Potassium in PDB 3q9c: Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine
Protein crystallography data
The structure of Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine, PDB code: 3q9c
was solved by
P.M.Lombardi,
D.W.Christianson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
50.00 /
2.30
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.461,
120.154,
118.448,
98.47,
94.41,
115.89
|
|
R / Rfree (%)
|
18.6 /
22.7
|
Other elements in 3q9c:
The structure of Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine also contains other interesting chemical elements:
Potassium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Potassium atom in the Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine
(pdb code 3q9c). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 12 binding sites of Potassium where determined in the
Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine, PDB code: 3q9c:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Potassium binding site 1 out
of 12 in 3q9c
Go back to
Potassium Binding Sites List in 3q9c
Potassium binding site 1 out
of 12 in the Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K342
b:19.5
occ:1.00
|
O
|
A:ASP195
|
2.5
|
12.5
|
1.0
|
|
OD1
|
A:ASP193
|
2.6
|
18.7
|
1.0
|
|
O
|
A:LEU217
|
2.6
|
15.0
|
1.0
|
|
O
|
A:ASP193
|
2.8
|
16.5
|
1.0
|
|
O
|
A:HIS197
|
2.8
|
13.1
|
1.0
|
|
OG
|
A:SER216
|
2.9
|
9.7
|
1.0
|
|
CG
|
A:ASP193
|
3.2
|
19.4
|
1.0
|
|
C
|
A:ASP193
|
3.5
|
15.2
|
1.0
|
|
C
|
A:ASP195
|
3.6
|
12.3
|
1.0
|
|
C
|
A:LEU217
|
3.6
|
14.2
|
1.0
|
|
N
|
A:ASP195
|
3.6
|
16.0
|
1.0
|
|
CB
|
A:ASP193
|
3.7
|
17.8
|
1.0
|
|
C
|
A:HIS197
|
3.7
|
12.8
|
1.0
|
|
N
|
A:LEU217
|
3.8
|
13.9
|
1.0
|
|
CB
|
A:HIS218
|
3.9
|
12.0
|
1.0
|
|
CB
|
A:SER216
|
4.0
|
12.6
|
1.0
|
|
CA
|
A:ASP195
|
4.1
|
13.3
|
1.0
|
|
C
|
A:VAL194
|
4.1
|
14.9
|
1.0
|
|
OD2
|
A:ASP193
|
4.1
|
21.2
|
1.0
|
|
CA
|
A:HIS198
|
4.1
|
16.8
|
1.0
|
|
N
|
A:VAL194
|
4.2
|
14.2
|
1.0
|
|
CB
|
A:ASP195
|
4.2
|
16.4
|
1.0
|
|
CA
|
A:ASP193
|
4.2
|
16.1
|
1.0
|
|
N
|
A:HIS198
|
4.3
|
14.4
|
1.0
|
|
CA
|
A:VAL194
|
4.3
|
14.0
|
1.0
|
|
ND1
|
A:HIS218
|
4.3
|
11.1
|
1.0
|
|
N
|
A:GLY199
|
4.3
|
15.2
|
1.0
|
|
CA
|
A:SER216
|
4.4
|
13.3
|
1.0
|
|
CA
|
A:HIS218
|
4.4
|
14.6
|
1.0
|
|
CA
|
A:LEU217
|
4.4
|
14.8
|
1.0
|
|
C
|
A:SER216
|
4.4
|
13.9
|
1.0
|
|
N
|
A:HIS218
|
4.4
|
13.5
|
1.0
|
|
O
|
A:HOH347
|
4.5
|
13.5
|
1.0
|
|
C
|
A:HIS198
|
4.5
|
16.5
|
1.0
|
|
CG
|
A:HIS218
|
4.5
|
