Potassium in PDB 1pwh: Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate
Enzymatic activity of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate
All present enzymatic activity of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate:
4.3.1.17;
Protein crystallography data
The structure of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate, PDB code: 1pwh
was solved by
T.Yamada,
J.Komoto,
Y.Takata,
H.Ogawa,
F.Takusagawa,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.01 /
2.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.241,
109.262,
98.940,
90.00,
91.66,
90.00
|
R / Rfree (%)
|
23 /
26
|
Potassium Binding Sites:
The binding sites of Potassium atom in the Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate
(pdb code 1pwh). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate, PDB code: 1pwh:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 1pwh
Go back to
Potassium Binding Sites List in 1pwh
Potassium binding site 1 out
of 4 in the Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K332
b:8.4
occ:1.00
|
O
|
A:ALA198
|
2.9
|
13.1
|
1.0
|
OE2
|
A:GLU194
|
2.9
|
14.1
|
1.0
|
O
|
A:VAL167
|
3.0
|
10.9
|
1.0
|
OG
|
A:SER200
|
3.1
|
15.5
|
1.0
|
O
|
A:LEU223
|
3.1
|
12.6
|
1.0
|
O
|
A:GLY168
|
3.1
|
15.4
|
1.0
|
N
|
A:SER200
|
3.8
|
14.0
|
1.0
|
C
|
A:VAL167
|
3.8
|
11.5
|
1.0
|
CA
|
A:GLY168
|
3.8
|
13.6
|
1.0
|
C
|
A:GLY168
|
3.9
|
14.2
|
1.0
|
C
|
A:ALA198
|
3.9
|
12.6
|
1.0
|
CD
|
A:GLU194
|
4.1
|
16.8
|
1.0
|
N
|
A:GLY168
|
4.1
|
13.5
|
1.0
|
C
|
A:LEU223
|
4.2
|
12.5
|
1.0
|
CB
|
A:SER200
|
4.3
|
15.5
|
1.0
|
O
|
A:VAL225
|
4.3
|
16.7
|
1.0
|
N
|
A:PHE201
|
4.3
|
15.3
|
1.0
|
CG1
|
A:VAL167
|
4.4
|
8.3
|
1.0
|
CA
|
A:SER200
|
4.5
|
14.5
|
1.0
|
CB
|
A:GLU194
|
4.5
|
14.8
|
1.0
|
CB
|
A:LEU223
|
4.6
|
10.7
|
1.0
|
C
|
A:HIS199
|
4.6
|
13.7
|
1.0
|
CA
|
A:HIS199
|
4.6
|
13.0
|
1.0
|
N
|
A:HIS199
|
4.7
|
13.0
|
1.0
|
N
|
A:VAL225
|
4.7
|
14.3
|
1.0
|
CA
|
A:LEU223
|
4.7
|
12.0
|
1.0
|
CB
|
A:VAL167
|
4.7
|
9.2
|
1.0
|
OE1
|
A:GLU194
|
4.8
|
17.7
|
1.0
|
CG1
|
A:VAL228
|
4.9
|
18.5
|
1.0
|
C
|
A:SER200
|
4.9
|
15.1
|
1.0
|
CG
|
A:LEU223
|
4.9
|
10.6
|
1.0
|
CA
|
A:VAL167
|
4.9
|
10.8
|
1.0
|
CG
|
A:GLU194
|
4.9
|
15.8
|
1.0
|
CA
|
A:ALA198
|
4.9
|
12.5
|
1.0
|
CB
|
A:ALA198
|
4.9
|
13.4
|
1.0
|
|
Potassium binding site 2 out
of 4 in 1pwh
