Potassium in PDB 7pwy: Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025
Enzymatic activity of Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025
All present enzymatic activity of Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025:
4.1.1.45;
Protein crystallography data
The structure of Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025, PDB code: 7pwy
was solved by
M.Cianci,
N.Giacche,
A.Carotti,
P.Liscio,
A.Amici,
L.Cialabrini,
F.Defranco,
R.Pellicciari,
N.Raffaelli,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.33 /
2.50
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
153.41,
92.579,
103.97,
90,
90,
90
|
R / Rfree (%)
|
21.1 /
25.2
|
Other elements in 7pwy:
The structure of Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025 also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025
(pdb code 7pwy). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the
Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025, PDB code: 7pwy:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
Potassium binding site 1 out
of 6 in 7pwy
Go back to
Potassium Binding Sites List in 7pwy
Potassium binding site 1 out
of 6 in the Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K403
b:56.0
occ:1.00
|
O
|
A:LYS168
|
2.8
|
59.4
|
1.0
|
O
|
A:LEU328
|
2.8
|
40.0
|
1.0
|
O
|
A:PRO139
|
2.8
|
48.0
|
1.0
|
OG
|
A:SER170
|
2.8
|
57.6
|
1.0
|
O
|
A:HOH636
|
3.3
|
60.2
|
1.0
|
O
|
A:HOH619
|
3.5
|
53.2
|
1.0
|
C
|
A:LEU328
|
3.6
|
52.0
|
1.0
|
N
|
A:SER170
|
3.6
|
44.3
|
1.0
|
C
|
A:LYS168
|
3.7
|
51.8
|
1.0
|
C
|
A:PRO139
|
3.9
|
42.1
|
1.0
|
CB
|
A:SER170
|
4.0
|
48.8
|
1.0
|
CA
|
A:CYS169
|
4.1
|
53.2
|
1.0
|
CA
|
A:PRO139
|
4.2
|
34.8
|
1.0
|
CB
|
A:PRO139
|
4.2
|
43.2
|
1.0
|
N
|
A:CYS169
|
4.2
|
51.4
|
1.0
|
C
|
A:CYS169
|
4.2
|
49.3
|
1.0
|
CA
|
A:LEU328
|
4.3
|
42.8
|
1.0
|
N
|
A:GLY329
|
4.4
|
47.8
|
1.0
|
O
|
A:HOH542
|
4.4
|
46.3
|
1.0
|
CA
|
A:SER170
|
4.4
|
47.9
|
1.0
|
O
|
A:PHE327
|
4.4
|
50.9
|
1.0
|
CA
|
A:GLY329
|
4.5
|
49.9
|
1.0
|
CA
|
A:LYS168
|
4.8
|
57.2
|
1.0
|
CB
|
A:LYS168
|
4.8
|
55.7
|
1.0
|
|
Potassium binding site 2 out
of 6 in 7pwy
Go back to
Potassium Binding Sites List in 7pwy
Potassium binding site 2 out
of 6 in the Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K404
b:70.4
occ:1.00
|
O
|
A:HOH538
|
2.8
|
42.4
|
1.0
|
OE2
|
A:GLU298
|
2.9
|
43.6
|
1.0
|
OE1
|
A:GLU298
|
3.0
|
46.4
|
1.0
|
CA
|
A:GLY302
|
3.2
|
40.5
|
1.0
|
N
|
A:ILE305
|
3.3
|
36.3
|
1.0
|
CD
|
A:GLU298
|
3.3
|
43.4
|
1.0
|
N
|
A:GLY302
|
3.4
|
43.8
|
1.0
|
C
|
A:GLY302
|
3.4
|
40.9
|
1.0
|
N
|
A:LEU304
|
3.4
|
43.7
|
1.0
|
CB
|
A:LEU304
|
3.5
|
42.5
|
1.0
|
CG1
|
A:ILE305
|
3.7
|
39.9
|
1.0
|
N
|
A:LYS303
|
3.8
|
42.4
|
1.0
|
CD1
|
A:LEU288
|
3.8
|
41.0
|
1.0
|
CA
|
A:LEU304
|
3.8
|
38.5
|
