM301 4.3 9.0 1.0
O2 B:KYN303 4.3 10.0 1.0
N1 B:KYN303 4.7 12.0 1.0
CG2 B:VAL244 4.7 11.6 1.0
N B:KYN303 4.7 10.4 1.0
N B:GLY125 4.9 10.8 1.0
CA B:GLY125 5.0 10.9 1.0
C1 B:KYN303 5.0 9.3 1.0

Iron binding site 3 out of 8 in 7p46

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Iron binding site 3 out of 8 in the Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo)


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 Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:16.6
occ:1.00
FE C:HEM301 0.0 16.6 1.0
ND C:HEM301 1.9 15.8 1.0
C C:CYN302 2.0 15.7 1.0
NA C:HEM301 2.0 14.9 1.0
NB C:HEM301 2.0 15.7 1.0
NC C:HEM301 2.1 14.5 1.0
NE2 C:HIS240 2.1 17.3 1.0
C4D C:HEM301 2.9 16.6 1.0
C1A C:HEM301 3.0 16.6 1.0
C1D C:HEM301 3.0 16.0 1.0
CE1 C:HIS240 3.0 19.2 1.0
C1C C:HEM301 3.0 14.8 1.0
C4A C:HEM301 3.0 16.5 1.0
C1B C:HEM301 3.0 14.9 1.0
C4B C:HEM301 3.1 14.7 1.0
C4C C:HEM301 3.1 15.5 1.0
CD2 C:HIS240 3.1 17.6 1.0
N C:CYN302 3.1 20.4 1.0
CHA C:HEM301 3.4 16.9 1.0
CHB C:HEM301 3.4 16.2 1.0
CHC C:HEM301 3.5 14.7 1.0
CHD C:HEM301 3.5 16.0 1.0
ND1 C:HIS240 4.2 17.6 1.0
C2C C:HEM301 4.2 14.0 1.0
C3D C:HEM301 4.2 16.6 1.0
C2A C:HEM301 4.2 16.6 1.0
CG C:HIS240 4.2 15.6 1.0
C2D C:HEM301 4.2 16.5 1.0
C3A C:HEM301 4.2 16.1 1.0
C3C C:HEM301 4.2 15.0 1.0
C2B C:HEM301 4.3 14.8 1.0
O2 C:KYN303 4.3 19.8 1.0
C3B C:HEM301 4.3 14.9 1.0
N1 C:KYN303 4.7 17.6 1.0
CG2 C:VAL244 4.7 16.5 1.0
N C:KYN303 4.7 16.6 1.0
N C:GLY125 4.9 19.5 1.0
C1 C:KYN303 4.9 19.0 1.0

Iron binding site 4 out of 8 in 7p46

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Iron binding site 4 out of 8 in the Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo)


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 Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:15.8
occ:1.00
FE D:HEM301 0.0 15.8 1.0
ND D:HEM301 1.9 12.6 1.0
NB D:HEM301 2.0 13.4 1.0
NA D:HEM301 2.0 14.3 1.0
NC D:HEM301 2.0 14.0 1.0
C D:CYN302 2.1 12.3 1.0
NE2 D:HIS240 2.1 12.7 1.0
C1D D:HEM301 2.9 14.2 1.0
C4B D:HEM301 3.0 14.5 1.0
CE1 D:HIS240 3.0 16.2 1.0
C4D D:HEM301 3.0 12.8 1.0
C1A D:HEM301 3.0 13.8 1.0
C4C D:HEM301 3.0 14.1 1.0
C4A D:HEM301 3.0 13.7 1.0
C1B D:HEM301 3.0 13.4 1.0
C1C D:HEM301 3.0 14.0 1.0
CD2 D:HIS240 3.1 15.3 1.0
N D:CYN302 3.3 20.2 1.0
CHD D:HEM301 3.4 13.7 1.0
CHC D:HEM301 3.4 15.5 1.0
CHB D:HEM301 3.4 14.4 1.0
CHA D:HEM301 3.5 14.0 1.0
ND1 D:HIS240 4.1 15.8 1.0
C3A D:HEM301 4.2 13.9 1.0
C2D D:HEM301 4.2 14.3 1.0
C2A D:HEM301 4.2 15.0 1.0
C2B D:HEM301 4.2 13.4 1.0
C3B D:HEM301 4.2 14.3 1.0
C3D D:HEM301 4.2 15.1 1.0
C3C D:HEM301 4.2 14.2 1.0
CG D:HIS240 4.2 14.1 1.0
C2C D:HEM301 4.2 13.7 1.0
O2 D:KYN303 4.4 18.7 1.0
N1 D:KYN303 4.7 18.1 1.0
CG2 D:VAL244 4.7 15.0 1.0
N D:KYN303 4.7 15.5 1.0
N D:GLY125 4.9 20.0 1.0
CA D:GLY125 4.9 17.2 1.0

