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Magnesium in PDB 1yw0: Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13.

Enzymatic activity of Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13.

All present enzymatic activity of Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13.:
1.13.11.11;

Protein crystallography data

The structure of Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13., PDB code: 1yw0 was solved by S.M.Vorobiev, M.Abashidze, F.Forouhar, A.Kuzin, R.Xiao, M.Ciano, T.B.Aton, G.T.Montelione, J.F.Hunt, L.Tong, Northeaststructural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.32 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.701, 110.223, 149.398, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 29.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13. (pdb code 1yw0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13., PDB code: 1yw0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1yw0

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Magnesium binding site 1 out of 8 in the Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:10.2
occ:1.00
 N A:GLN38 2.8 21.9 1.0
O A:ALA36 2.9 16.4 1.0
O D:TYR27 2.9 16.9 1.0
CA A:GLN37 3.5 18.6 1.0
C A:GLN37 3.6 19.4 1.0
O D:LEU28 3.7 20.8 1.0
CA A:GLN38 3.7 23.7 1.0
C A:ALA36 3.8 16.6 1.0
C D:LEU28 3.9 21.6 1.0
CG2 A:ILE52 3.9 10.9 1.0
CA D:LEU28 3.9 20.1 1.0
CD1 A:ILE52 4.0 10.3 1.0
CB A:GLN38 4.0 25.2 1.0
C D:TYR27 4.0 17.3 1.0
C A:GLN38 4.0 24.2 1.0
O A:GLN38 4.0 23.8 1.0
N A:GLN37 4.1 18.1 1.0
CG D:ARG29 4.1 37.4 1.0
CG A:GLN38 4.2 29.1 1.0
O D:HOH535 4.2 10.9 1.0
N D:LEU28 4.4 18.6 1.0
NE2 A:GLN56 4.5 17.8 1.0
N D:ARG29 4.7 23.2 1.0
CB D:ARG29 4.7 29.2 1.0
CB A:GLN37 4.7 19.8 1.0
CG1 A:ILE52 4.8 11.7 1.0
O A:GLN37 4.8 18.0 1.0
N A:PRO39 4.8 24.4 1.0
CB A:ILE52 5.0 10.9 1.0

Magnesium binding site 2 out of 8 in 1yw0

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Magnesium binding site 2 out of 8 in the Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:19.2
occ:1.00
 N A:SER128 3.0 55.6 1.0
CA A:GLN127 3.0 66.7 1.0
C A:GLN127 3.4 61.8 1.0
CB A:GLN127 3.5 69.9 1.0
O A:PHE126 3.7 71.9 1.0
NH2 A:ARG132 3.9 53.4 1.0
CG A:GLN127 4.1 74.6 1.0
N A:GLN127 4.1 69.7 1.0
CA A:SER128 4.1 49.5 1.0
CB A:SER128 4.3 48.2 1.0
C A:PHE126 4.3 72.6 1.0
O A:SER128 4.5 46.6 1.0
CD2 A:TYR131 4.6 29.3 1.0
O A:GLN127 4.7 61.2 1.0
C A:SER128 4.8 46.5 1.0
CB A:TYR131 4.9 31.2 1.0
CG A:TYR131 4.9 29.6 1.0
CZ A:ARG132 5.0 51.8 1.0

Magnesium binding site 3 out of 8 in 1yw0

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Magnesium binding site 3 out of 8 in the Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:15.6
occ:1.00
 N B:GLN38 2.8 20.0 1.0
O B:ALA36 2.9 20.1 1.0
O C:TYR27 3.0 18.8 1.0
CG C:ARG29 3.5 14.0 1.0
CA B:GLN37 3.6 17.7 1.0
C B:GLN37 3.7 19.9 1.0
CA B:GLN38 3.7 19.5 1.0
C B:ALA36 3.8 18.5 1.0
CB B:GLN38 3.8 17.1 1.0
C C:LEU28 3.9 18.9 1.0
MG B:MG405 3.9 13.2 1.0
CG2 B:ILE52 3.9 10.9 1.0
CA C:LEU28 4.0 18.8 1.0
O C:LEU28 4.0 20.2 1.0
C C:TYR27 4.1 20.9 1.0
C B:GLN38 4.1 21.8 1.0
N B:GLN37 4.1 17.8 1.0
O B:GLN38 4.2 18.3 1.0
CB C:ARG29 4.2 13.3 1.0
N C:ARG29 4.3 15.9 1.0
CG B:GLN38 4.4 13.8 1.0
CD1 B:ILE52 4.4 9.2 1.0
NE2 B:GLN56 4.5 17.3 1.0
N C:LEU28 4.5 19.4 1.0
CD B:PRO39 4.6 30.6 1.0
CD C:ARG29 4.7 12.5 1.0
N B:PRO39 4.8 25.4 1.0
CB B:GLN37 4.9 16.0 1.0
O B:GLN37 4.9 20.3 1.0
CG1 B:ILE52 4.9 12.6 1.0
CA C:ARG29 4.9 14.6 1.0

