Potassium in PDB 5w1b: Tryptophan Indole-Lyase

Enzymatic activity of Tryptophan Indole-Lyase

All present enzymatic activity of Tryptophan Indole-Lyase:
4.1.99.1;

Protein crystallography data

The structure of Tryptophan Indole-Lyase, PDB code: 5w1b was solved by R.S.Phillips, Z.A.Wood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.58 / 2.00
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.785, 152.577, 205.013, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.2

Potassium Binding Sites:

The binding sites of Potassium atom in the Tryptophan Indole-Lyase (pdb code 5w1b). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Tryptophan Indole-Lyase, PDB code: 5w1b:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5w1b

Go back to Potassium Binding Sites List in 5w1b
Potassium binding site 1 out of 4 in the Tryptophan Indole-Lyase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Tryptophan Indole-Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K501

b:42.1
occ:1.00
 OE2 B:GLU70 2.7 40.8 1.0
O B:HOH595 2.7 34.8 1.0
O A:GLY53 2.8 30.6 1.0
O A:HOH645 2.8 31.9 1.0
O A:HOH649 3.1 34.8 1.0
O A:ASN271 3.2 36.8 1.0
O B:GLU70 3.3 35.3 1.0
C A:GLY53 3.5 32.2 1.0
CA A:GLY53 3.8 31.1 1.0
CB B:GLU70 3.8 33.7 1.0
CD B:GLU70 3.8 40.9 1.0
CA B:GLU70 4.0 30.4 1.0
C B:GLU70 4.1 33.5 1.0
C A:ASN271 4.1 35.6 1.0
CB A:ASN271 4.1 42.8 1.0
O B:HOH609 4.2 28.6 1.0
CA A:ASN271 4.3 36.2 1.0
CG B:GLU70 4.3 33.6 1.0
N B:GLY306 4.5 33.9 1.0
CA B:ALA305 4.5 35.7 1.0
N A:THR54 4.6 30.7 1.0
O A:SER52 4.8 34.5 1.0
ND2 A:ASN271 4.8 35.1 1.0
CE A:LYS265 4.9 32.5 1.0
OE1 B:GLU70 4.9 37.9 1.0
O B:LEU304 4.9 33.3 1.0
CG A:ASN271 5.0 40.2 1.0
CB B:ALA305 5.0 24.9 1.0

Potassium binding site 2 out of 4 in 5w1b

Go back to Potassium Binding Sites List in 5w1b
Potassium binding site 2 out of 4 in the Tryptophan Indole-Lyase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Tryptophan Indole-Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:38.8
occ:1.00
 OE1 A:GLU70 2.8 33.3 1.0
O B:GLY53 2.9 33.1 1.0
O A:HOH640 2.9 32.1 1.0
O B:ASN271 2.9 29.9 1.0
O A:HOH695 3.0 35.2 1.0
O B:HOH647 3.0 31.9 1.0
O A:GLU70 3.4 35.0 1.0
C B:GLY53 3.6 28.1 1.0
CA B:GLY53 3.9 33.3 1.0
C B:ASN271 3.9 34.7 1.0
CB A:GLU70 3.9 40.2 1.0
CD A:GLU70 3.9 37.6 1.0
CB B:ASN271 4.0 33.8 1.0
CA B:ASN271 4.1 31.0 1.0
O A:HOH704 4.1 30.2 1.0
C A:GLU70 4.2 31.9 1.0
CA A:GLU70 4.2 35.1 1.0
CA A:ALA305 4.3 30.6 1.0
N A:GLY306 4.4 30.5 1.0
CG A:GLU70 4.4 35.0 1.0
N B:THR54 4.7 30.0 1.0
CB A:ALA305 4.7 27.9 1.0
ND2 B:ASN271 4.7 29.9 1.0
O A:LEU304 4.8 33.9 1.0
CG B:ASN271 4.8 33.5 1.0
C A:ALA305 4.9 31.7 1.0
CE B:LYS265 4.9 37.3 1.0
O B:SER52 4.9 28.5 1.0
OE2 A:GLU70 5.0 38.2 1.0