1.0
|
CD1
|
A:ILE305
|
3.8
|
44.0
|
1.0
|
O
|
A:GLY302
|
3.9
|
46.4
|
1.0
|
O
|
A:HOH504
|
3.9
|
43.7
|
1.0
|
CB
|
A:ILE305
|
4.0
|
51.0
|
1.0
|
C
|
A:LEU304
|
4.0
|
42.7
|
1.0
|
CA
|
A:ILE305
|
4.2
|
49.1
|
1.0
|
C
|
A:LYS303
|
4.4
|
41.7
|
1.0
|
CG
|
A:LEU304
|
4.5
|
40.4
|
1.0
|
C
|
A:PRO301
|
4.6
|
44.5
|
1.0
|
CA
|
A:LYS303
|
4.7
|
46.2
|
1.0
|
CG
|
A:GLU298
|
4.8
|
41.5
|
1.0
|
CD2
|
A:LEU304
|
4.8
|
37.9
|
1.0
|
O
|
A:HOH562
|
4.9
|
41.1
|
1.0
|
|
Potassium binding site 3 out
of 6 in 7pwy
Go back to
Potassium Binding Sites List in 7pwy
Potassium binding site 3 out
of 6 in the Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K403
b:55.7
occ:1.00
|
O
|
B:LYS168
|
2.7
|
61.6
|
1.0
|
O
|
B:PRO139
|
2.8
|
58.5
|
1.0
|
O
|
B:LEU328
|
2.8
|
57.8
|
1.0
|
OG
|
B:SER170
|
2.9
|
57.0
|
1.0
|
C
|
B:LEU328
|
3.6
|
57.1
|
1.0
|
N
|
B:SER170
|
3.7
|
53.2
|
1.0
|
O
|
B:HOH542
|
3.7
|
62.9
|
1.0
|
C
|
B:LYS168
|
3.8
|
54.7
|
1.0
|
C
|
B:PRO139
|
3.8
|
49.2
|
1.0
|
CB
|
B:SER170
|
4.1
|
51.8
|
1.0
|
CA
|
B:PRO139
|
4.2
|
53.8
|
1.0
|
CA
|
B:CYS169
|
4.2
|
48.0
|
1.0
|
O
|
B:HOH548
|
4.3
|
51.8
|
1.0
|
C
|
B:CYS169
|
4.4
|
49.8
|
1.0
|
N
|
B:GLY329
|
4.4
|
56.6
|
1.0
|
CA
|
B:LEU328
|
4.4
|
57.8
|
1.0
|
N
|
B:CYS169
|
4.4
|
56.6
|
1.0
|
CB
|
B:PRO139
|
4.4
|
42.1
|
1.0
|
NZ
|
B:LYS219
|
4.4
|
80.7
|
1.0
|
CA
|
B:SER170
|
4.5
|
48.6
|
1.0
|
O
|
B:PHE327
|
4.5
|
56.8
|
1.0
|
CA
|
B:GLY329
|
4.5
|
49.9
|
1.0
|
CB
|
B:LYS168
|
4.8
|
62.3
|
1.0
|
CA
|
B:LYS168
|
4.9
|
49.0
|
1.0
|
N
|
B:GLY140
|
5.0
|
47.3
|
1.0
|
|
Potassium binding site 4 out
of 6 in 7pwy
Go back to
Potassium Binding Sites List in 7pwy
Potassium binding site 4 out
of 6 in the Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K404
b:81.0
occ:1.00
|
OE1
|
B:GLN120
|
2.7
|
59.4
|
0.3
|
O
|
B:HOH557
|
2.9
|
62.8
|
1.0
|
O
|
B:VAL147
|
3.1
|
45.0
|
1.0
|
OD1
|
B:ASN148
|
3.2
|
51.7
|
1.0
|
CB
|
B:ASN148
|
3.3
|
44.0
|
1.0
|
CE3
|
B:TRP150
|
3.4
|
43.4
|
1.0
|
CD2
|
B:TRP150
|
3.5
|
38.6
|
1.0
|
CG
|
B:ASN148
|
3.7
|
49.8
|
1.0
|
CZ3
|
B:TRP150
|
3.7
|
45.0
|
1.0
|
CE2
|
B:TRP150
|
3.8
|
44.4
|
1.0
|
CD
|
B:GLN120
|
3.9
|
52.9
|
0.3
|
C
|
B:VAL147
|
3.9
|
43.0
|
1.0
|
CG
|
B:TRP150
|
4.0
|
48.4
|
1.0
|
CH2
|
B:TRP150
|
4.0
|
44.7
|
1.0
|
CG1
|
B:VAL147
|
4.1
|
40.8
|
1.0
|
CZ2
|
B:TRP150
|
4.1
|
46.4
|
1.0
|
CA
|
B:ASN148
|
4.3
|
47.5
|
1.0
|
N
|
B:GLU149
|
4.4
|
48.1
|
1.0
|
N
|
B:ASN148
|
4.4
|
41.4
|
1.0
|
NE1
|
B:TRP150
|
4.4
|
38.8
|
1.0
|
CB
|
B:GLN120
|
4.5
|
47.5
|
0.7
|
CA
|
B:GLN120
|
4.6
|
61.7
|
0.7
|
CD1
|
B:TRP150
|
4.6
|
51.2
|
1.0
|
CA
|
B:GLN120
|
4.6
|
59.5
|
0.3
|
CB
|
B:VAL147
|
4.6
|
41.8
|
1.0
|
NE2
|
B:GLN120
|
4.6
|
48.5
|
0.3
|
CB
|
B:TRP150
|
4.6
|
42.1
|
1.0
|
O
|
B:HOH585
|
4.6
|
93.3
|
1.0
|
CB
|
B:GLN120
|
4.7
|
48.2
|
0.3
|
N
|
