Potassium in PDB 3h8f: High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida
Enzymatic activity of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida
All present enzymatic activity of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida:
3.4.11.1;
Protein crystallography data
The structure of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida, PDB code: 3h8f
was solved by
A.Kale,
B.W.Dijkstra,
T.Sonke,
A.M.W.H.Thunnissen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.45 /
2.20
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.786,
95.931,
96.308,
68.43,
76.31,
94.86
|
R / Rfree (%)
|
19.2 /
25.1
|
Other elements in 3h8f:
The structure of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida
(pdb code 3h8f). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the
High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida, PDB code: 3h8f:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
Potassium binding site 1 out
of 6 in 3h8f
Go back to
Potassium Binding Sites List in 3h8f
Potassium binding site 1 out
of 6 in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K503
b:9.3
occ:1.00
|
O
|
A:LEU192
|
2.7
|
8.0
|
1.0
|
O
|
A:HOH520
|
2.7
|
9.1
|
1.0
|
O
|
A:LYS288
|
2.9
|
6.5
|
1.0
|
O
|
A:GLY190
|
2.9
|
5.1
|
1.0
|
O
|
A:LEU189
|
3.0
|
4.1
|
1.0
|
SD
|
A:MET291
|
3.3
|
8.8
|
1.0
|
C
|
A:GLY190
|
3.5
|
6.4
|
1.0
|
C
|
A:LEU192
|
3.9
|
7.8
|
1.0
|
SG
|
A:CYS197
|
3.9
|
8.9
|
1.0
|
CA
|
A:GLY190
|
3.9
|
5.6
|
1.0
|
C
|
A:LYS288
|
3.9
|
6.8
|
1.0
|
CG
|
A:MET291
|
3.9
|
6.5
|
1.0
|
CB
|
A:LYS288
|
4.0
|
6.7
|
1.0
|
C
|
A:LEU189
|
4.0
|
5.2
|
1.0
|
CB
|
A:CYS197
|
4.1
|
8.2
|
1.0
|
CE
|
A:MET291
|
4.1
|
6.5
|
1.0
|
N
|
A:LEU192
|
4.3
|
8.1
|
1.0
|
CG
|
A:LYS288
|
4.3
|
7.4
|
1.0
|
CA
|
A:LYS288
|
4.4
|
7.0
|
1.0
|
N
|
A:GLY190
|
4.4
|
5.0
|
1.0
|
CA
|
A:LEU192
|
4.5
|
8.0
|
1.0
|
N
|
A:ASN191
|
4.5
|
6.7
|
1.0
|
CB
|
A:LEU192
|
4.6
|
7.9
|
1.0
|
C
|
A:ASN191
|
4.6
|
8.3
|
1.0
|
O
|
A:THR270
|
4.6
|
7.2
|
1.0
|
CD
|
A:LYS288
|
4.7
|
8.6
|
1.0
|
N
|
A:PRO193
|
4.9
|
7.5
|
1.0
|
N
|
A:TYR289
|
5.0
|
5.4
|
1.0
|
CA
|
A:ASN191
|
5.0
|
7.5
|
1.0
|
|
Potassium binding site 2 out
of 6 in 3h8f
Go back to