10.9
|
1.0
|
|
C
|
A:PHE196
|
4.5
|
12.2
|
1.0
|
|
N
|
A:HIS197
|
4.6
|
10.9
|
1.0
|
|
O
|
A:PHE196
|
4.7
|
14.3
|
1.0
|
|
N
|
A:PHE196
|
4.7
|
11.2
|
1.0
|
|
O
|
A:VAL194
|
4.7
|
14.3
|
1.0
|
|
CA
|
A:HIS197
|
4.8
|
12.1
|
1.0
|
|
OD1
|
A:ASP195
|
5.0
|
18.1
|
1.0
|
|
Potassium binding site 2 out
of 12 in 3q9c
Go back to
Potassium Binding Sites List in 3q9c
Potassium binding site 2 out
of 12 in the Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K342
b:25.2
occ:1.00
|
OD1
|
B:ASP193
|
2.5
|
20.1
|
1.0
|
|
O
|
B:ASP195
|
2.6
|
20.3
|
1.0
|
|
O
|
B:LEU217
|
2.6
|
17.4
|
1.0
|
|
O
|
B:HIS197
|
2.7
|
19.6
|
1.0
|
|
O
|
B:ASP193
|
2.9
|
19.1
|
1.0
|
|
OG
|
B:SER216
|
3.0
|
14.9
|
1.0
|
|
CG
|
B:ASP193
|
3.2
|
22.3
|
1.0
|
|
C
|
B:ASP195
|
3.5
|
20.9
|
1.0
|
|
C
|
B:ASP193
|
3.6
|
18.8
|
1.0
|
|
C
|
B:LEU217
|
3.6
|
17.5
|
1.0
|
|
C
|
B:HIS197
|
3.7
|
18.3
|
1.0
|
|
N
|
B:ASP195
|
3.7
|
20.0
|
1.0
|
|
CB
|
B:ASP193
|
3.7
|
19.5
|
1.0
|
|
CB
|
B:HIS218
|
3.8
|
12.9
|
1.0
|
|
N
|
B:LEU217
|
3.9
|
16.9
|
1.0
|
|
CA
|
B:ASP195
|
4.0
|
20.5
|
1.0
|
|
OD2
|
B:ASP193
|
4.1
|
22.4
|
1.0
|
|
C
|
B:VAL194
|
4.1
|
20.6
|
1.0
|
|
CB
|
B:SER216
|
4.1
|
16.0
|
1.0
|
|
CA
|
B:HIS198
|
4.1
|
17.9
|
1.0
|
|
CB
|
B:ASP195
|
4.2
|
22.5
|
1.0
|
|
N
|
B:VAL194
|
4.2
|
19.6
|
1.0
|
|
ND1
|
B:HIS218
|
4.3
|
10.0
|
1.0
|
|
N
|
B:GLY199
|
4.3
|
17.1
|
1.0
|
|
CA
|
B:ASP193
|
4.3
|
19.5
|
1.0
|
|
N
|
B:HIS198
|
4.3
|
18.4
|
1.0
|
|
CA
|
B:HIS218
|
4.4
|
15.7
|
1.0
|
|
N
|
B:HIS218
|
4.4
|
15.9
|
1.0
|
|
CA
|
B:VAL194
|
4.4
|
19.7
|
1.0
|
|
C
|
B:HIS198
|
4.5
|
18.0
|
1.0
|
|
N
|
B:HIS197
|
4.5
|
16.8
|
1.0
|
|
CA
|
B:LEU217
|
4.5
|
17.2
|
1.0
|
|
C
|
B:PHE196
|
4.5
|
19.2
|
1.0
|
|
CG
|
B:HIS218
|
4.5
|
11.4
|
1.0
|
|
CA
|
B:SER216
|
4.5
|
17.7
|
1.0
|
|
C
|
B:SER216
|
4.6
|
18.5
|
1.0
|
|
N
|
B:PHE196
|
4.6
|
20.0
|
1.0
|
|
OD1
|
B:ASP195
|
4.7
|
24.2
|
1.0
|
|
O
|
B:PHE196
|
4.7
|
19.3
|
1.0
|
|
O
|
B:HOH350
|
4.7
|
12.8
|
1.0
|
|
CA
|
B:HIS197
|
4.7
|
17.3
|
1.0
|
|
O
|
B:VAL194
|
4.8
|
22.0
|
1.0
|
|
ND1
|
B:HIS158
|
4.9
|
23.5
|
1.0
|
|
CE1
|
B:HIS158
|
4.9
|
22.4
|
1.0
|
|
CG
|
B:ASP195
|
5.0
|
25.8
|
1.0
|
|
CA
|
B:PHE196
|
5.0
|
19.2
|
1.0
|
|
Potassium binding site 3 out
of 12 in 3q9c
Go back to
Potassium Binding Sites List in 3q9c
Potassium binding site 3 out
of 12 in the Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K342
b:18.4
occ:1.00
|
OD1
|
C:ASP193
|
2.4
|
16.1
|
1.0
|
|
O
|
C:ASP195
|
2.5
|
14.8
|
1.0
|
|
O
|
C:LEU217
