Potassium in PDB 9bnj: Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole
Enzymatic activity of Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole
All present enzymatic activity of Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole:
4.1.99.1;
Protein crystallography data
The structure of Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole, PDB code: 9bnj
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)
|
91.27 /
1.51
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
113.945,
118.225,
152.47,
90,
90,
90
|
|
R / Rfree (%)
|
15.8 /
18.1
|
Other elements in 9bnj:
The structure of Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole
(pdb code 9bnj). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole, PDB code: 9bnj:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 9bnj
Go back to
Potassium Binding Sites List in 9bnj
Potassium binding site 1 out
of 4 in the Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K501
b:21.5
occ:1.00
|
O
|
B:HOH743
|
2.7
|
19.2
|
1.0
|
|
OE1
|
B:GLU70
|
2.7
|
18.8
|
1.0
|
|
O
|
A:GLY53
|
2.8
|
17.1
|
1.0
|
|
O
|
A:HOH783
|
2.8
|
21.3
|
1.0
|
|
O
|
A:ASN271
|
2.9
|
17.0
|
1.0
|
|
HB3
|
B:GLU70
|
3.0
|
22.0
|
1.0
|
|
O
|
A:HOH799
|
3.1
|
20.2
|
1.0
|
|
O
|
B:GLU70
|
3.2
|
20.7
|
1.0
|
|
HB3
|
A:ASN271
|
3.2
|
19.4
|
1.0
|
|
HA3
|
A:GLY53
|
3.3
|
20.5
|
1.0
|
|
HA
|
B:ALA305
|
3.5
|
19.9
|
1.0
|
|
C
|
A:GLY53
|
3.6
|
17.1
|
1.0
|
|
H
|
B:GLY306
|
3.6
|
20.4
|
1.0
|
|
HA
|
B:GLU70
|
3.6
|
23.4
|
1.0
|
|
HA
|
A:ASN271
|
3.8
|
15.5
|
1.0
|
|
CB
|
B:GLU70
|
3.8
|
18.4
|
1.0
|
|
CD
|
B:GLU70
|
3.8
|
20.0
|
1.0
|
|
C
|
A:ASN271
|
3.9
|
14.3
|
1.0
|
|
CA
|
A:GLY53
|
3.9
|
17.1
|
1.0
|
|
C
|
B:GLU70
|
4.0
|
22.0
|
1.0
|
|
HE3
|
A:LYS265
|
4.0
|
20.5
|
1.0
|
|
CA
|
B:GLU70
|
4.0
|
19.5
|
1.0
|
|
CB
|
A:ASN271
|
4.1
|
16.1
|
1.0
|
|
CA
|
A:ASN271
|
4.1
|
12.9
|
1.0
|
|
HA2
|
A:GLY53
|
4.2
|
20.5
|
1.0
|
|
HD22
|
A:ASN271
|
4.2
|
21.6
|
1.0
|
|
CG
|
B:GLU70
|
4.3
|
19.1
|
1.0
|
|
O
|
B:HOH724
|
4.4
|
21.0
|
1.0
|
|
N
|
B:GLY306
|
4.4
|
17.0
|
1.0
|
|
CA
|
B:ALA305
|
4.4
|
16.6
|
1.0
|
|
HZ1
|
A:LYS265
|
4.5
|
23.2
|
1.0
|
|
HB2
|
B:GLU70
|
4.6
|
22.0
|
1.0
|
|
HG3
|
B:GLU70
|
4.6
|
23.0
|
1.0
|
|
HA
|
A:THR54
|
4.6
|
19.2
|
1.0
|
|
HB2
|
A:ASN271
|
4.7
|
19.4
|
1.0
|
|
N
|
A:THR54
|
4.7
|
16.9
|
1.0
|
|
HB1
|