Potassium Binding Sites List in 3h8f
Potassium binding site 2 out
of 6 in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K503
b:13.2
occ:1.00
|
O
|
B:LEU192
|
2.5
|
6.3
|
1.0
|
O
|
B:HOH3687
|
2.7
|
2.0
|
1.0
|
O
|
B:GLY190
|
2.7
|
4.6
|
1.0
|
O
|
B:LEU189
|
2.9
|
5.8
|
1.0
|
O
|
B:LYS288
|
2.9
|
7.0
|
1.0
|
SD
|
B:MET291
|
3.4
|
25.4
|
1.0
|
C
|
B:GLY190
|
3.5
|
5.0
|
1.0
|
C
|
B:LEU192
|
3.7
|
5.8
|
1.0
|
CG
|
B:MET291
|
3.7
|
5.7
|
1.0
|
CA
|
B:GLY190
|
3.9
|
4.6
|
1.0
|
C
|
B:LYS288
|
3.9
|
7.1
|
1.0
|
SG
|
B:CYS197
|
3.9
|
15.0
|
1.0
|
C
|
B:LEU189
|
4.0
|
6.5
|
1.0
|
CB
|
B:LYS288
|
4.0
|
5.5
|
1.0
|
CB
|
B:CYS197
|
4.1
|
8.9
|
1.0
|
CG
|
B:LYS288
|
4.1
|
7.4
|
1.0
|
N
|
B:LEU192
|
4.2
|
6.3
|
1.0
|
CA
|
B:LEU192
|
4.4
|
6.2
|
1.0
|
CA
|
B:LYS288
|
4.4
|
6.9
|
1.0
|
N
|
B:GLY190
|
4.4
|
5.5
|
1.0
|
N
|
B:ASN191
|
4.4
|
4.8
|
1.0
|
C
|
B:ASN191
|
4.5
|
5.9
|
1.0
|
CD
|
B:LYS288
|
4.6
|
7.8
|
1.0
|
CB
|
B:LEU192
|
4.6
|
6.7
|
1.0
|
N
|
B:PRO193
|
4.8
|
5.3
|
1.0
|
O
|
B:THR270
|
4.8
|
3.1
|
1.0
|
CE
|
B:MET291
|
4.9
|
18.8
|
1.0
|
N
|
B:TYR289
|
4.9
|
5.9
|
1.0
|
CA
|
B:ASN191
|
4.9
|
5.3
|
1.0
|
|
Potassium binding site 3 out
of 6 in 3h8f
Go back to
Potassium Binding Sites List in 3h8f
Potassium binding site 3 out
of 6 in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K503
b:12.6
occ:1.00
|
O
|
C:LEU192
|
2.7
|
3.5
|
1.0
|
O
|
C:HOH2007
|
2.8
|
7.7
|
1.0
|
O
|
C:LEU189
|
2.8
|
4.6
|
1.0
|
O
|
C:GLY190
|
2.9
|
5.5
|
1.0
|
O
|
C:LYS288
|
2.9
|
4.8
|
1.0
|
SD
|
C:MET291
|
3.3
|
7.5
|
1.0
|
C
|
C:GLY190
|
3.5
|
5.4
|
1.0
|
CA
|
C:GLY190
|
3.8
|
5.2
|
1.0
|
C
|
C:LEU192
|
3.8
|
4.3
|
1.0
|
C
|
C:LEU189
|
3.9
|
3.8
|
1.0
|
C
|
C:LYS288
|
3.9
|
5.3
|
1.0
|
CG
|
C:MET291
|
3.9
|
2.1
|
1.0
|
SG
|
C:CYS197
|
4.0
|
10.7
|
1.0
|
CB
|
C:LYS288
|
4.1
|
6.1
|
1.0
|
CB
|
C:CYS197
|
4.1
|
7.0
|
1.0
|
N
|
C:LEU192
|
4.2
|
5.4
|
1.0
|
CE
|
C:MET291
|
4.3
|
5.9
|
1.0
|
N
|
C:GLY190
|
4.3
|
4.7
|
1.0
|
CG
|
C:LYS288
|
4.3
|
6.0
|
1.0
|
N
|
C:ASN191
|
4.4
|
5.3
|
1.0
|
CA
|
C:LEU192
|
4.4
|
4.7
|
1.0
|
CA
|
C:LYS288
|
4.5
|
5.6
|
1.0
|
C
|
C:ASN191
|
4.5
|
5.9
|
1.0
|
CB
|
C:LEU192
|
4.6
|
5.0
|
1.0
|
CD
|
C:LYS288
|
4.8
|