|
2.6
|
14.5
|
1.0
|
|
O
|
C:HIS197
|
2.8
|
16.4
|
1.0
|
|
O
|
C:ASP193
|
2.9
|
14.5
|
1.0
|
|
OG
|
C:SER216
|
2.9
|
11.9
|
1.0
|
|
CG
|
C:ASP193
|
3.2
|
17.1
|
1.0
|
|
C
|
C:ASP193
|
3.5
|
13.9
|
1.0
|
|
C
|
C:ASP195
|
3.5
|
14.8
|
1.0
|
|
N
|
C:ASP195
|
3.6
|
16.0
|
1.0
|
|
C
|
C:LEU217
|
3.7
|
12.6
|
1.0
|
|
C
|
C:HIS197
|
3.7
|
16.1
|
1.0
|
|
CB
|
C:ASP193
|
3.8
|
13.6
|
1.0
|
|
CB
|
C:HIS218
|
3.9
|
10.1
|
1.0
|
|
N
|
C:LEU217
|
3.9
|
11.9
|
1.0
|
|
OD2
|
C:ASP193
|
4.0
|
15.5
|
1.0
|
|
CA
|
C:ASP195
|
4.0
|
14.7
|
1.0
|
|
C
|
C:VAL194
|
4.0
|
17.1
|
1.0
|
|
N
|
C:VAL194
|
4.1
|
16.4
|
1.0
|
|
CB
|
C:ASP195
|
4.2
|
17.9
|
1.0
|
|
CA
|
C:HIS198
|
4.2
|
17.4
|
1.0
|
|
CB
|
C:SER216
|
4.2
|
10.8
|
1.0
|
|
CA
|
C:ASP193
|
4.2
|
14.3
|
1.0
|
|
CA
|
C:VAL194
|
4.3
|
16.3
|
1.0
|
|
ND1
|
C:HIS218
|
4.3
|
5.9
|
1.0
|
|
N
|
C:HIS198
|
4.4
|
16.9
|
1.0
|
|
N
|
C:GLY199
|
4.4
|
16.3
|
1.0
|
|
CA
|
C:HIS218
|
4.4
|
11.8
|
1.0
|
|
N
|
C:HIS218
|
4.5
|
11.8
|
1.0
|
|
C
|
C:PHE196
|
4.5
|
16.7
|
1.0
|
|
CA
|
C:LEU217
|
4.5
|
12.6
|
1.0
|
|
C
|
C:SER216
|
4.5
|
12.1
|
1.0
|
|
CA
|
C:SER216
|
4.5
|
11.6
|
1.0
|
|
C
|
C:HIS198
|
4.6
|
17.2
|
1.0
|
|
N
|
C:HIS197
|
4.6
|
14.1
|
1.0
|
|
CG
|
C:HIS218
|
4.6
|
4.3
|
1.0
|
|
O
|
C:PHE196
|
4.6
|
15.7
|
1.0
|
|
N
|
C:PHE196
|
4.6
|
13.1
|
1.0
|
|
O
|
C:VAL194
|
4.7
|
17.5
|
1.0
|
|
OD1
|
C:ASP195
|
4.7
|
20.1
|
1.0
|
|
O
|
C:HOH360
|
4.7
|
12.4
|
1.0
|
|
CA
|
C:HIS197
|
4.8
|
15.0
|
1.0
|
|
CE1
|
C:HIS158
|
4.8
|
20.2
|
1.0
|
|
ND1
|
C:HIS158
|
4.9
|
21.6
|
1.0
|
|
CG
|
C:ASP195
|
5.0
|
19.9
|
1.0
|
|
Potassium binding site 4 out
of 12 in 3q9c
Go back to
Potassium Binding Sites List in 3q9c
Potassium binding site 4 out
of 12 in the Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K342
b:20.2
occ:1.00
|
OD1
|
D:ASP193
|
2.6
|
23.0
|
1.0
|
|
O
|
D:ASP195
|
2.7
|
15.9
|
1.0
|
|
O
|
D:HIS197
|
2.8
|
19.2
|
1.0
|
|
O
|
D:LEU217
|
2.8
|
16.9
|
1.0
|
|
O
|
D:ASP193
|
2.8
|
21.6
|
1.0
|
|
OG
|
D:SER216
|
2.9
|
16.9
|
1.0
|
|
CG
|
D:ASP193
|
3.1
|
23.1
|
1.0
|
|
C
|
D:ASP193
|
3.4
|
20.0
|
1.0
|
|
CB
|
D:ASP193
|
3.5
|
20.3
|
1.0
|
|
C
|
D:ASP195
|
3.7
|
16.1
|
1.0
|
|
C
|
D:LEU217
|
3.7
|
15.7
|
1.0
|
|
N
|
D:ASP195
|
3.8
|
16.8
|
1.0
|
|
C
|
D:HIS197
|
3.8
|
18.5
|
1.0
|
|
CB
|
D:HIS218
|
3.9
|
14.9
|
1.0
|
|
N
|
D:LEU217
|
4.0
|
15.6
|
1.0
|
|
OD2
|
D:ASP193
|
4.0
|
24.1
|
1.0
|
|
CB
|
D:SER216
|
4.0
|
16.8
|
1.0
|
|
CA
|
D:ASP193
|
4.1
|
20.2
|
1.0
|
|
CA
|
D:HIS198
|
4.2
|