Magnesium binding site 4 out of 8 in 1yw0

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Magnesium binding site 4 out of 8 in the Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:15.6
occ:1.00
 NE B:ARG246 2.7 18.9 1.0
OE1 D:GLU224 2.9 10.3 1.0
NH2 B:ARG246 3.0 15.2 1.0
CZ B:ARG246 3.3 18.1 1.0
NH2 D:ARG279 3.3 9.1 1.0
O B:LEU108 3.4 13.5 1.0
CD D:GLU224 3.7 9.6 1.0
O B:ARG246 3.8 20.8 1.0
O B:GLU106 3.8 16.6 1.0
CD B:ARG246 3.8 19.8 1.0
OE2 D:GLU224 3.8 8.4 1.0
CB B:ARG246 3.9 21.1 1.0
CG B:ARG246 3.9 21.4 1.0
CD B:PRO110 4.1 13.5 1.0
CA B:THR109 4.2 14.1 1.0
C B:ARG246 4.2 22.0 1.0
C B:LEU108 4.3 12.9 1.0
CZ D:ARG279 4.5 15.2 1.0
NH1 B:ARG246 4.6 17.2 1.0
N B:THR109 4.7 12.8 1.0
CA B:ARG246 4.7 20.8 1.0
CB B:THR109 4.8 15.6 1.0
NH1 D:ARG279 4.8 15.4 1.0
C B:GLU106 4.9 16.8 1.0
CG2 B:THR109 4.9 14.7 1.0
CG B:PRO110 4.9 14.3 1.0
CG1 D:VAL227 4.9 10.8 1.0
N B:VAL247 4.9 24.4 1.0

Magnesium binding site 5 out of 8 in 1yw0

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Magnesium binding site 5 out of 8 in the Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:13.2
occ:1.00
 O B:GLN38 2.9 18.3 1.0
O C:TYR27 3.0 18.8 1.0
CB B:GLN38 3.3 17.1 1.0
CD2 B:LEU40 3.7 27.6 1.0
C C:TYR27 3.8 20.9 1.0
CD1 C:TYR27 3.8 23.0 1.0
C B:GLN38 3.9 21.8 1.0
CA C:TYR27 3.9 22.2 1.0
MG B:MG403 3.9 15.6 1.0
O C:GLY26 4.1 21.6 1.0
CA B:GLN38 4.1 19.5 1.0
CG B:LEU40 4.3 28.8 1.0
CE1 C:TYR27 4.3 23.7 1.0
CG C:ARG29 4.4 14.0 1.0
CG B:GLN38 4.4 13.8 1.0
CD C:ARG29 4.4 12.5 1.0
CG C:TYR27 4.5 23.3 1.0
N B:GLN38 4.7 20.0 1.0
CB C:TYR27 4.7 22.8 1.0
N C:TYR27 4.9 21.4 1.0
C C:GLY26 4.9 21.5 1.0
N C:LEU28 5.0 19.4 1.0

