Sodium in PDB 4pv2: Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations
Enzymatic activity of Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations
All present enzymatic activity of Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations:
3.5.1.1;
Protein crystallography data
The structure of Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations, PDB code: 4pv2
was solved by
M.Bejger,
M.Gilski,
B.Imiolczyk,
D.Clavel,
M.Jaskolski,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.77 /
1.79
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.885,
102.632,
123.754,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.4 /
20.7
|
Other elements in 4pv2:
The structure of Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations
(pdb code 4pv2). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations, PDB code: 4pv2:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 4pv2
Go back to
Sodium Binding Sites List in 4pv2
Sodium binding site 1 out
of 4 in the Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na201
b:18.7
occ:0.70
|
K
|
A:K203
|
1.8
|
36.2
|
0.3
|
O
|
A:ARG68
|
2.2
|
24.6
|
1.0
|
O
|
A:ASP61
|
2.3
|
21.1
|
1.0
|
O
|
A:SER66
|
2.3
|
21.8
|
1.0
|
O
|
A:GLU59
|
2.4
|
23.8
|
1.0
|
C
|
A:GLU59
|
3.2
|
24.8
|
1.0
|
O
|
A:LEU58
|
3.2
|
23.4
|
1.0
|
C
|
A:ARG68
|
3.3
|
19.9
|
1.0
|
C
|
A:ASP61
|
3.4
|
23.4
|
1.0
|
C
|
A:SER66
|
3.5
|
20.8
|
1.0
|
N
|
A:ARG68
|
3.6
|
22.6
|
1.0
|
O
|
A:HOH379
|
3.6
|
28.1
|
1.0
|
O
|
A:PHE64
|
3.7
|
22.9
|
1.0
|
CA
|
A:GLU59
|
3.7
|
19.0
|
1.0
|
OG
|
A:SER66
|
3.9
|
29.7
|
1.0
|
C
|
A:GLY67
|
3.9
|
23.6
|
1.0
|
CA
|
A:PRO62
|
3.9
|
25.0
|
1.0
|
N
|
A:ASP61
|
4.0
|
20.9
|
1.0
|
CA
|
A:ARG68
|
4.1
|
20.5
|
1.0
|
N
|
A:PRO62
|
4.1
|
21.6
|
1.0
|
C
|
A:THR60
|
4.1
|
22.7
|
1.0
|
CA
|
A:GLY67
|
4.2
|
20.8
|
1.0
|
N
|
A:THR60
|
4.2
|
16.7
|
1.0
|
C
|
A:LEU58
|
4.2
|
22.1
|
1.0
|
N
|
A:GLY67
|
4.2
|
20.4
|
1.0
|
N
|
A:SER66
|
4.3
|
18.9
|
1.0
|
C
|
A:PRO62
|
4.3
|
30.2
|
1.0
|
CA
|
A:ASP61
|
4.3
|
24.3
|
1.0
|
N
|
A:GLY69
|
4.3
|
22.5
|
1.0
|
CA
|
A:SER66
|
4.4
|
18.8
|
1.0
|
O
|
A:THR60
|
4.4
|
20.3
|
1.0
|
N
|
A:GLU59
|
4.5
|
18.9
|
1.0
|
O
|
A:GLY67
|
4.5
|
21.6
|
1.0
|
CA
|
A:GLY69
|
4.5
|
21.4
|
1.0
|
CA
|
A:THR60
|
4.6
|
18.9
|
1.0
|
C
|
A:PHE64
|
4.7
|
23.1
|
1.0
|
CB
|
A:ARG68
|
4.7
|
25.9
|
1.0
|
N
|
A:LEU63
|
4.8
|
25.4
|
1.0
|
O
|
A:PRO62
|
4.8
|
28.8
|
1.0
|
CB
|
A:SER66
|
4.8
|
21.6
|
1.0
|
N
|
A:PHE64
|
4.8
|
24.3