16.8
|
1.0
|
|
N
|
D:VAL194
|
4.2
|
18.7
|
1.0
|
|
CA
|
D:ASP195
|
4.2
|
16.7
|
1.0
|
|
C
|
D:VAL194
|
4.2
|
20.1
|
1.0
|
|
N
|
D:GLY199
|
4.2
|
17.9
|
1.0
|
|
CB
|
D:ASP195
|
4.2
|
17.6
|
1.0
|
|
ND1
|
D:HIS218
|
4.4
|
13.1
|
1.0
|
|
N
|
D:HIS198
|
4.4
|
17.6
|
1.0
|
|
C
|
D:HIS198
|
4.5
|
16.7
|
1.0
|
|
CA
|
D:VAL194
|
4.5
|
20.1
|
1.0
|
|
CA
|
D:HIS218
|
4.5
|
16.3
|
1.0
|
|
CA
|
D:SER216
|
4.5
|
17.6
|
1.0
|
|
N
|
D:HIS218
|
4.5
|
14.9
|
1.0
|
|
C
|
D:SER216
|
4.6
|
17.7
|
1.0
|
|
CA
|
D:LEU217
|
4.6
|
15.3
|
1.0
|
|
CG
|
D:HIS218
|
4.6
|
14.3
|
1.0
|
|
N
|
D:HIS197
|
4.7
|
16.9
|
1.0
|
|
O
|
D:HOH346
|
4.7
|
14.0
|
1.0
|
|
C
|
D:PHE196
|
4.7
|
17.5
|
1.0
|
|
CE1
|
D:HIS158
|
4.8
|
19.6
|
1.0
|
|
ND1
|
D:HIS158
|
4.8
|
22.3
|
1.0
|
|
N
|
D:PHE196
|
4.8
|
16.3
|
1.0
|
|
CA
|
D:HIS197
|
4.9
|
18.5
|
1.0
|
|
O
|
D:PHE196
|
4.9
|
17.3
|
1.0
|
|
O
|
D:VAL194
|
4.9
|
19.9
|
1.0
|
|
OD1
|
D:ASP195
|
4.9
|
18.6
|
1.0
|
|
Potassium binding site 5 out
of 12 in 3q9c
Go back to
Potassium Binding Sites List in 3q9c
Potassium binding site 5 out
of 12 in the Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K342
b:20.4
occ:1.00
|
O
|
E:ASP195
|
2.6
|
19.5
|
1.0
|
|
O
|
E:LEU217
|
2.7
|
19.9
|
1.0
|
|
OD1
|
E:ASP193
|
2.7
|
25.1
|
1.0
|
|
O
|
E:HIS197
|
2.7
|
18.5
|
1.0
|
|
OG
|
E:SER216
|
2.9
|
18.9
|
1.0
|
|
O
|
E:ASP193
|
3.0
|
17.5
|
1.0
|
|
CG
|
E:ASP193
|
3.3
|
22.0
|
1.0
|
|
C
|
E:ASP193
|
3.6
|
19.3
|
1.0
|
|
C
|
E:LEU217
|
3.6
|
18.7
|
1.0
|
|
C
|
E:ASP195
|
3.6
|
19.1
|
1.0
|
|
C
|
E:HIS197
|
3.7
|
17.5
|
1.0
|
|
CB
|
E:ASP193
|
3.8
|
20.1
|
1.0
|
|
N
|
E:ASP195
|
3.8
|
21.3
|
1.0
|
|
CB
|
E:HIS218
|
3.8
|
14.6
|
1.0
|
|
N
|
E:LEU217
|
3.9
|
18.3
|
1.0
|
|
OD2
|
E:ASP193
|
4.0
|
21.8
|
1.0
|
|
CA
|
E:HIS198
|
4.1
|
18.7
|
1.0
|
|
CB
|
E:SER216
|
4.1
|
19.2
|
1.0
|
|
CA
|
E:ASP195
|
4.1
|
20.5
|
1.0
|
|
C
|
E:VAL194
|
4.2
|
21.4
|
1.0
|
|
CB
|
E:ASP195
|
4.2
|
21.2
|
1.0
|
|
N
|
E:GLY199
|
4.3
|
20.7
|
1.0
|
|
N
|
E:VAL194
|
4.3
|
19.5
|
1.0
|
|
CA
|
E:HIS218
|
4.3
|
18.0
|
1.0
|
|
N
|
E:HIS198
|
4.3
|
17.6
|
1.0
|
|
CA
|
E:ASP193
|
4.3
|
19.3
|
1.0
|
|
N
|
E:HIS218
|
4.3
|
17.9
|
1.0
|
|
ND1
|
E:HIS218
|
4.3
|
14.0
|
1.0
|
|
C
|
E:HIS198
|
4.4
|
19.6
|
1.0
|
|
CA
|
E:LEU217
|
4.5
|
18.6
|
1.0
|
|
C
|
E:SER216
|
4.5
|
18.7
|
1.0
|
|
CA
|
E:SER216
|
4.5
|
18.5
|
1.0
|
|
CG
|
E:HIS218
|
4.5
|
14.0
|
1.0
|
|
CA
|
E:VAL194
|
4.5
|
20.6
|
1.0
|
|
C
|
E:PHE196
|
4.5
|
18.7
|
1.0
|
|
N
|
E:HIS197
|
4.6
|
17.4
|
1.0
|