B:ALA305
|
4.7
|
20.3
|
1.0
|
|
CE
|
A:LYS265
|
4.7
|
17.1
|
1.0
|
|
HE2
|
A:LYS265
|
4.8
|
20.5
|
1.0
|
|
ND2
|
A:ASN271
|
4.8
|
17.9
|
1.0
|
|
OE2
|
B:GLU70
|
4.9
|
18.5
|
1.0
|
|
HG22
|
A:THR54
|
4.9
|
27.9
|
1.0
|
|
O
|
B:LEU304
|
4.9
|
18.1
|
1.0
|
|
HB
|
A:ILE272
|
4.9
|
19.1
|
1.0
|
|
O
|
A:SER52
|
4.9
|
19.0
|
1.0
|
|
HB2
|
B:ALA305
|
4.9
|
20.3
|
1.0
|
|
HA
|
B:TYR72
|
4.9
|
24.9
|
1.0
|
|
CG
|
A:ASN271
|
5.0
|
15.4
|
1.0
|
|
C
|
B:ALA305
|
5.0
|
19.0
|
1.0
|
|
CB
|
B:ALA305
|
5.0
|
16.9
|
1.0
|
|
Potassium binding site 2 out
of 4 in 9bnj
Go back to
Potassium Binding Sites List in 9bnj
Potassium binding site 2 out
of 4 in the Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K506
b:19.1
occ:1.00
|
OE1
|
A:GLU70
|
2.7
|
16.7
|
1.0
|
|
O
|
A:HOH756
|
2.7
|
17.2
|
1.0
|
|
O
|
B:GLY53
|
2.8
|
14.9
|
1.0
|
|
O
|
B:ASN271
|
2.9
|
15.6
|
1.0
|
|
O
|
B:HOH739
|
2.9
|
20.1
|
1.0
|
|
HB3
|
A:GLU70
|
3.0
|
19.4
|
1.0
|
|
O
|
B:HOH811
|
3.1
|
18.9
|
1.0
|
|
HB3
|
B:ASN271
|
3.2
|
17.3
|
1.0
|
|
O
|
A:GLU70
|
3.2
|
17.1
|
1.0
|
|
HA3
|
B:GLY53
|
3.3
|
17.8
|
1.0
|
|
HA
|
A:ALA305
|
3.5
|
17.9
|
1.0
|
|
HA
|
A:GLU70
|
3.6
|
19.6
|
1.0
|
|
H
|
A:GLY306
|
3.6
|
19.2
|
1.0
|
|
C
|
B:GLY53
|
3.6
|
16.3
|
1.0
|
|
HA
|
B:ASN271
|
3.7
|
16.4
|
1.0
|
|
CB
|
A:GLU70
|
3.8
|
16.1
|
1.0
|
|
CD
|
A:GLU70
|
3.8
|
16.6
|
1.0
|
|
C
|
B:ASN271
|
3.9
|
13.7
|
1.0
|
|
CA
|
B:GLY53
|
3.9
|
14.8
|
1.0
|
|
HE3
|
B:LYS265
|
4.0
|
19.2
|
1.0
|
|
CA
|
A:GLU70
|
4.0
|
16.3
|
1.0
|
|
C
|
A:GLU70
|
4.0
|
17.9
|
1.0
|
|
CB
|
B:ASN271
|
4.0
|
14.4
|
1.0
|
|
CA
|
B:ASN271
|
4.1
|
13.7
|
1.0
|
|
HA2
|
B:GLY53
|
4.2
|
17.8
|
1.0
|
|
HD22
|
B:ASN271
|
4.3
|
19.3
|
1.0
|
|
CG
|
A:GLU70
|
4.3
|
17.9
|
1.0
|
|
O
|
A:HOH761
|
4.3
|
18.1
|
1.0
|
|
CA
|
A:ALA305
|
4.4
|
14.9
|
1.0
|
|
N
|
A:GLY306
|
4.4
|
16.0
|
1.0
|
|
HZ1
|
B:LYS265
|
4.5
|
20.6
|
1.0
|
|
HG3
|
A:GLU70
|
4.5
|
21.4
|
1.0
|
|
HB2
|
A:GLU70
|
4.6
|
19.4
|
1.0
|
|
HB2
|
B:ASN271
|
4.6
|
17.3
|
1.0
|
|
HB1
|
A:ALA305
|
4.6
|
18.1
|
1.0
|
|
HE2
|
B:LYS265
|
4.7
|
19.2
|
1.0
|
|
HA
|
B:THR54
|
4.7
|
17.8
|
1.0
|
|
CE
|
B:LYS265
|
4.7
|
16.0
|
1.0
|
|
N
|
B:THR54
|
4.7
|
14.2
|
1.0
|
|
OE2
|
A:GLU70
|
4.8
|
16.9
|
1.0
|
|
ND2
|
B:ASN271
|
4.9
|
16.1
|
1.0
|
|
O
|
B:SER52
|
4.9
|
17.6
|
1.0
|
|
HB
|
B:ILE272
|
4.9
|
20.2
|
1.0
|
|
HB2
|
A:ALA305