|
1.0
|
C
|
A:GLY69
|
4.9
|
24.7
|
1.0
|
CB
|
A:GLU59
|
4.9
|
22.2
|
1.0
|
|
Sodium binding site 2 out
of 4 in 4pv2
Go back to
Sodium Binding Sites List in 4pv2
Sodium binding site 2 out
of 4 in the Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na202
b:28.1
occ:0.70
|
K
|
A:K204
|
1.3
|
34.5
|
0.3
|
O
|
A:SER115
|
2.2
|
35.7
|
1.0
|
O
|
A:VAL111
|
2.3
|
19.2
|
1.0
|
O
|
A:HOH422
|
2.4
|
35.4
|
1.0
|
O
|
A:MET112
|
2.8
|
20.9
|
1.0
|
O
|
A:HIS117
|
2.8
|
25.8
|
1.0
|
O
|
A:HOH420
|
2.9
|
18.7
|
0.7
|
C
|
A:SER115
|
3.3
|
34.3
|
1.0
|
C
|
A:MET112
|
3.4
|
29.4
|
1.0
|
O
|
A:HOH423
|
3.4
|
40.7
|
1.0
|
C
|
A:VAL111
|
3.4
|
15.2
|
1.0
|
CA
|
A:MET112
|
3.6
|
21.7
|
1.0
|
N
|
A:SER115
|
3.8
|
30.0
|
1.0
|
O
|
A:HOH421
|
3.9
|
48.7
|
1.0
|
CA
|
A:SER115
|
3.9
|
26.3
|
1.0
|
C
|
A:HIS117
|
3.9
|
25.9
|
1.0
|
N
|
A:MET112
|
4.0
|
17.8
|
1.0
|
CB
|
A:SER115
|
4.0
|
22.3
|
1.0
|
N
|
A:HIS117
|
4.3
|
36.3
|
1.0
|
N
|
A:PRO116
|
4.4
|
33.7
|
1.0
|
C
|
A:PRO116
|
4.4
|
40.7
|
1.0
|
N
|
A:ASP113
|
4.4
|
22.4
|
1.0
|
O
|
A:CYS92
|
4.5
|
18.3
|
1.0
|
OG
|
A:SER115
|
4.6
|
33.8
|
1.0
|
CA
|
A:PRO116
|
4.6
|
40.8
|
1.0
|
N
|
A:LYS114
|
4.6
|
30.6
|
1.0
|
CG1
|
A:VAL111
|
4.7
|
17.6
|
1.0
|
CA
|
A:VAL111
|
4.7
|
14.5
|
1.0
|
CA
|
A:SER118
|
4.7
|
24.7
|
1.0
|
N
|
A:SER118
|
4.8
|
22.8
|
1.0
|
CA
|
A:HIS117
|
4.8
|
30.0
|
1.0
|
O
|
A:PRO116
|
4.8
|
43.1
|
1.0
|
C
|
A:LYS114
|
4.9
|
42.2
|
1.0
|
C
|
A:ASP113
|
4.9
|
24.5
|
1.0
|
|
Sodium binding site 3 out
of 4 in 4pv2
Go back to
Sodium Binding Sites List in 4pv2
Sodium binding site 3 out
of 4 in the Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na201
b:13.2
occ:0.70
|
K
|
C:K203
|
2.0
|
26.8
|
0.3
|
O
|
C:ARG68
|
2.2
|
19.8
|
1.0
|
O
|
C:SER66
|
2.2
|
20.5
|
1.0
|
O
|
C:ASP61
|
2.3
|
17.5
|
1.0
|
O
|
C:GLU59
|
2.3
|
21.3
|
1.0
|
C
|
C:GLU59
|
3.2
|
18.6
|
1.0
|
C
|
C:ARG68
|
3.3
|
18.4
|
1.0
|
O
|
C:LEU58
|
3.3
|
20.5
|
1.0
|
C
|
C:SER66
|
3.4
|
19.0
|
1.0
|
C
|
C:ASP61
|
3.4
|
17.6
|
1.0
|
N
|
C:ARG68
|
3.7
|
19.9
|
1.0
|
O
|
C:PHE64
|
3.7
|
21.6
|
1.0
|
O
|
C:HOH304
|
3.7
|
24.5
|
1.0
|
CA
|
C:GLU59
|
3.8
|
16.6
|
1.0
|
C
|
C:GLY67
|
3.9
|
18.7
|
1.0
|
CA
|
C:PRO62
|
3.9
|
19.1
|
1.0
|
N
|
C:ASP61
|
4.1
|
16.2
|
1.0
|
CA
|
C:ARG68
|
4.1
|
22.4
|
1.0
|
OG
|
C:SER66
|
4.1
|
26.1
|
1.0
|
CA
|
C:GLY67
|
4.1
|
13.5
|
1.0
|
N
|
C:PRO62
|
4.1
|
19.1
|
1.0
|
C
|
C:THR60
|
4.2
|
16.9
|
1.0
|
N
|
C:GLY67
|
4.2
|
14.6
|
1.0
|
N
|
C:SER66
|
4.2
|
