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Sodium in PDB 9dy7: Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+

Enzymatic activity of Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+

All present enzymatic activity of Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+:
4.1.99.1;

Protein crystallography data

The structure of Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+, PDB code: 9dy7 was solved by R.S.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.16 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 111.33, 113.676, 149.414, 90, 90, 90
R / Rfree (%) 15.6 / 18.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+ (pdb code 9dy7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+, PDB code: 9dy7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 9dy7

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Sodium binding site 1 out of 8 in the Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:19.7
occ:0.69
 NA B:NA501 0.0 19.7 0.7
NA B:NA501 1.1 20.2 0.3
O A:HOH882 2.4 57.5 1.0
O B:HOH731 2.5 44.1 1.0
OE1 B:GLU70 2.6 34.0 1.0
O B:HOH764 2.7 44.8 1.0
O A:ASN271 2.9 25.9 1.0
O A:GLY53 2.9 28.2 1.0
C A:GLY53 3.7 28.1 1.0
O B:GLU70 3.7 31.1 1.0
CD B:GLU70 3.7 35.4 1.0
C A:ASN271 3.8 26.4 1.0
CA A:GLY53 3.9 24.3 1.0
CB A:ASN271 3.9 24.9 1.0
CA A:ASN271 4.1 24.8 1.0
CA B:ALA305 4.2 31.9 1.0
CB B:GLU70 4.2 29.7 1.0
N B:GLY306 4.3 32.4 1.0
CA B:GLU70 4.4 26.1 1.0
CG B:GLU70 4.4 23.5 1.0
C B:GLU70 4.5 35.9 1.0
O B:HOH698 4.5 34.9 1.0
CB B:ALA305 4.6 30.9 1.0
OE2 B:GLU70 4.7 31.6 1.0
CE A:LYS265 4.7 30.5 1.0
N A:THR54 4.8 23.0 1.0
C B:ALA305 4.8 28.9 1.0
ND2 A:ASN271 4.8 28.4 1.0
O B:LEU304 4.9 39.4 1.0
CG A:ASN271 4.9 37.0 1.0
O A:SER52 5.0 30.4 1.0

Sodium binding site 2 out of 8 in 9dy7

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Sodium binding site 2 out of 8 in the Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:20.2
occ:0.31
 NA B:NA501 0.0 20.2 0.3
NA B:NA501 1.1 19.7 0.7
O B:HOH764 2.2 44.8 1.0
O B:HOH731 2.5 44.1 1.0
OE1 B:GLU70 2.6 34.0 1.0
O A:HOH882 2.6 57.5 1.0
O B:GLU70 2.7 31.1 1.0
O A:GLY53 3.0 28.2 1.0
C B:GLU70 3.5 35.9 1.0
CB B:GLU70 3.6 29.7 1.0
CA B:GLU70 3.6 26.1 1.0
CD B:GLU70 3.7 35.4 1.0
O B:HOH698 3.7 34.9 1.0
C A:GLY53 3.8 28.1 1.0
O A:ASN271 3.9 25.9 1.0
CG B:GLU70 4.2 23.5 1.0
CA A:GLY53 4.3 24.3 1.0
N B:GLY306 4.3 32.4 1.0
O B:ALA71 4.5 32.7 1.0
N B:ALA71 4.7 28.2 1.0
CB A:ASN271 4.7 24.9 1.0
CA B:ALA305 4.7 31.9 1.0
N A:THR54 4.7 23.0 1.0
C B:ALA71 4.7 33.7 1.0
CG2 A:THR54 4.8 22.1 1.0
OE2 B:GLU70 4.8 31.6 1.0
C A:ASN271 4.9 26.4 1.0
O A:SER52 4.9 30.4 1.0
CA A:ASN271 4.9 24.8 1.0

Sodium binding site 3 out of 8 in 9dy7

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Sodium binding site 3 out of 8 in the Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:27.0
occ:0.86
 NA B:NA502 0.0 27.0 0.9
NA B:NA502 0.1 27.7 0.1
O A:HOH860 2.4 41.2 1.0
O A:HOH692 2.5 45.0 1.0
OE1 A:GLU70 2.6 32.0 1.0
O B:HOH794 2.6 54.5 1.0
O B:GLY53 2.7 33.3 1.0
O A:GLU70 3.0 38.3 1.0
O B:ASN271 3.1 39.1 1.0
C B:GLY53 3.5 33.0 1.0
CD A:GLU70 3.7 32.4 1.0
CB A:GLU70 3.7 30.3 1.0
C A:GLU70 3.8 34.3 1.0
CA B:GLY53 3.9 26.1 1.0
CA A:GLU70 3.9 25.5 1.0
C B:ASN271 4.1 36.1 1.0
CB B:ASN271 4.1 31.8 1.0
O A:HOH714 4.2 32.6 1.0
CG A:GLU70 4.2 25.4 1.0
CA B:ASN271 4.3 32.9 1.0
CA A:ALA305 4.3 35.8 1.0
N A:GLY306 4.4 30.5 1.0
N B:THR54 4.6 32.4 1.0
ND2 B:ASN271 4.8 36.4 1.0
CB A:ALA305 4.8 33.9 1.0
OE2 A:GLU70 4.8 30.7 1.0
O B:SER52 4.9 40.1 1.0
C A:ALA305 4.9 34.1 1.0
CE B:LYS265 5.0 47.1 1.0
O A:ALA71 5.0 30.2 1.0
CG B:ASN271 5.0 32.6 1.0