|
4.9
|
18.1
|
1.0
|
|
CB
|
A:ALA305
|
4.9
|
15.1
|
1.0
|
|
O
|
A:LEU304
|
4.9
|
17.2
|
1.0
|
|
C
|
A:ALA305
|
4.9
|
15.5
|
1.0
|
|
HG23
|
B:THR54
|
4.9
|
23.0
|
1.0
|
|
CG
|
B:ASN271
|
5.0
|
16.4
|
1.0
|
|
Potassium binding site 3 out
of 4 in 9bnj
Go back to
Potassium Binding Sites List in 9bnj
Potassium binding site 3 out
of 4 in the Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K501
b:20.1
occ:1.00
|
OE1
|
D:GLU70
|
2.7
|
20.2
|
1.0
|
|
O
|
D:HOH727
|
2.8
|
19.0
|
1.0
|
|
O
|
C:GLY53
|
2.8
|
17.1
|
1.0
|
|
O
|
C:ASN271
|
2.9
|
15.5
|
1.0
|
|
O
|
C:HOH761
|
2.9
|
20.6
|
1.0
|
|
HB3
|
D:GLU70
|
3.0
|
22.5
|
1.0
|
|
O
|
C:HOH735
|
3.0
|
19.0
|
1.0
|
|
O
|
D:GLU70
|
3.1
|
20.7
|
1.0
|
|
HB3
|
C:ASN271
|
3.2
|
20.5
|
1.0
|
|
HA3
|
C:GLY53
|
3.3
|
19.4
|
1.0
|
|
HA
|
D:ALA305
|
3.5
|
20.1
|
1.0
|
|
HA
|
D:GLU70
|
3.6
|
21.7
|
1.0
|
|
H
|
D:GLY306
|
3.6
|
20.1
|
1.0
|
|
C
|
C:GLY53
|
3.6
|
18.1
|
1.0
|
|
HA
|
C:ASN271
|
3.7
|
17.0
|
1.0
|
|
CB
|
D:GLU70
|
3.8
|
18.7
|
1.0
|
|
CD
|
D:GLU70
|
3.8
|
19.2
|
1.0
|
|
C
|
C:ASN271
|
3.9
|
14.4
|
1.0
|
|
C
|
D:GLU70
|
3.9
|
19.6
|
1.0
|
|
CA
|
C:GLY53
|
3.9
|
16.2
|
1.0
|
|
CA
|
D:GLU70
|
3.9
|
18.1
|
1.0
|
|
HE3
|
C:LYS265
|
4.0
|
20.6
|
1.0
|
|
CB
|
C:ASN271
|
4.0
|
17.1
|
1.0
|
|
CA
|
C:ASN271
|
4.1
|
14.2
|
1.0
|
|
HA2
|
C:GLY53
|
4.2
|
19.4
|
1.0
|
|
HD22
|
C:ASN271
|
4.2
|
20.2
|
1.0
|
|
HZ1
|
C:LYS265
|
4.3
|
23.6
|
1.0
|
|
O
|
D:HOH714
|
4.3
|
19.6
|
1.0
|
|
CG
|
D:GLU70
|
4.3
|
18.6
|
1.0
|
|
N
|
D:GLY306
|
4.4
|
16.8
|
1.0
|
|
CA
|
D:ALA305
|
4.4
|
16.7
|
1.0
|
|
HB2
|
D:GLU70
|
4.5
|
22.5
|
1.0
|
|
HG3
|
D:GLU70
|
4.6
|
22.4
|
1.0
|
|
HE2
|
C:LYS265
|
4.6
|
20.6
|
1.0
|
|
HB2
|
C:ASN271
|
4.7
|
20.5
|
1.0
|
|
HB1
|
D:ALA305
|
4.7
|
21.7
|
1.0
|
|
HA
|
C:THR54
|
4.7
|
20.5
|
1.0
|
|
CE
|
C:LYS265
|
4.7
|
17.1
|
1.0
|
|
N
|
C:THR54
|
4.7
|
17.6
|
1.0
|
|
OE2
|
D:GLU70
|
4.8
|
17.6
|
1.0
|
|
ND2
|
C:ASN271
|
4.9
|
16.9
|
1.0
|
|
HG22
|
C:THR54
|
4.9
|
26.1
|
1.0
|
|
HB2
|
D:ALA305
|
4.9
|
21.7
|
1.0
|
|
C
|
D:ALA305
|
4.9
|
16.6
|
1.0
|
|
O
|
D:LEU304
|
4.9
|
17.9
|
1.0
|
|
NZ
|
C:LYS265
|
4.9
|
19.7
|
1.0
|
|
HB
|
C:ILE272
|
4.9
|
19.1
|
1.0
|
|
CB
|
D:ALA305
|
5.0
|
18.1
|
1.0
|
|
O
|
C:SER52
|
5.0
|
20.7
|
1.0
|
|
CG
|
C:ASN271
|
5.0
|
18.3
|
1.0
|
|
HA
|
D:TYR72
|
5.0
|
23.2
|
1.0
|
|
Potassium binding site 4 out