Go back to
Potassium Binding Sites List in 1pwh
Potassium binding site 2 out
of 4 in the Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K333
b:18.8
occ:1.00
|
O
|
B:ALA198
|
2.8
|
11.8
|
1.0
|
OE2
|
B:GLU194
|
2.9
|
20.0
|
1.0
|
O
|
B:GLY168
|
3.0
|
16.0
|
1.0
|
OG
|
B:SER200
|
3.1
|
14.4
|
1.0
|
O
|
B:VAL167
|
3.1
|
13.4
|
1.0
|
O
|
B:LEU223
|
3.1
|
11.7
|
1.0
|
N
|
B:SER200
|
3.7
|
14.6
|
1.0
|
C
|
B:GLY168
|
3.8
|
16.4
|
1.0
|
CA
|
B:GLY168
|
3.8
|
15.1
|
1.0
|
C
|
B:VAL167
|
3.8
|
13.3
|
1.0
|
C
|
B:ALA198
|
3.9
|
13.6
|
1.0
|
CD
|
B:GLU194
|
4.1
|
21.0
|
1.0
|
CB
|
B:SER200
|
4.2
|
14.5
|
1.0
|
N
|
B:GLY168
|
4.2
|
14.3
|
1.0
|
O
|
B:VAL225
|
4.2
|
15.5
|
1.0
|
C
|
B:LEU223
|
4.2
|
13.3
|
1.0
|
N
|
B:PHE201
|
4.3
|
15.2
|
1.0
|
CA
|
B:SER200
|
4.4
|
14.7
|
1.0
|
CG1
|
B:VAL167
|
4.4
|
9.3
|
1.0
|
C
|
B:HIS199
|
4.6
|
14.1
|
1.0
|
CB
|
B:GLU194
|
4.6
|
15.5
|
1.0
|
CA
|
B:HIS199
|
4.6
|
13.9
|
1.0
|
CB
|
B:LEU223
|
4.7
|
12.0
|
1.0
|
N
|
B:VAL225
|
4.7
|
14.5
|
1.0
|
N
|
B:HIS199
|
4.7
|
14.0
|
1.0
|
CA
|
B:LEU223
|
4.8
|
13.3
|
1.0
|
CG1
|
B:VAL228
|
4.8
|
15.6
|
1.0
|
CB
|
B:VAL167
|
4.8
|
10.4
|
1.0
|
C
|
B:SER200
|
4.8
|
15.4
|
1.0
|
OE1
|
B:GLU194
|
4.9
|
22.1
|
1.0
|
CA
|
B:ALA198
|
4.9
|
14.0
|
1.0
|
CA
|
B:VAL167
|
5.0
|
12.0
|
1.0
|
CG
|
B:LEU223
|
5.0
|
12.4
|
1.0
|
CG
|
B:GLU194
|
5.0
|
19.7
|
1.0
|
CB
|
B:ALA198
|
5.0
|
14.1
|
1.0
|
|
Potassium binding site 3 out
of 4 in 1pwh
Go back to
Potassium Binding Sites List in 1pwh
Potassium binding site 3 out
of 4 in the Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K334
b:17.8
occ:1.00
|
O
|
C:ALA198
|
2.8
|
16.4
|
1.0
|
OE2
|
C:GLU194
|
2.9
|
21.6
|
1.0
|
OG
|
C:SER200
|
3.0
|
16.6
|
1.0
|
O
|
C:VAL167
|
3.1
|
15.7
|
1.0
|
O
|
C:GLY168
|
3.2
|
17.1
|
1.0
|
O
|
C:LEU223
|
3.3
|
15.4
|
1.0
|
N
|
C:SER200
|
3.6
|
17.1
|
1.0
|
C
|
C:VAL167
|
3.8
|
14.6
|
1.0
|
CA
|
C:GLY168
|
3.9
|
16.1
|
1.0
|
C
|
C:ALA198
|
3.9
|
16.4
|
1.0
|
C
|
C:GLY168
|
3.9
|
16.6
|
1.0
|
CD
|
C:GLU194
|
4.0
|
21.8
|
1.0
|
CB
|
C:SER200
|
4.1
|
17.4
|
1.0
|
N
|
C:PHE201
|
4.1
|
17.1
|
1.0
|
N
|
C:GLY168
|
4.2
|
15.8
|
1.0
|
CA
|
C:SER200
|
4.3
|
16.7
|
1.0
|
O
|
C:VAL225
|
4.4
|
14.9
|
1.0
|
C
|
C:LEU223
|
4.4
|
14.8
|
1.0
|
CG1
|
C:VAL167
|
4.5
|
10.6
|
1.0
|
CB
|
C:GLU194
|
4.5
|
17.4
|
1.0
|
C
|
C:HIS199
|
4.5
|
16.7
|
1.0
|