6.8
|
1.0
|
O
|
C:THR270
|
4.9
|
2.0
|
1.0
|
N
|
C:TYR289
|
4.9
|
3.7
|
1.0
|
CA
|
C:ASN191
|
4.9
|
5.6
|
1.0
|
N
|
C:PRO193
|
4.9
|
4.1
|
1.0
|
|
Potassium binding site 4 out
of 6 in 3h8f
Go back to
Potassium Binding Sites List in 3h8f
Potassium binding site 4 out
of 6 in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K503
b:10.9
occ:1.00
|
O
|
D:LEU192
|
2.6
|
7.8
|
1.0
|
O
|
D:GLY190
|
2.7
|
7.7
|
1.0
|
O
|
D:LEU189
|
2.9
|
9.3
|
1.0
|
O
|
D:HOH511
|
2.9
|
21.2
|
1.0
|
O
|
D:LYS288
|
3.0
|
8.0
|
1.0
|
SD
|
D:MET291
|
3.4
|
15.1
|
1.0
|
C
|
D:GLY190
|
3.4
|
8.0
|
1.0
|
C
|
D:LEU192
|
3.7
|
8.4
|
1.0
|
CA
|
D:GLY190
|
3.8
|
8.3
|
1.0
|
SG
|
D:CYS197
|
3.8
|
11.9
|
1.0
|
C
|
D:LYS288
|
3.9
|
8.4
|
1.0
|
C
|
D:LEU189
|
4.0
|
9.6
|
1.0
|
CB
|
D:LYS288
|
4.0
|
9.1
|
1.0
|
N
|
D:LEU192
|
4.1
|
7.8
|
1.0
|
CB
|
D:CYS197
|
4.1
|
11.9
|
1.0
|
CG
|
D:MET291
|
4.1
|
11.9
|
1.0
|
CG
|
D:LYS288
|
4.2
|
8.8
|
1.0
|
CA
|
D:LEU192
|
4.3
|
8.3
|
1.0
|
CE
|
D:MET291
|
4.4
|
13.2
|
1.0
|
N
|
D:GLY190
|
4.4
|
9.6
|
1.0
|
CD
|
D:LYS288
|
4.4
|
7.6
|
1.0
|
CA
|
D:LYS288
|
4.4
|
8.5
|
1.0
|
N
|
D:ASN191
|
4.5
|
7.9
|
1.0
|
C
|
D:ASN191
|
4.5
|
7.7
|
1.0
|
CB
|
D:LEU192
|
4.5
|
8.5
|
1.0
|
N
|
D:PRO193
|
4.8
|
8.6
|
1.0
|
N
|
D:TYR289
|
4.9
|
8.0
|
1.0
|
CA
|
D:ASN191
|
4.9
|
7.7
|
1.0
|
O
|
D:THR270
|
4.9
|
10.1
|
1.0
|
C
|
D:PRO193
|
5.0
|
8.7
|
1.0
|
|
Potassium binding site 5 out
of 6 in 3h8f
Go back to
Potassium Binding Sites List in 3h8f
Potassium binding site 5 out
of 6 in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K503
b:12.6
occ:1.00
|
O
|
E:HOH556
|
2.6
|
3.1
|
1.0
|
O
|
E:GLY190
|
2.8
|
6.3
|
1.0
|
O
|
E:LEU192
|
2.8
|
6.7
|
1.0
|
O
|
E:LEU189
|
2.8
|
6.5
|
1.0
|
O
|
E:LYS288
|
2.9
|
9.1
|
1.0
|
SD
|
E:MET291
|
3.3
|
7.9
|
1.0
|
C
|
E:GLY190
|
3.5
|
6.9
|
1.0
|
C
|
E:LEU192
|
3.8
|
6.8
|
1.0
|
CA
|
E:GLY190
|
3.9
|
5.9
|
1.0
|
C
|
E:LEU189
|
3.9
|
6.3
|
1.0
|
SG
|
E:CYS197
|
3.9
|
10.7
|
1.0
|
C
|
E:LYS288
|
3.9
|
8.4
|
1.0
|
CG
|
E:MET291
|
4.0
|
6.2
|
1.0
|
CB
|
E:LYS288
|
4.0
|
8.1
|
1.0
|
CB
|
E:CYS197
|
4.1
|
7.5
|
1.0
|
N
|
E:LEU192
|
4.1
|
6.9
|
1.0
|
CA
|
E:LEU192
|
4.3
|
6.8
|
1.0
|
N
|
E:GLY190
|
4.3
|
6.1