13.6
|
1.0
|
N
|
C:THR60
|
4.2
|
14.1
|
1.0
|
C
|
C:PRO62
|
4.3
|
22.4
|
1.0
|
C
|
C:LEU58
|
4.3
|
20.1
|
1.0
|
N
|
C:GLY69
|
4.3
|
20.2
|
1.0
|
CA
|
C:SER66
|
4.4
|
15.4
|
1.0
|
CA
|
C:ASP61
|
4.4
|
18.1
|
1.0
|
O
|
C:GLY67
|
4.4
|
21.4
|
1.0
|
O
|
C:THR60
|
4.5
|
18.1
|
1.0
|
CA
|
C:GLY69
|
4.5
|
18.4
|
1.0
|
N
|
C:GLU59
|
4.5
|
17.3
|
1.0
|
CA
|
C:THR60
|
4.6
|
15.5
|
1.0
|
O
|
C:PRO62
|
4.6
|
22.9
|
1.0
|
CB
|
C:ARG68
|
4.7
|
25.2
|
0.5
|
CB
|
C:ARG68
|
4.7
|
25.2
|
0.5
|
C
|
C:PHE64
|
4.7
|
16.5
|
1.0
|
C
|
C:GLY69
|
4.8
|
22.1
|
1.0
|
N
|
C:LEU63
|
4.8
|
17.2
|
1.0
|
CB
|
C:SER66
|
4.9
|
21.1
|
1.0
|
CB
|
C:GLU59
|
4.9
|
17.4
|
1.0
|
N
|
C:PHE64
|
5.0
|
16.7
|
1.0
|
|
Sodium binding site 4 out
of 4 in 4pv2
Go back to
Sodium Binding Sites List in 4pv2
Sodium binding site 4 out
of 4 in the Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with K+ and Na+ Cations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na202
b:25.0
occ:0.70
|
K
|
C:K204
|
2.1
|
47.8
|
0.3
|
O
|
C:SER115
|
2.4
|
40.1
|
1.0
|
O
|
C:VAL111
|
2.4
|
18.2
|
1.0
|
O
|
C:HIS117
|
2.5
|
25.3
|
1.0
|
O
|
C:HOH449
|
2.6
|
51.6
|
0.7
|
O
|
C:HOH450
|
2.6
|
26.1
|
1.0
|
O
|
C:MET112
|
3.0
|
26.0
|
1.0
|
C
|
C:SER115
|
3.4
|
31.9
|
1.0
|
C
|
C:VAL111
|
3.5
|
18.4
|
1.0
|
C
|
C:MET112
|
3.5
|
25.6
|
1.0
|
O
|
C:HOH451
|
3.6
|
44.5
|
1.0
|
C
|
C:HIS117
|
3.6
|
26.9
|
1.0
|
CA
|
C:MET112
|
3.6
|
20.3
|
1.0
|
O
|
C:HOH452
|
3.9
|
45.4
|
1.0
|
N
|
C:SER115
|
4.0
|
31.6
|
1.0
|
CB
|
C:SER115
|
4.0
|
19.9
|
1.0
|
CA
|
C:SER115
|
4.0
|
31.2
|
1.0
|
N
|
C:MET112
|
4.0
|
17.3
|
1.0
|
N
|
C:HIS117
|
4.1
|
32.1
|
1.0
|
C
|
C:PRO116
|
4.3
|
31.5
|
1.0
|
O
|
C:CYS92
|
4.4
|
17.4
|
1.0
|
N
|
C:PRO116
|
4.4
|
32.3
|
1.0
|
N
|
C:SER118
|
4.5
|
16.8
|
1.0
|
CA
|
C:HIS117
|
4.5
|
28.9
|
1.0
|
CA
|
C:SER118
|
4.5
|
18.6
|
1.0
|
OG
|
C:SER115
|
4.6
|
35.3
|
1.0
|
N
|
C:ASP113
|
4.6
|
20.2
|
1.0
|
CA
|
C:PRO116
|
4.6
|
34.0
|
1.0
|
CG1
|
C:VAL111
|
4.6
|
14.4
|
1.0
|
CA
|
C:VAL111
|
4.7
|
18.3
|
1.0
|
O
|
C:PRO116
|
4.8
|
42.4
|
1.0
|
N
|
C:LYS114
|
4.9
|
29.6
|
1.0
|
OG
|
C:SER118
|
4.9
|
35.1
|
1.0
|
|
Reference:
M.Bejger,
B.Imiolczyk,
D.Clavel,
M.Gilski,
A.Pajak,
F.Marsolais,
M.Jaskolski.
Na+/K+ Exchange Switches the Catalytic Apparatus of Potassium-Dependent Plant L-Asparaginase Acta Crystallogr.,Sect.D V. 70 1854 2014.
ISSN: ISSN 0907-4449
PubMed: 25004963
DOI: 10.1107/S1399004714008700
Page generated: Mon Oct 7 17:48:55 2024
|