|
O
|
E:PHE196
|
4.7
|
20.4
|
1.0
|
|
O
|
E:HOH349
|
4.7
|
15.0
|
1.0
|
|
N
|
E:PHE196
|
4.7
|
17.8
|
1.0
|
|
CA
|
E:HIS197
|
4.8
|
17.3
|
1.0
|
|
O
|
E:VAL194
|
4.8
|
24.4
|
1.0
|
|
OD1
|
E:ASP195
|
4.9
|
22.1
|
1.0
|
|
Potassium binding site 6 out
of 12 in 3q9c
Go back to
Potassium Binding Sites List in 3q9c
Potassium binding site 6 out
of 12 in the Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:K342
b:20.3
occ:1.00
|
OD1
|
F:ASP193
|
2.6
|
23.1
|
1.0
|
|
O
|
F:LEU217
|
2.6
|
14.2
|
1.0
|
|
O
|
F:HIS197
|
2.6
|
17.7
|
1.0
|
|
O
|
F:ASP195
|
2.6
|
18.5
|
1.0
|
|
O
|
F:ASP193
|
2.9
|
19.6
|
1.0
|
|
OG
|
F:SER216
|
3.0
|
18.6
|
1.0
|
|
CG
|
F:ASP193
|
3.3
|
23.0
|
1.0
|
|
C
|
F:HIS197
|
3.6
|
18.6
|
1.0
|
|
C
|
F:ASP193
|
3.6
|
19.8
|
1.0
|
|
C
|
F:LEU217
|
3.6
|
16.0
|
1.0
|
|
C
|
F:ASP195
|
3.6
|
17.7
|
1.0
|
|
CB
|
F:ASP193
|
3.8
|
18.2
|
1.0
|
|
N
|
F:ASP195
|
3.8
|
18.9
|
1.0
|
|
CB
|
F:HIS218
|
3.8
|
15.1
|
1.0
|
|
N
|
F:LEU217
|
3.9
|
16.5
|
1.0
|
|
CA
|
F:HIS198
|
4.0
|
20.0
|
1.0
|
|
ND1
|
F:HIS218
|
4.1
|
17.3
|
1.0
|
|
OD2
|
F:ASP193
|
4.1
|
23.9
|
1.0
|
|
N
|
F:HIS198
|
4.2
|
19.2
|
1.0
|
|
CA
|
F:ASP195
|
4.2
|
17.9
|
1.0
|
|
C
|
F:VAL194
|
4.2
|
20.3
|
1.0
|
|
CB
|
F:SER216
|
4.2
|
18.2
|
1.0
|
|
N
|
F:GLY199
|
4.2
|
18.0
|
1.0
|
|
N
|
F:VAL194
|
4.2
|
20.5
|
1.0
|
|
CA
|
F:ASP193
|
4.3
|
19.4
|
1.0
|
|
CB
|
F:ASP195
|
4.3
|
20.1
|
1.0
|
|
CG
|
F:HIS218
|
4.4
|
16.2
|
1.0
|
|
C
|
F:HIS198
|
4.4
|
19.4
|
1.0
|
|
CA
|
F:HIS218
|
4.4
|
15.6
|
1.0
|
|
CA
|
F:VAL194
|
4.4
|
20.0
|
1.0
|
|
N
|
F:HIS218
|
4.4
|
14.4
|
1.0
|
|
N
|
F:HIS197
|
4.5
|
18.2
|
1.0
|
|
CA
|
F:LEU217
|
4.5
|
17.1
|
1.0
|
|
C
|
F:PHE196
|
4.5
|
19.0
|
1.0
|
|
CA
|
F:SER216
|
4.5
|
17.8
|
1.0
|
|
C
|
F:SER216
|
4.5
|
17.4
|
1.0
|
|
CA
|
F:HIS197
|
4.6
|
18.6
|
1.0
|
|
N
|
F:PHE196
|
4.7
|
17.8
|
1.0
|
|
O
|
F:PHE196
|
4.8
|
17.1
|
1.0
|
|
OD1
|
F:ASP195
|
4.8
|
22.6
|
1.0
|
|
O
|
F:VAL194
|
4.9
|
22.6
|
1.0
|
|
CE1
|
F:HIS158
|
4.9
|
21.9
|
1.0
|
|
ND1
|
F:HIS158
|
4.9
|
21.0
|
1.0
|
|
O
|
F:HOH349
|
4.9
|
20.2
|
1.0
|
|
Potassium binding site 7 out
of 12 in 3q9c
Go back to
Potassium Binding Sites List in 3q9c
Potassium binding site 7 out
of 12 in the Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:K342
b:21.4
occ:1.00
|
O
|
G:LEU217
|
2.5
|
17.7
|
1.0
|
|
O
|
G:ASP195
|
2.5
|
16.6
|
1.0
|
|
OD1
|
G:ASP193
|
2.6
|
23.7
|
1.0
|
|
O
|
G:HIS197
|
2.8
|
13.6
|
1.0
|
|
O
|
G:ASP193
|
3.1
|
18.5
|
1.0
|
|
OG
|
G:SER216
|
3.2