Potassium binding site 3 out of 4 in 5w1b

Go back to Potassium Binding Sites List in 5w1b
Potassium binding site 3 out of 4 in the Tryptophan Indole-Lyase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Tryptophan Indole-Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K501

b:39.3
occ:1.00
 OE1 C:GLU70 2.8 36.2 1.0
O D:GLY53 2.9 24.4 1.0
O C:HOH640 2.9 35.0 1.0
O C:HOH728 3.0 34.3 1.0
O D:HOH571 3.0 32.4 1.0
O D:ASN271 3.0 36.7 1.0
O C:GLU70 3.3 31.8 1.0
C D:GLY53 3.6 33.8 1.0
CA D:GLY53 3.9 30.5 1.0
CB C:GLU70 3.9 34.0 1.0
C D:ASN271 4.0 35.2 1.0
CD C:GLU70 4.0 45.8 1.0
C C:GLU70 4.1 33.6 1.0
CB D:ASN271 4.1 32.0 1.0
CA C:GLU70 4.1 34.1 1.0
O C:HOH692 4.1 31.7 1.0
CA D:ASN271 4.2 28.2 1.0
N C:GLY306 4.4 35.3 1.0
CA C:ALA305 4.4 31.5 1.0
CG C:GLU70 4.5 36.1 1.0
N D:THR54 4.7 28.9 1.0
O C:LEU304 4.8 39.7 1.0
CE D:LYS265 4.8 34.3 1.0
O D:SER52 4.9 31.9 1.0
ND2 D:ASN271 4.9 34.8 1.0
C C:ALA305 4.9 31.8 1.0
CB C:ALA305 5.0 24.4 1.0
CG D:ASN271 5.0 35.6 1.0

Potassium binding site 4 out of 4 in 5w1b

Go back to Potassium Binding Sites List in 5w1b
Potassium binding site 4 out of 4 in the Tryptophan Indole-Lyase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Tryptophan Indole-Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K502

b:34.3
occ:1.00
 O D:HOH586 2.7 31.1 1.0
OE1 D:GLU70 2.8 31.3 1.0
O C:GLY53 2.9 27.2 1.0
O C:ASN271 2.9 28.1 1.0
O C:HOH683 3.1 37.4 1.0
O C:HOH697 3.1 40.5 1.0
O D:GLU70 3.5 29.9 1.0
C C:GLY53 3.7 24.3 1.0
C C:ASN271 3.9 29.3 1.0
CA C:GLY53 3.9 29.1 1.0
CD D:GLU70 4.0 37.9 1.0
CB D:GLU70 4.0 30.7 1.0
CB C:ASN271 4.1 31.2 1.0
CA C:ASN271 4.2 29.6 1.0
O D:HOH589 4.3 30.2 1.0
CA D:GLU70 4.3 30.1 1.0
CA D:ALA305 4.3 30.1 1.0
C D:GLU70 4.3 27.6 1.0
N D:GLY306 4.4 32.3 1.0
CG D:GLU70 4.5 35.5 1.0
CB D:ALA305 4.7 31.6 1.0
CE C:LYS265 4.8 30.8 1.0
O D:LEU304 4.8 38.6 1.0
N C:THR54 4.8 28.9 1.0
ND2 C:ASN271 4.8 32.0 1.0
C D:ALA305 4.9 28.6 1.0
CG C:ASN271 4.9 33.4 1.0
O C:SER52 4.9 32.4 1.0
OE2 D:GLU70 5.0 38.6 1.0
NZ C:LYS265 5.0 36.0 1.0

Reference:

R.S.Phillips, A.A.Buisman, S.Choi, A.Hussaini, Z.A.Wood. The Crystal Structure of Proteus Vulgaris Tryptophan Indole-Lyase Complexed with Oxindolyl-L-Alanine: Implications For the Reaction Mechanism. Acta Crystallogr D Struct V. 74 748 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30082510
DOI: 10.1107/S2059798318003352
Page generated: Mon Dec 14 00:10:38 2020

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