CA
|
C:HIS199
|
4.5
|
16.2
|
1.0
|
N
|
C:HIS199
|
4.6
|
16.2
|
1.0
|
OE1
|
C:GLU194
|
4.7
|
23.3
|
1.0
|
C
|
C:SER200
|
4.7
|
17.2
|
1.0
|
CB
|
C:LEU223
|
4.7
|
13.1
|
1.0
|
CG1
|
C:VAL228
|
4.8
|
19.3
|
1.0
|
CB
|
C:VAL167
|
4.8
|
13.1
|
1.0
|
CG
|
C:GLU194
|
4.8
|
20.3
|
1.0
|
N
|
C:VAL225
|
4.8
|
16.3
|
1.0
|
CA
|
C:ALA198
|
4.9
|
16.9
|
1.0
|
CA
|
C:LEU223
|
4.9
|
14.5
|
1.0
|
CA
|
C:VAL167
|
5.0
|
13.5
|
1.0
|
CB
|
C:ALA198
|
5.0
|
18.0
|
1.0
|
CB
|
C:PHE201
|
5.0
|
15.8
|
1.0
|
|
Potassium binding site 4 out
of 4 in 1pwh
Go back to
Potassium Binding Sites List in 1pwh
Potassium binding site 4 out
of 4 in the Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Rat Liver L-Serine Dehydratase- Complex with Pyridoxyl-(O-Methyl- Serine)-5-Monophosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K335
b:18.1
occ:1.00
|
O
|
D:ALA198
|
2.9
|
15.3
|
1.0
|
OE2
|
D:GLU194
|
2.9
|
16.1
|
1.0
|
O
|
D:VAL167
|
3.0
|
13.2
|
1.0
|
OG
|
D:SER200
|
3.1
|
14.0
|
1.0
|
O
|
D:GLY168
|
3.1
|
17.2
|
1.0
|
O
|
D:LEU223
|
3.1
|
13.1
|
1.0
|
N
|
D:SER200
|
3.8
|
14.7
|
1.0
|
C
|
D:VAL167
|
3.8
|
13.8
|
1.0
|
CA
|
D:GLY168
|
3.8
|
15.6
|
1.0
|
C
|
D:GLY168
|
3.8
|
16.2
|
1.0
|
C
|
D:ALA198
|
3.9
|
15.4
|
1.0
|
CD
|
D:GLU194
|
4.1
|
18.9
|
1.0
|
N
|
D:GLY168
|
4.1
|
14.8
|
1.0
|
CB
|
D:SER200
|
4.2
|
14.5
|
1.0
|
C
|
D:LEU223
|
4.2
|
13.4
|
1.0
|
O
|
D:VAL225
|
4.3
|
16.5
|
1.0
|
N
|
D:PHE201
|
4.3
|
14.7
|
1.0
|
CG1
|
D:VAL167
|
4.4
|
7.9
|
1.0
|
CA
|
D:SER200
|
4.4
|
14.5
|
1.0
|
CB
|
D:GLU194
|
4.5
|
14.8
|
1.0
|
C
|
D:HIS199
|
4.6
|
15.2
|
1.0
|
CA
|
D:HIS199
|
4.6
|
15.1
|
1.0
|
CB
|
D:LEU223
|
4.6
|
12.2
|
1.0
|
N
|
D:HIS199
|
4.7
|
15.4
|
1.0
|
N
|
D:VAL225
|
4.7
|
14.7
|
1.0
|
CB
|
D:VAL167
|
4.8
|
11.0
|
1.0
|
CG1
|
D:VAL228
|
4.8
|
17.8
|
1.0
|
CA
|
D:LEU223
|
4.8
|
13.0
|
1.0
|
OE1
|
D:GLU194
|
4.9
|
20.8
|
1.0
|
C
|
D:SER200
|
4.9
|
14.5
|
1.0
|
CA
|
D:VAL167
|
4.9
|
12.1
|
1.0
|
CG
|
D:GLU194
|
4.9
|
18.2
|
1.0
|
CA
|
D:ALA198
|
4.9
|
14.6
|
1.0
|
CG
|
D:LEU223
|
5.0
|
13.2
|
1.0
|
CB
|
D:ALA198
|
5.0
|
13.2
|
1.0
|
|
Reference:
T.Yamada,
J.Komoto,
Y.Takata,
H.Ogawa,
H.C.Pitot,
F.Takusagawa.
Crystal Structure of Serine Dehydratase From Rat Liver. Biochemistry V. 42 12854 2003.
ISSN: ISSN 0006-2960
PubMed: 14596599
DOI: 10.1021/BI035324P
Page generated: Mon Aug 12 05:13:42 2024
|