B:TRP150
|
4.7
|
53.3
|
1.0
|
C
|
B:ASN148
|
4.8
|
53.7
|
1.0
|
O
|
B:GLN120
|
4.8
|
55.0
|
1.0
|
CG
|
B:GLN120
|
4.9
|
51.1
|
0.3
|
CA
|
B:VAL147
|
4.9
|
35.7
|
1.0
|
ND2
|
B:ASN148
|
5.0
|
44.3
|
1.0
|
|
Potassium binding site 5 out
of 6 in 7pwy
Go back to
Potassium Binding Sites List in 7pwy
Potassium binding site 5 out
of 6 in the Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K402
b:79.5
occ:1.00
|
O
|
C:LYS168
|
2.7
|
85.7
|
1.0
|
O
|
C:LEU328
|
2.7
|
79.8
|
1.0
|
O
|
C:PRO139
|
2.8
|
70.8
|
1.0
|
OG
|
C:SER170
|
3.0
|
70.6
|
1.0
|
NZ
|
C:LYS219
|
3.5
|
88.2
|
1.0
|
C
|
C:LEU328
|
3.6
|
79.8
|
1.0
|
C
|
C:LYS168
|
3.7
|
84.0
|
1.0
|
N
|
C:SER170
|
3.7
|
71.8
|
1.0
|
C
|
C:PRO139
|
3.8
|
71.7
|
1.0
|
CB
|
C:SER170
|
4.0
|
68.1
|
1.0
|
CA
|
C:PRO139
|
4.1
|
72.8
|
1.0
|
CA
|
C:LEU328
|
4.2
|
73.0
|
1.0
|
CA
|
C:CYS169
|
4.2
|
68.9
|
1.0
|
C
|
C:CYS169
|
4.2
|
78.7
|
1.0
|
CE
|
C:LYS219
|
4.3
|
89.6
|
1.0
|
N
|
C:CYS169
|
4.4
|
77.3
|
1.0
|
CA
|
C:SER170
|
4.4
|
71.8
|
1.0
|
CB
|
C:PRO139
|
4.4
|
72.7
|
1.0
|
N
|
C:GLY329
|
4.5
|
75.7
|
1.0
|
O
|
C:PHE327
|
4.5
|
75.3
|
1.0
|
CA
|
C:GLY329
|
4.7
|
80.6
|
1.0
|
CB
|
C:LYS168
|
4.7
|
72.7
|
1.0
|
CA
|
C:LYS168
|
4.8
|
74.2
|
1.0
|
N
|
C:GLY140
|
4.9
|
61.6
|
1.0
|
|
Potassium binding site 6 out
of 6 in 7pwy
Go back to
Potassium Binding Sites List in 7pwy
Potassium binding site 6 out
of 6 in the Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Structure of Human Dimeric Acmsd in Complex with the Inhibitor Tes- 1025 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K402
b:82.9
occ:1.00
|
O
|
D:LYS168
|
2.7
|
76.7
|
1.0
|
O
|
D:LEU328
|
2.8
|
65.8
|
1.0
|
OG
|
D:SER170
|
3.0
|
67.3
|
1.0
|
O
|
D:PRO139
|
3.1
|
78.1
|
1.0
|
C
|
D:LEU328
|
3.5
|
68.0
|
1.0
|
C
|
D:LYS168
|
3.7
|
78.6
|
1.0
|
N
|
D:SER170
|
3.9
|
77.1
|
1.0
|
C
|
D:PRO139
|
4.1
|
78.7
|
1.0
|
N
|
D:GLY329
|
4.2
|
67.5
|
1.0
|
CB
|
D:SER170
|
4.2
|
74.4
|
1.0
|
CA
|
D:LEU328
|
4.2
|
60.1
|
1.0
|
O
|
D:PHE327
|
4.3
|
61.0
|
1.0
|
C
|
D:CYS169
|
4.3
|
77.3
|
1.0
|
CA
|
D:CYS169
|
4.3
|
71.7
|
1.0
|
N
|
D:CYS169
|
4.4
|
75.5
|
1.0
|
CA
|
D:GLY329
|
4.4
|
67.8
|
1.0
|
CB
|
D:PRO139
|
4.4
|
66.7
|
1.0
|
CA
|
D:PRO139
|
4.5
|
63.8
|
1.0
|
CA
|
D:SER170
|
4.5
|
72.4
|
1.0
|
CB
|
D:LYS168
|
4.7
|
73.5
|
1.0
|
CA
|
D:LYS168
|
4.7
|
84.3
|
1.0
|
O
|
D:GLY329
|
4.9
|
73.4
|
1.0
|
|
Reference:
M.Cianci,
N.Giacche,
L.Cialabrini,
A.Carotti,
P.Liscio,
E.Rosatelli,
F.De Franco,
M.Gasparrini,
J.Robertson,
A.Amici,
N.Raffaelli,
R.Pellicciari.
Structural Basis of Human Dimeric Alpha-Amino-Beta-Carboxymuconate-Epsilon-Semialdehyde Decarboxylase Inhibition with Tes-1025. Front Mol Biosci V. 9 34700 2022.
ISSN: ESSN 2296-889X
PubMed: 35463964
DOI: 10.3389/FMOLB.2022.834700
Page generated: Mon Aug 12 19:58:38 2024
|