Sodium binding site 4 out of 8 in 9dy7

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Sodium binding site 4 out of 8 in the Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:27.7
occ:0.14
 NA B:NA502 0.0 27.7 0.1
NA B:NA502 0.1 27.0 0.9
O A:HOH860 2.5 41.2 1.0
O A:HOH692 2.5 45.0 1.0
O B:HOH794 2.6 54.5 1.0
OE1 A:GLU70 2.6 32.0 1.0
O B:GLY53 2.6 33.3 1.0
O A:GLU70 3.0 38.3 1.0
O B:ASN271 3.1 39.1 1.0
C B:GLY53 3.5 33.0 1.0
CD A:GLU70 3.8 32.4 1.0
CB A:GLU70 3.8 30.3 1.0
CA B:GLY53 3.8 26.1 1.0
C A:GLU70 3.9 34.3 1.0
CA A:GLU70 4.0 25.5 1.0
C B:ASN271 4.1 36.1 1.0
CB B:ASN271 4.1 31.8 1.0
CA B:ASN271 4.2 32.9 1.0
CG A:GLU70 4.2 25.4 1.0
O A:HOH714 4.3 32.6 1.0
CA A:ALA305 4.4 35.8 1.0
N A:GLY306 4.4 30.5 1.0
N B:THR54 4.5 32.4 1.0
ND2 B:ASN271 4.7 36.4 1.0
CB A:ALA305 4.8 33.9 1.0
O B:SER52 4.8 40.1 1.0
OE2 A:GLU70 4.8 30.7 1.0
CE B:LYS265 4.9 47.1 1.0
C A:ALA305 5.0 34.1 1.0
CG B:ASN271 5.0 32.6 1.0
CA B:THR54 5.0 31.2 1.0

Sodium binding site 5 out of 8 in 9dy7

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Sodium binding site 5 out of 8 in the Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:17.4
occ:0.15
 NA D:NA501 0.0 17.4 0.1
NA D:NA501 0.8 20.0 0.8
O D:HOH719 2.3 33.8 1.0
O D:HOH735 2.4 34.9 1.0
O D:GLU70 2.5 29.4 1.0
O C:HOH873 2.7 43.4 1.0
OE1 D:GLU70 2.7 26.1 1.0
O C:GLY53 3.0 23.6 1.0
C D:GLU70 3.4 32.1 1.0
CB D:GLU70 3.6 23.8 1.0
O D:HOH706 3.6 27.7 1.0
CA D:GLU70 3.6 24.6 1.0
C C:GLY53 3.7 26.5 1.0
O C:ASN271 3.8 22.3 1.0
CD D:GLU70 3.8 31.8 1.0
CA C:GLY53 4.2 23.4 1.0
CG D:GLU70 4.3 24.6 1.0
N D:GLY306 4.3 23.9 1.0
O D:ALA71 4.5 24.9 1.0
CB C:ASN271 4.6 19.7 1.0
N D:ALA71 4.6 25.6 1.0
CA D:ALA305 4.6 26.1 1.0
N C:THR54 4.7 22.5 1.0
C C:ASN271 4.7 27.1 1.0
C D:ALA71 4.7 24.0 1.0
O C:SER52 4.8 25.9 1.0
CA C:ASN271 4.8 21.7 1.0
OE2 D:GLU70 4.9 26.7 1.0
CG2 C:THR54 4.9 26.6 1.0

Sodium binding site 6 out of 8 in 9dy7

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Sodium binding site 6 out of 8 in the Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:20.0
occ:0.85
 NA D:NA501 0.0 20.0 0.8
NA D:NA501 0.8 17.4 0.1
O D:HOH735 2.5 34.9 1.0
OE1 D:GLU70 2.5 26.1 1.0
O C:HOH873 2.7 43.4 1.0
O D:HOH719 2.7 33.8 1.0
O C:GLY53 2.8 23.6 1.0
O C:ASN271 3.0 22.3 1.0
O D:GLU70 3.3 29.4 1.0
C C:GLY53 3.6 26.5 1.0
CD D:GLU70 3.7 31.8 1.0
CA C:GLY53 3.9 23.4 1.0
C C:ASN271 3.9 27.1 1.0
CB D:GLU70 3.9 23.8 1.0
CB C:ASN271 4.0 19.7 1.0
CA C:ASN271 4.1 21.7 1.0
C D:GLU70 4.1 32.1 1.0
CA D:GLU70 4.2 24.6 1.0
O D:HOH706 4.2 27.7 1.0
CA D:ALA305 4.2 26.1 1.0
N D:GLY306 4.3 23.9 1.0
CG D:GLU70 4.3 24.6 1.0
N C:THR54 4.7 22.5 1.0
OE2 D:GLU70 4.7 26.7 1.0
CB D:ALA305 4.7 27.9 1.0
C D:ALA305 4.8 28.8 1.0
ND2 C:ASN271 4.8 27.1 1.0
CE C:LYS265 4.8 26.7 1.0
O C:SER52 4.9 25.9 1.0
O D:LEU304 4.9 31.3 1.0
CG C:ASN271 4.9 26.4 1.0