of 4 in 9bnj
Go back to
Potassium Binding Sites List in 9bnj
Potassium binding site 4 out
of 4 in the Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Proteus Vulgaris Tryptophan Indole-Lyase Aminoacrylate Complex with Benzimidazole within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K504
b:19.6
occ:1.00
|
O
|
C:HOH767
|
2.7
|
18.4
|
1.0
|
|
OE1
|
C:GLU70
|
2.7
|
18.2
|
1.0
|
|
O
|
D:GLY53
|
2.8
|
15.9
|
1.0
|
|
O
|
D:HOH709
|
2.9
|
21.3
|
1.0
|
|
O
|
D:ASN271
|
2.9
|
14.7
|
1.0
|
|
O
|
D:HOH781
|
3.0
|
20.8
|
1.0
|
|
HB3
|
C:GLU70
|
3.1
|
22.5
|
1.0
|
|
O
|
C:GLU70
|
3.1
|
21.8
|
1.0
|
|
HB3
|
D:ASN271
|
3.2
|
18.7
|
1.0
|
|
HA3
|
D:GLY53
|
3.3
|
15.6
|
1.0
|
|
HA
|
C:ALA305
|
3.5
|
18.7
|
1.0
|
|
H
|
C:GLY306
|
3.6
|
19.8
|
1.0
|
|
C
|
D:GLY53
|
3.6
|
16.1
|
1.0
|
|
HA
|
C:GLU70
|
3.6
|
20.1
|
1.0
|
|
HA
|
D:ASN271
|
3.7
|
16.0
|
1.0
|
|
CB
|
C:GLU70
|
3.8
|
18.7
|
1.0
|
|
CD
|
C:GLU70
|
3.8
|
17.9
|
1.0
|
|
CA
|
D:GLY53
|
3.9
|
12.9
|
1.0
|
|
C
|
D:ASN271
|
3.9
|
13.2
|
1.0
|
|
C
|
C:GLU70
|
3.9
|
19.9
|
1.0
|
|
HE3
|
D:LYS265
|
4.0
|
20.6
|
1.0
|
|
CA
|
C:GLU70
|
4.0
|
16.8
|
1.0
|
|
CB
|
D:ASN271
|
4.0
|
15.5
|
1.0
|
|
CA
|
D:ASN271
|
4.1
|
13.3
|
1.0
|
|
HA2
|
D:GLY53
|
4.2
|
15.6
|
1.0
|
|
HD22
|
D:ASN271
|
4.2
|
20.4
|
1.0
|
|
O
|
C:HOH768
|
4.3
|
21.5
|
1.0
|
|
N
|
C:GLY306
|
4.4
|
16.5
|
1.0
|
|
HZ1
|
D:LYS265
|
4.4
|
22.6
|
1.0
|
|
CG
|
C:GLU70
|
4.4
|
19.7
|
1.0
|
|
CA
|
C:ALA305
|
4.4
|
15.6
|
1.0
|
|
HB2
|
C:GLU70
|
4.6
|
22.5
|
1.0
|
|
HG3
|
C:GLU70
|
4.6
|
23.7
|
1.0
|
|
HB2
|
D:ASN271
|
4.6
|
18.7
|
1.0
|
|
HB1
|
C:ALA305
|
4.7
|
20.5
|
1.0
|
|
HA
|
D:THR54
|
4.7
|
18.1
|
1.0
|
|
CE
|
D:LYS265
|
4.7
|
17.2
|
1.0
|
|
HE2
|
D:LYS265
|
4.7
|
20.6
|
1.0
|
|
N
|
D:THR54
|
4.7
|
16.1
|
1.0
|
|
ND2
|
D:ASN271
|
4.9
|
17.0
|
1.0
|
|
OE2
|
C:GLU70
|
4.9
|
19.0
|
1.0
|
|
HB2
|
C:ALA305
|
4.9
|
20.5
|
1.0
|
|
HG23
|
D:THR54
|
4.9
|
28.4
|
1.0
|
|
O
|
C:LEU304
|
4.9
|
18.3
|
1.0
|
|
O
|
D:SER52
|
4.9
|
19.1
|
1.0
|
|
CB
|
C:ALA305
|
4.9
|
17.1
|
1.0
|
|
C
|
C:ALA305
|
4.9
|
17.8
|
1.0
|
|
HA
|
C:TYR72
|
5.0
|
24.5
|
1.0
|
|
CG
|
D:ASN271
|
5.0
|
18.4
|
1.0
|
|
HB
|
D:ILE272
|
5.0
|
18.4
|
1.0
|
|
Reference:
R.S.Phillips,
R.S.Phillips.
N/A N/A.
Page generated: Sat Aug 9 18:29:39 2025
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