|
13.5
|
1.0
|
|
CG
|
G:ASP193
|
3.2
|
19.6
|
1.0
|
|
C
|
G:ASP193
|
3.6
|
18.5
|
1.0
|
|
C
|
G:LEU217
|
3.6
|
16.3
|
1.0
|
|
C
|
G:ASP195
|
3.6
|
17.9
|
1.0
|
|
N
|
G:ASP195
|
3.7
|
19.9
|
1.0
|
|
CB
|
G:ASP193
|
3.7
|
17.1
|
1.0
|
|
C
|
G:HIS197
|
3.7
|
14.5
|
1.0
|
|
CB
|
G:HIS218
|
3.8
|
11.3
|
1.0
|
|
N
|
G:LEU217
|
3.8
|
15.6
|
1.0
|
|
C
|
G:VAL194
|
4.0
|
20.3
|
1.0
|
|
OD2
|
G:ASP193
|
4.0
|
16.7
|
1.0
|
|
CA
|
G:HIS198
|
4.0
|
14.9
|
1.0
|
|
CA
|
G:ASP195
|
4.1
|
19.4
|
1.0
|
|
N
|
G:VAL194
|
4.1
|
19.3
|
1.0
|
|
CB
|
G:ASP195
|
4.3
|
22.7
|
1.0
|
|
CA
|
G:ASP193
|
4.3
|
18.2
|
1.0
|
|
N
|
G:HIS198
|
4.3
|
14.4
|
1.0
|
|
CB
|
G:SER216
|
4.3
|
15.2
|
1.0
|
|
CA
|
G:VAL194
|
4.3
|
20.0
|
1.0
|
|
N
|
G:GLY199
|
4.3
|
14.9
|
1.0
|
|
ND1
|
G:HIS218
|
4.3
|
11.0
|
1.0
|
|
CA
|
G:HIS218
|
4.4
|
14.8
|
1.0
|
|
N
|
G:HIS218
|
4.4
|
13.8
|
1.0
|
|
CA
|
G:LEU217
|
4.4
|
16.2
|
1.0
|
|
C
|
G:HIS198
|
4.4
|
17.1
|
1.0
|
|
O
|
G:HOH350
|
4.5
|
14.7
|
1.0
|
|
C
|
G:SER216
|
4.5
|
15.2
|
1.0
|
|
CG
|
G:HIS218
|
4.5
|
11.7
|
1.0
|
|
C
|
G:PHE196
|
4.6
|
17.7
|
1.0
|
|
CA
|
G:SER216
|
4.6
|
14.6
|
1.0
|
|
O
|
G:VAL194
|
4.6
|
19.9
|
1.0
|
|
N
|
G:HIS197
|
4.6
|
16.0
|
1.0
|
|
O
|
G:PHE196
|
4.6
|
18.7
|
1.0
|
|
N
|
G:PHE196
|
4.7
|
17.6
|
1.0
|
|
CA
|
G:HIS197
|
4.8
|
14.1
|
1.0
|
|
OD1
|
G:ASP195
|
5.0
|
25.8
|
1.0
|
|
ND1
|
G:HIS158
|
5.0
|
22.9
|
1.0
|
|
CE1
|
G:HIS158
|
5.0
|
22.5
|
1.0
|
|
Potassium binding site 8 out
of 12 in 3q9c
Go back to
Potassium Binding Sites List in 3q9c
Potassium binding site 8 out
of 12 in the Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:K342
b:22.5
occ:1.00
|
OD1
|
H:ASP193
|
2.6
|
20.5
|
1.0
|
|
O
|
H:LEU217
|
2.6
|
18.8
|
1.0
|
|
O
|
H:ASP195
|
2.7
|
19.9
|
1.0
|
|
O
|
H:HIS197
|
2.7
|
17.3
|
1.0
|
|
O
|
H:ASP193
|
3.0
|
18.6
|
1.0
|
|
OG
|
H:SER216
|
3.1
|
18.5
|
1.0
|
|
CG
|
H:ASP193
|
3.2
|
20.9
|
1.0
|
|
C
|
H:ASP193
|
3.6
|
20.2
|
1.0
|
|
CB
|
H:ASP193
|
3.6
|
19.4
|
1.0
|
|
C
|
H:ASP195
|
3.6
|
17.8
|
1.0
|
|
C
|
H:HIS197
|
3.6
|
17.9
|
1.0
|
|
C
|
H:LEU217
|
3.6
|
18.1
|
1.0
|
|
N
|
H:ASP195
|
3.7
|
18.1
|
1.0
|
|
CB
|
H:HIS218
|
3.8
|
17.1
|
1.0
|
|
OD2
|
H:ASP193
|
4.0
|
19.2
|
1.0
|
|
N
|
H:LEU217
|
4.0
|
20.7
|
1.0
|
|
CA
|
H:HIS198
|
4.1
|
17.8
|
1.0
|
|
CA
|
H:ASP195
|
4.1
|
17.6
|
1.0
|
|
C
|
H:VAL194
|
4.1
|
19.4
|
1.0
|
|
CB
|
H:ASP195
|
4.1
|
18.7
|
1.0
|
|
N
|
H:HIS198
|
4.2
|
17.2
|
1.0
|
|
N
|
H:GLY199
|
4.2
|
17.5
|
1.0
|
|
CA
|
H:ASP193
|
4.2
|
20.1
|