Sodium binding site 7 out of 8 in 9dy7

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Sodium binding site 7 out of 8 in the Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:21.9
occ:0.42
 NA D:NA502 0.0 21.9 0.4
NA D:NA502 0.8 20.6 0.6
O D:HOH807 2.4 52.8 1.0
O D:ASN271 2.5 30.5 1.0
O C:HOH803 2.6 39.5 1.0
O C:HOH641 2.7 45.6 1.0
OE1 C:GLU70 2.7 35.2 1.0
O D:GLY53 2.8 35.6 1.0
C D:ASN271 3.5 28.4 1.0
C D:GLY53 3.6 31.4 1.0
CA D:GLY53 3.7 27.3 1.0
O C:GLU70 3.8 29.7 1.0
CB D:ASN271 3.8 27.9 1.0
CD C:GLU70 3.9 34.1 1.0
CA D:ASN271 3.9 32.9 1.0
CA C:ALA305 4.1 31.2 1.0
CB C:GLU70 4.2 28.7 1.0
CE D:LYS265 4.4 32.6 1.0
N C:GLY306 4.5 35.2 1.0
CA C:GLU70 4.5 28.5 1.0
CB C:ALA305 4.5 35.4 1.0
CG C:GLU70 4.6 31.8 1.0
C C:GLU70 4.6 34.6 1.0
O C:HOH713 4.6 31.4 1.0
O C:LEU304 4.7 40.1 1.0
N D:ILE272 4.7 27.8 1.0
N D:THR54 4.8 29.1 1.0
NZ D:LYS265 4.8 48.0 1.0
OE2 C:GLU70 4.8 31.7 1.0
C C:ALA305 4.8 29.8 1.0
CG D:ASN271 4.9 41.2 1.0
ND2 D:ASN271 4.9 30.3 1.0
O D:SER52 4.9 34.3 1.0
N C:ALA305 5.0 33.4 1.0

Sodium binding site 8 out of 8 in 9dy7

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Sodium binding site 8 out of 8 in the Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Proteus Vulgaris Tryptophan Indole-Lyase Complexed with L-Ethionine and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:20.6
occ:0.59
 NA D:NA502 0.0 20.6 0.6
NA D:NA502 0.8 21.9 0.4
O C:HOH641 2.3 45.6 1.0
OE1 C:GLU70 2.4 35.2 1.0
O C:HOH803 2.5 39.5 1.0
O D:HOH807 2.6 52.8 1.0
O D:GLY53 2.7 35.6 1.0
O C:GLU70 3.0 29.7 1.0
O D:ASN271 3.3 30.5 1.0
CB C:GLU70 3.6 28.7 1.0
CD C:GLU70 3.6 34.1 1.0
C D:GLY53 3.6 31.4 1.0
C C:GLU70 3.7 34.6 1.0
CA C:GLU70 3.8 28.5 1.0
O C:HOH713 4.0 31.4 1.0
CA D:GLY53 4.0 27.3 1.0
CG C:GLU70 4.1 31.8 1.0
CB D:ASN271 4.2 27.9 1.0
C D:ASN271 4.2 28.4 1.0
N C:GLY306 4.3 35.2 1.0
CA D:ASN271 4.4 32.9 1.0
CA C:ALA305 4.4 31.2 1.0
N D:THR54 4.6 29.1 1.0
OE2 C:GLU70 4.6 31.7 1.0
CB C:ALA305 4.9 35.4 1.0
C C:ALA305 4.9 29.8 1.0
ND2 D:ASN271 4.9 30.3 1.0
O D:SER52 4.9 34.3 1.0
O C:LEU304 5.0 40.1 1.0
N C:ALA71 5.0 30.8 1.0
O C:ALA71 5.0 31.6 1.0

Reference:

R.S.Phillips, S.M.Brown. Structure and Dynamics of Proteus Vulgaris Tryptophan Indole-Lyase Complexes with L-Ethionine and L-Alanine. Arch.Biochem.Biophys. V. 768 10402 2025.
ISSN: ESSN 1096-0384
PubMed: 40147499
DOI: 10.1016/J.ABB.2025.110402
Page generated: Mon Aug 18 16:47:01 2025

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