Iron binding site 5 out of 8 in 7p46

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Iron binding site 5 out of 8 in the Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:26.9
occ:1.00
FE E:HEM301 0.0 26.9 1.0
ND E:HEM301 2.0 24.4 1.0
NA E:HEM301 2.0 27.5 1.0
NC E:HEM301 2.0 27.0 1.0
NB E:HEM301 2.1 24.2 1.0
NE2 E:HIS240 2.2 24.2 1.0
O E:HOH538 2.5 29.7 1.0
C4D E:HEM301 3.0 24.6 1.0
C1D E:HEM301 3.0 23.9 1.0
C4B E:HEM301 3.0 25.7 1.0
C1A E:HEM301 3.0 26.1 1.0
C4A E:HEM301 3.0 28.1 1.0
C1C E:HEM301 3.1 26.3 1.0
C4C E:HEM301 3.1 28.9 1.0
C1B E:HEM301 3.1 25.9 1.0
CE1 E:HIS240 3.1 28.1 1.0
CD2 E:HIS240 3.2 25.1 1.0
CHC E:HEM301 3.4 26.0 1.0
CHA E:HEM301 3.4 27.2 1.0
CHD E:HEM301 3.4 27.1 1.0
CHB E:HEM301 3.5 27.5 1.0
O2 E:KYN302 4.2 31.5 1.0
C2D E:HEM301 4.2 24.8 1.0
C3A E:HEM301 4.3 29.1 1.0
C2C E:HEM301 4.3 28.2 1.0
C3D E:HEM301 4.3 26.5 1.0
C2A E:HEM301 4.3 27.0 1.0
ND1 E:HIS240 4.3 24.3 1.0
C2B E:HEM301 4.3 25.6 1.0
C3C E:HEM301 4.3 28.9 1.0
C3B E:HEM301 4.3 25.6 1.0
CG E:HIS240 4.3 22.4 1.0
N1 E:KYN302 4.6 27.1 1.0
N E:KYN302 4.7 33.4 1.0
CG2 E:VAL244 4.7 27.7 1.0
N E:GLY125 4.9 31.6 1.0
C1 E:KYN302 5.0 29.1 1.0
CA E:GLY125 5.0 31.7 1.0

Iron binding site 6 out of 8 in 7p46

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Iron binding site 6 out of 8 in the Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe301

b:20.1
occ:1.00
FE F:HEM301 0.0 20.1 1.0
C F:CYN302 1.9 17.9 1.0
ND F:HEM301 2.0 18.1 1.0
NA F:HEM301 2.0 19.4 1.0
NC F:HEM301 2.0 18.1 1.0
NB F:HEM301 2.1 17.5 1.0
NE2 F:HIS240 2.1 19.4 1.0
C1D F:HEM301 3.0 20.2 1.0
C4D F:HEM301 3.0 21.5 1.0
C4B F:HEM301 3.0 19.3 1.0
CE1 F:HIS240 3.0 23.0 1.0
C1A F:HEM301 3.0 21.3 1.0
C4C F:HEM301 3.0 21.1 1.0
C4A F:HEM301 3.1 22.2 1.0
C1C F:HEM301 3.1 19.5 1.0
C1B F:HEM301 3.1 20.6 1.0
N F:CYN302 3.2 19.9 1.0
CD2 F:HIS240 3.2 22.8 1.0
CHD F:HEM301 3.4 21.0 1.0
CHC F:HEM301 3.4 20.0 1.0
CHA F:HEM301 3.5 20.9 1.0
CHB F:HEM301 3.5 20.2 1.0
ND1 F:HIS240 4.2 21.7 1.0
C2D F:HEM301 4.2 20.8 1.0
C3D F:HEM301 4.2 22.8 1.0
C2A F:HEM301 4.2 21.2 1.0
C3A F:HEM301 4.3 22.1 1.0
C3B F:HEM301 4.3 17.7 1.0
C2B F:HEM301 4.3 20.0 1.0
C2C F:HEM301 4.3 20.3 1.0
C3C F:HEM301 4.3 21.2 1.0
CG F:HIS240 4.3 19.3 1.0
O2 F:KYN303 4.4 23.8 1.0
CG2 F:VAL244 4.7 21.4 1.0
N1 F:KYN303 4.8 23.1 1.0
N F:KYN303 4.8 21.7 1.0
N F:GLY125 4.8 24.1 1.0
CA F:GLY125 4.9 23.7 1.0
C1 F:KYN303 5.0 22.0 1.0