1.0
|
|
N
|
H:VAL194
|
4.2
|
20.1
|
1.0
|
|
CB
|
H:SER216
|
4.2
|
19.3
|
1.0
|
|
ND1
|
H:HIS218
|
4.2
|
19.5
|
1.0
|
|
CA
|
H:HIS218
|
4.4
|
17.6
|
1.0
|
|
N
|
H:HIS218
|
4.4
|
17.0
|
1.0
|
|
C
|
H:HIS198
|
4.4
|
18.0
|
1.0
|
|
N
|
H:HIS197
|
4.5
|
18.3
|
1.0
|
|
CG
|
H:HIS218
|
4.5
|
17.4
|
1.0
|
|
CA
|
H:VAL194
|
4.5
|
20.1
|
1.0
|
|
C
|
H:PHE196
|
4.5
|
18.7
|
1.0
|
|
CA
|
H:LEU217
|
4.5
|
19.1
|
1.0
|
|
CA
|
H:SER216
|
4.6
|
20.9
|
1.0
|
|
CA
|
H:HIS197
|
4.6
|
18.2
|
1.0
|
|
C
|
H:SER216
|
4.7
|
21.1
|
1.0
|
|
N
|
H:PHE196
|
4.7
|
17.7
|
1.0
|
|
O
|
H:HOH365
|
4.7
|
28.9
|
1.0
|
|
O
|
H:PHE196
|
4.7
|
19.8
|
1.0
|
|
O
|
H:VAL194
|
4.7
|
19.1
|
1.0
|
|
OD1
|
H:ASP195
|
4.8
|
22.7
|
1.0
|
|
CE1
|
H:HIS158
|
4.8
|
24.3
|
1.0
|
|
ND1
|
H:HIS158
|
4.8
|
25.6
|
1.0
|
|
Potassium binding site 9 out
of 12 in 3q9c
Go back to
Potassium Binding Sites List in 3q9c
Potassium binding site 9 out
of 12 in the Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 9 of Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K342
b:28.3
occ:1.00
|
OD1
|
I:ASP193
|
2.6
|
23.8
|
1.0
|
|
O
|
I:HIS197
|
2.6
|
19.7
|
1.0
|
|
O
|
I:LEU217
|
2.6
|
18.9
|
1.0
|
|
O
|
I:ASP195
|
2.7
|
14.3
|
1.0
|
|
OG
|
I:SER216
|
2.9
|
12.1
|
1.0
|
|
O
|
I:ASP193
|
3.0
|
18.0
|
1.0
|
|
CG
|
I:ASP193
|
3.3
|
21.7
|
1.0
|
|
C
|
I:HIS197
|
3.6
|
17.6
|
1.0
|
|
C
|
I:LEU217
|
3.6
|
18.2
|
1.0
|
|
C
|
I:ASP193
|
3.7
|
18.3
|
1.0
|
|
C
|
I:ASP195
|
3.7
|
12.9
|
1.0
|
|
CB
|
I:HIS218
|
3.7
|
16.3
|
1.0
|
|
CB
|
I:ASP193
|
3.8
|
18.9
|
1.0
|
|
N
|
I:ASP195
|
3.8
|
16.3
|
1.0
|
|
N
|
I:LEU217
|
3.9
|
16.3
|
1.0
|
|
CA
|
I:HIS198
|
4.0
|
20.9
|
1.0
|
|
CB
|
I:SER216
|
4.0
|
14.0
|
1.0
|
|
OD2
|
I:ASP193
|
4.2
|
21.2
|
1.0
|
|
N
|
I:GLY199
|
4.2
|
20.6
|
1.0
|
|
N
|
I:HIS198
|
4.2
|
18.9
|
1.0
|
|
CA
|
I:ASP195
|
4.2
|
14.3
|
1.0
|
|
C
|
I:VAL194
|
4.3
|
15.9
|
1.0
|
|
N
|
I:VAL194
|
4.3
|
16.9
|
1.0
|
|
C
|
I:HIS198
|
4.3
|
21.2
|
1.0
|
|
CA
|
I:HIS218
|
4.3
|
15.2
|
1.0
|
|
CA
|
I:ASP193
|
4.4
|
19.9
|
1.0
|
|
CB
|
I:ASP195
|
4.4
|
16.6
|
1.0
|
|
N
|
I:HIS218
|
4.4
|
15.8
|
1.0
|
|
CA
|
I:SER216
|
4.5
|
17.0
|
1.0
|
|
C
|
I:SER216
|
4.5
|
17.0
|
1.0
|
|
ND1
|
I:HIS218
|
4.5
|
16.4
|
1.0
|
|
N
|
I:HIS197
|
4.5
|
14.2
|
1.0
|
|
CA
|
I:VAL194
|
4.5
|
16.3
|
1.0
|
|
CA
|
I:LEU217
|
4.5
|
17.1
|
1.0
|
|
CG
|
I:HIS218
|
4.5
|
16.5
|
1.0
|
|
C
|
I:PHE196
|
4.5
|
15.1
|
1.0
|
|
CA
|
I:HIS197
|
4.7
|
16.5
|
1.0
|
|
OD1
|
I:ASP195
|
4.7
|
17.6
|
1.0
|
|
N
|
I:PHE196
|
4.7