|
1.0
|
CE
|
E:MET291
|
4.4
|
4.6
|
1.0
|
CA
|
E:LYS288
|
4.4
|
8.6
|
1.0
|
N
|
E:ASN191
|
4.4
|
6.0
|
1.0
|
CB
|
E:LEU192
|
4.5
|
7.2
|
1.0
|
CG
|
E:LYS288
|
4.5
|
9.8
|
1.0
|
C
|
E:ASN191
|
4.5
|
7.0
|
1.0
|
CD
|
E:LYS288
|
4.6
|
10.2
|
1.0
|
O
|
E:THR270
|
4.8
|
4.7
|
1.0
|
N
|
E:PRO193
|
4.9
|
6.6
|
1.0
|
CA
|
E:ASN191
|
5.0
|
6.5
|
1.0
|
N
|
E:TYR289
|
5.0
|
7.8
|
1.0
|
|
Potassium binding site 6 out
of 6 in 3h8f
Go back to
Potassium Binding Sites List in 3h8f
Potassium binding site 6 out
of 6 in the High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of High pH Native Structure of Leucine Aminopeptidase From Pseudomonas Putida within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:K503
b:22.0
occ:1.00
|
O
|
F:LEU192
|
2.6
|
9.5
|
1.0
|
O
|
F:GLY190
|
2.7
|
8.2
|
1.0
|
O
|
F:HOH508
|
2.8
|
2.0
|
1.0
|
O
|
F:LEU189
|
2.9
|
7.9
|
1.0
|
O
|
F:LYS288
|
3.0
|
9.3
|
1.0
|
C
|
F:GLY190
|
3.5
|
8.6
|
1.0
|
SD
|
F:MET291
|
3.6
|
15.9
|
1.0
|
C
|
F:LEU192
|
3.7
|
9.0
|
1.0
|
CB
|
F:LYS288
|
3.9
|
9.5
|
1.0
|
C
|
F:LYS288
|
3.9
|
8.7
|
1.0
|
SG
|
F:CYS197
|
3.9
|
8.2
|
1.0
|
C
|
F:LEU189
|
4.0
|
8.7
|
1.0
|
CA
|
F:GLY190
|
4.0
|
8.6
|
1.0
|
N
|
F:LEU192
|
4.1
|
8.5
|
1.0
|
CB
|
F:CYS197
|
4.1
|
8.6
|
1.0
|
CG
|
F:MET291
|
4.2
|
10.3
|
1.0
|
CG
|
F:LYS288
|
4.2
|
8.4
|
1.0
|
CD
|
F:LYS288
|
4.3
|
6.8
|
1.0
|
CA
|
F:LEU192
|
4.3
|
9.1
|
1.0
|
CA
|
F:LYS288
|
4.4
|
8.2
|
1.0
|
CB
|
F:LEU192
|
4.4
|
8.8
|
1.0
|
N
|
F:ASN191
|
4.4
|
8.2
|
1.0
|
N
|
F:GLY190
|
4.5
|
8.7
|
1.0
|
C
|
F:ASN191
|
4.5
|
8.1
|
1.0
|
CE
|
F:MET291
|
4.5
|
15.0
|
1.0
|
N
|
F:PRO193
|
4.8
|
8.7
|
1.0
|
O
|
F:THR270
|
4.8
|
5.6
|
1.0
|
N
|
F:TYR289
|
4.9
|
8.0
|
1.0
|
CA
|
F:ASN191
|
4.9
|
7.8
|
1.0
|
C
|
F:PRO193
|
4.9
|
8.5
|
1.0
|
|
Reference:
A.Kale,
T.Pijning,
T.Sonke,
B.W.Dijkstra,
A.M.Thunnissen.
Crystal Structure of the Leucine Aminopeptidase From Pseudomonas Putida Reveals the Molecular Basis For Its Enantioselectivity and Broad Substrate Specificity. J.Mol.Biol. V. 398 703 2010.
ISSN: ISSN 0022-2836
PubMed: 20359484
DOI: 10.1016/J.JMB.2010.03.042
Page generated: Mon Aug 12 08:25:27 2024
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