Iron binding site 7 out of 8 in 7p46

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Iron binding site 7 out of 8 in the Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe301

b:25.2
occ:1.00
FE G:HEM301 0.0 25.2 1.0
ND G:HEM301 1.9 21.9 1.0
NA G:HEM301 2.0 20.9 1.0
NB G:HEM301 2.1 23.0 1.0
NC G:HEM301 2.1 23.1 1.0
NE2 G:HIS240 2.2 21.3 1.0
O G:HOH495 2.6 28.4 1.0
C4D G:HEM301 2.9 22.6 1.0
C1D G:HEM301 3.0 23.2 1.0
C1A G:HEM301 3.0 24.8 1.0
C4B G:HEM301 3.0 24.0 1.0
C4A G:HEM301 3.0 23.9 1.0
C1B G:HEM301 3.0 25.9 1.0
C4C G:HEM301 3.1 24.9 1.0
C1C G:HEM301 3.1 24.7 1.0
CE1 G:HIS240 3.1 23.8 1.0
CD2 G:HIS240 3.2 24.4 1.0
CHA G:HEM301 3.4 23.4 1.0
CHD G:HEM301 3.4 24.0 1.0
CHC G:HEM301 3.5 23.9 1.0
CHB G:HEM301 3.5 23.6 1.0
C2A G:HEM301 4.2 23.6 1.0
C3A G:HEM301 4.2 23.3 1.0
C3D G:HEM301 4.2 23.6 1.0
C2D G:HEM301 4.2 23.0 1.0
C2B G:HEM301 4.3 23.8 1.0
ND1 G:HIS240 4.3 23.5 1.0
C3B G:HEM301 4.3 23.1 1.0
C3C G:HEM301 4.3 27.7 1.0
C2C G:HEM301 4.3 25.1 1.0
CG G:HIS240 4.3 21.9 1.0
O2 G:KYN302 4.3 29.1 1.0
N1 G:KYN302 4.6 26.6 1.0
N G:KYN302 4.7 29.0 1.0
CG2 G:VAL244 4.7 23.3 1.0
N G:GLY125 4.9 28.7 1.0
CA G:GLY125 4.9 28.7 1.0
C1 G:KYN302 5.0 27.0 1.0
CA G:KYN302 5.0 26.7 1.0

Iron binding site 8 out of 8 in 7p46

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Iron binding site 8 out of 8 in the Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Xanthomonas Campestris Tryptophan 2,3-Dioxygenase (Tdo) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe301

b:21.7
occ:1.00
FE H:HEM301 0.0 21.7 1.0
ND H:HEM301 1.9 20.4 1.0
C H:CYN302 2.0 22.8 1.0
NA H:HEM301 2.0 21.3 1.0
NC H:HEM301 2.1 20.2 1.0
NB H:HEM301 2.1 20.5 1.0
CE1 H:HIS240 2.1 16.9 1.0
NE2 H:HIS240 2.9 23.0 1.0
C1D H:HEM301 3.0 21.1 1.0
C4D H:HEM301 3.0 21.5 1.0
C1A H:HEM301 3.0 22.9 1.0
C4B H:HEM301 3.0 22.2 1.0
C4C H:HEM301 3.1 21.7 1.0
C4A H:HEM301 3.1 24.4 1.0
C1B H:HEM301 3.1 25.1 1.0
C1C H:HEM301 3.1 22.4 1.0
N H:CYN302 3.2 22.6 1.0
ND1 H:HIS240 3.3 22.7 1.0
CHD H:HEM301 3.4 21.7 1.0
CHA H:HEM301 3.4 22.1 1.0
CHB H:HEM301 3.5 24.1 1.0
CHC H:HEM301 3.5 20.9 1.0
CD2 H:HIS240 4.1 18.3 1.0
C2A H:HEM301 4.2 24.0 1.0
C2D H:HEM301 4.2 19.9 1.0
C3A H:HEM301 4.3 24.1 1.0
C3D H:HEM301 4.3 21.1 1.0
C2B H:HEM301 4.3 23.4 1.0
C3C H:HEM301 4.3 22.1 1.0
C2C H:HEM301 4.3 21.8 1.0
CG H:HIS240 4.3 18.8 1.0
C3B H:HEM301 4.3 21.7 1.0
O2 H:KYN303 4.3 24.3 1.0
N1 H:KYN303 4.7 23.7 1.0
CG2 H:VAL244 4.7 22.1 1.0
N H:KYN303 4.7 24.1 1.0
N H:GLY125 4.9 24.2 1.0
C1 H:KYN303 5.0 23.7 1.0
CA H:GLY125 5.0 25.2 1.0

Reference:

J.Basran, E.S.Booth, L.P.Campbell, S.J.Thackray, M.H.Jesani, J.Clayden, P.C.E.Moody, C.G.Mowat, H.Kwon, E.L.Raven. Binding of L-Kynurenine to X. Campestris Tryptophan 2,3-Dioxygenase. J.Inorg.Biochem. V. 225 11604 2021.
ISSN: ISSN 0162-0134
PubMed: 34571402
DOI: 10.1016/J.JINORGBIO.2021.111604
Page generated: Thu Aug 8 14:56:21 2024

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