|
12.6
|
1.0
|
|
O
|
I:HOH353
|
4.7
|
16.8
|
1.0
|
|
O
|
I:PHE196
|
4.8
|
15.7
|
1.0
|
|
CE1
|
I:HIS158
|
4.9
|
19.4
|
1.0
|
|
ND1
|
I:HIS158
|
4.9
|
17.8
|
1.0
|
|
O
|
I:VAL194
|
4.9
|
16.9
|
1.0
|
|
Potassium binding site 10 out
of 12 in 3q9c
Go back to
Potassium Binding Sites List in 3q9c
Potassium binding site 10 out
of 12 in the Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 10 of Crystal Structure of H159A Apah Complexed with N8-Acetylspermidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:K342
b:26.6
occ:1.00
|
O
|
J:ASP195
|
2.5
|
22.0
|
1.0
|
|
OD1
|
J:ASP193
|
2.6
|
25.4
|
1.0
|
|
O
|
J:LEU217
|
2.6
|
24.6
|
1.0
|
|
O
|
J:HIS197
|
2.8
|
23.7
|
1.0
|
|
O
|
J:ASP193
|
2.9
|
23.2
|
1.0
|
|
OG
|
J:SER216
|
3.0
|
17.0
|
1.0
|
|
CG
|
J:ASP193
|
3.2
|
24.6
|
1.0
|
|
C
|
J:ASP193
|
3.5
|
23.7
|
1.0
|
|
C
|
J:ASP195
|
3.5
|
23.9
|
1.0
|
|
C
|
J:LEU217
|
3.6
|
24.0
|
1.0
|
|
CB
|
J:ASP193
|
3.7
|
22.9
|
1.0
|
|
N
|
J:ASP195
|
3.7
|
25.0
|
1.0
|
|
C
|
J:HIS197
|
3.8
|
23.3
|
1.0
|
|
N
|
J:LEU217
|
3.8
|
23.3
|
1.0
|
|
CB
|
J:HIS218
|
3.9
|
20.7
|
1.0
|
|
CA
|
J:ASP195
|
4.0
|
23.2
|
1.0
|
|
CB
|
J:SER216
|
4.1
|
21.1
|
1.0
|
|
C
|
J:VAL194
|
4.1
|
24.8
|
1.0
|
|
OD2
|
J:ASP193
|
4.1
|
23.0
|
1.0
|
|
CB
|
J:ASP195
|
4.2
|
24.9
|
1.0
|
|
CA
|
J:HIS198
|
4.2
|
23.7
|
1.0
|
|
ND1
|
J:HIS218
|
4.2
|
19.4
|
1.0
|
|
N
|
J:VAL194
|
4.2
|
23.6
|
1.0
|
|
CA
|
J:ASP193
|
4.2
|
24.0
|
1.0
|
|
N
|
J:HIS198
|
4.4
|
23.3
|
1.0
|
|
CA
|
J:SER216
|
4.4
|
23.2
|
1.0
|
|
C
|
J:SER216
|
4.4
|
23.8
|
1.0
|
|
N
|
J:GLY199
|
4.4
|
23.3
|
1.0
|
|
CA
|
J:HIS218
|
4.4
|
23.4
|
1.0
|
|
N
|
J:HIS218
|
4.4
|
23.1
|
1.0
|
|
CA
|
J:VAL194
|
4.4
|
25.1
|
1.0
|
|
CA
|
J:LEU217
|
4.4
|
24.5
|
1.0
|
|
CG
|
J:HIS218
|
4.5
|
19.5
|
1.0
|
|
C
|
J:HIS198
|
4.5
|
22.5
|
1.0
|
|
C
|
J:PHE196
|
4.6
|
23.7
|
1.0
|
|
O
|
J:HOH359
|
4.6
|
28.9
|
1.0
|
|
N
|
J:HIS197
|
4.6
|
22.4
|
1.0
|
|
N
|
J:PHE196
|
4.6
|
23.1
|
1.0
|
|
O
|
J:VAL194
|
4.7
|
26.2
|
1.0
|
|
OD1
|
J:ASP195
|
4.7
|
26.0
|
1.0
|
|
O
|
J:PHE196
|
4.8
|
24.4
|
1.0
|
|
CA
|
J:HIS197
|
4.8
|
23.1
|
1.0
|
|
CG
|
J:ASP195
|
5.0
|
26.1
|
1.0
|
|
Reference:
P.M.Lombardi,
H.D.Angell,
D.A.Whittington,
E.F.Flynn,
K.R.Rajashankar,
D.W.Christianson.
Structure of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships with Eukaryotic Histone Deacetylases . Biochemistry V. 50 1808 2011.
ISSN: ISSN 0006-2960
PubMed: 21268586
DOI: 10.1021/BI101859K
Page generated: Mon Aug 12 09:10:47 2024
|