Magnesium binding site 6 out of 8 in 1yw0

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Magnesium binding site 6 out of 8 in the Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg400

b:5.4
occ:1.00
 O C:ALA36 2.6 14.1 1.0
N C:GLN38 2.9 21.6 1.0
O B:TYR27 3.2 13.9 1.0
CA C:GLN37 3.3 18.9 1.0
O B:LEU28 3.5 17.7 1.0
C C:ALA36 3.6 15.6 1.0
C C:GLN37 3.6 19.3 1.0
C B:LEU28 3.8 19.1 1.0
CG2 C:ILE52 3.8 10.8 1.0
CA B:LEU28 3.9 18.1 1.0
N C:GLN37 3.9 17.4 1.0
CA C:GLN38 3.9 23.2 1.0
NE2 C:GLN56 3.9 18.6 1.0
CD1 C:ILE52 4.0 11.6 1.0
CG B:ARG29 4.1 31.7 1.0
C B:TYR27 4.2 15.7 1.0
CB C:GLN38 4.2 26.2 1.0
C C:GLN38 4.2 22.6 1.0
O C:GLN38 4.3 21.5 1.0
CG C:GLN38 4.5 31.1 1.0
CB C:GLN37 4.5 20.4 1.0
CB B:ARG29 4.5 25.3 1.0
N B:LEU28 4.5 16.7 1.0
N B:ARG29 4.5 21.0 1.0
O B:HOH569 4.6 28.3 1.0
CG1 C:ILE52 4.7 13.3 1.0
O C:GLN37 4.8 16.8 1.0
CB C:ILE52 4.9 11.8 1.0
CA C:ALA36 5.0 14.9 1.0
CD C:GLN56 5.0 19.1 1.0

Magnesium binding site 7 out of 8 in 1yw0

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Magnesium binding site 7 out of 8 in the Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg407

b:20.0
occ:1.00
 O C:GLN37 2.6 16.8 1.0
N C:GLN37 3.0 17.4 1.0
C C:SER35 3.1 16.6 1.0
CA C:SER35 3.2 16.4 1.0
C C:GLN37 3.2 19.3 1.0
O C:SER35 3.3 16.4 1.0
CA C:GLN37 3.4 18.9 1.0
NE2 C:GLN37 3.5 22.6 1.0
N C:ALA36 3.6 15.7 1.0
O C:LEU34 3.6 10.5 1.0
CB C:GLN37 3.7 20.4 1.0
OE1 C:GLN38 3.7 37.2 1.0
NZ B:LYS63 3.7 7.9 1.0
C C:ALA36 4.0 15.6 1.0
N C:SER35 4.1 13.7 1.0
CD C:GLN38 4.1 34.9 1.0
C C:LEU34 4.2 13.3 1.0
CB C:SER35 4.2 16.6 1.0
CA C:ALA36 4.4 14.9 1.0
CD C:GLN37 4.4 20.8 1.0
N C:GLN38 4.4 21.6 1.0
NE2 C:GLN38 4.5 37.2 1.0
CG C:GLN37 4.7 19.4 1.0
CG C:GLN38 4.8 31.1 1.0

Magnesium binding site 8 out of 8 in 1yw0

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Magnesium binding site 8 out of 8 in the Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:14.2
occ:1.00
 O D:GLN38 2.9 19.8 1.0
O A:TYR27 3.0 15.9 1.0
CB D:GLN38 3.3 15.1 1.0
C A:TYR27 3.8 18.0 1.0
CD1 A:TYR27 3.8 15.6 1.0
CA A:TYR27 3.9 18.3 1.0
C D:GLN38 3.9 19.6 1.0
CD2 D:LEU40 3.9 16.7 1.0
CG D:LEU40 4.0 20.5 1.0
CA D:GLN38 4.1 18.1 1.0
O A:GLY26 4.1 16.9 1.0
O D:HOH528 4.2 8.3 1.0
CD1 D:LEU40 4.2 19.6 1.0
CE1 A:TYR27 4.4 16.4 1.0
CG D:GLN38 4.4 11.9 1.0
CG A:TYR27 4.5 16.9 1.0
CG A:ARG29 4.6 16.9 1.0
N D:GLN38 4.7 18.1 1.0
CB A:TYR27 4.7 18.6 1.0
N A:TYR27 4.9 17.8 1.0
C A:GLY26 4.9 16.9 1.0
CD A:ARG29 5.0 14.1 1.0

Reference:

S.M.Vorobiev, M.Abashidze, F.Forouhar, A.Kuzin, R.Xiao, M.Ciano, T.B.Aton, G.T.Montelione, J.F.Hunt, L.Tong. Crystal Structure of the Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris. Northeast Structural Genomics Target XCR13. To Be Published.
Page generated: Mon Dec 14 07:10:41 2020

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