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Sodium in PDB 4pv3: Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with Na+ Cations

Enzymatic activity of Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with Na+ Cations

All present enzymatic activity of Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with 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 Na+ Cations, PDB code: 4pv3 was solved by M.Bejger, M.Gilski, B.Imiolczyk, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.55 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.403, 103.424, 124.556, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 23.1

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 Na+ Cations (pdb code 4pv3). 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 Na+ Cations, PDB code: 4pv3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4pv3

Go back to Sodium Binding Sites List in 4pv3
Sodium binding site 1 out of 4 in the Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with 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 Na+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:40.2
occ:1.00
 O A:ARG68 2.2 31.0 1.0
O A:ASP61 2.3 31.1 1.0
O A:SER66 2.4 31.5 1.0
O A:GLU59 2.6 38.4 1.0
O A:LEU58 3.0 39.2 1.0
C A:GLU59 3.3 31.5 1.0
C A:ASP61 3.3 32.1 1.0
O A:PHE64 3.3 39.6 1.0
O A:HOH358 3.4 40.8 1.0
C A:ARG68 3.4 34.4 1.0
C A:SER66 3.5 30.6 1.0
CA A:GLU59 3.7 34.6 1.0
N A:ARG68 3.8 32.4 1.0
CA A:PRO62 3.9 37.3 1.0
C A:LEU58 4.0 37.0 1.0
C A:GLY67 4.1 30.0 1.0
N A:ASP61 4.1 31.3 1.0
N A:PRO62 4.1 33.8 1.0
N A:SER66 4.2 33.2 1.0
OG A:SER66 4.2 38.5 1.0
C A:THR60 4.2 32.4 1.0
CA A:ARG68 4.2 34.0 1.0
CA A:ASP61 4.3 32.0 1.0
C A:PRO62 4.3 37.8 1.0
N A:THR60 4.3 32.3 1.0
CA A:GLY67 4.3 27.2 1.0
N A:GLU59 4.3 34.7 1.0
N A:GLY67 4.3 27.2 1.0
C A:PHE64 4.4 37.0 1.0
N A:GLY69 4.4 33.0 1.0
CA A:SER66 4.4 31.9 1.0
CA A:GLY69 4.5 33.0 1.0
O A:THR60 4.5 30.2 1.0
N A:PHE64 4.6 32.1 1.0
O A:GLY67 4.7 34.4 1.0
O A:PRO62 4.7 37.5 1.0
N A:LEU63 4.7 34.8 1.0
CA A:THR60 4.8 33.2 1.0
CB A:ARG68 4.9 38.5 1.0
C A:GLY69 4.9 35.2 1.0
CB A:ASP61 5.0 34.4 1.0
CB A:SER66 5.0 34.8 1.0
CB A:GLU59 5.0 35.2 1.0

Sodium binding site 2 out of 4 in 4pv3

Go back to Sodium Binding Sites List in 4pv3
Sodium binding site 2 out of 4 in the Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with 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 Na+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:44.5
occ:1.00
 O A:HOH352 2.2 36.7 1.0
O A:HOH353 2.3 34.5 1.0
O A:HIS117 2.3 36.2 1.0
O A:SER115 2.4 41.7 1.0
O A:VAL111 2.7 27.9 1.0
O A:MET112 3.4 36.7 1.0
C A:HIS117 3.4 37.4 1.0
C A:SER115 3.5 43.2 1.0
C A:VAL111 3.6 31.5 1.0
C A:MET112 3.7 34.5 1.0
CA A:MET112 3.8 32.4 1.0
CB A:SER115 4.0 38.8 1.0
N A:HIS117 4.1 44.3 1.0
N A:SER115 4.1 43.4 1.0
CA A:SER115 4.1 45.5 1.0
N A:MET112 4.1 29.7 1.0
N A:SER118 4.2 30.6 1.0
CA A:SER118 4.2 32.7 1.0
C A:PRO116 4.2 48.4 1.0
O A:CYS92 4.3 25.7 1.0
CA A:HIS117 4.4 42.2 1.0
CG1 A:VAL111 4.5 25.5 1.0
OG A:SER118 4.5 46.7 1.0
N A:PRO116 4.5 44.9 1.0
CA A:PRO116 4.6 45.8 1.0
N A:ASP113 4.6 36.9 1.0
O A:PRO116 4.6 49.6 1.0
OG A:SER115 4.6 44.5 1.0
CA A:VAL111 4.8 28.7 1.0
CB A:SER118 4.9 32.9 1.0

Sodium binding site 3 out of 4 in 4pv3

Go back to Sodium Binding Sites List in 4pv3
Sodium binding site 3 out of 4 in the Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with 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 Na+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:40.8
occ:1.00
 O C:SER66 2.2 33.3 1.0
O C:ASP61 2.3 33.4 1.0
O C:ARG68 2.3 32.1 1.0
O C:GLU59 2.6 40.5 1.0
O C:LEU58 2.8 36.7 1.0
O C:PHE64 3.2 33.6 1.0
O C:HOH369 3.3 39.8 1.0
C C:GLU59 3.3 35.1 1.0
C C:SER66 3.4 30.4 1.0
C C:ASP61 3.4 34.8 1.0
C C:ARG68 3.5 31.2 1.0
CA C:GLU59 3.7 33.5 1.0
N C:ARG68 3.9 29.0 1.0
C C:LEU58 3.9 36.3 1.0
OG C:SER66 4.0 40.1 1.0
CA C:PRO62 4.0 36.5 1.0
N C:SER66 4.1 31.9 1.0
N C:ASP61 4.1 34.8 1.0
C C:GLY67 4.1 28.5 1.0
N C:PRO62 4.2 36.1 1.0
C C:PHE64 4.2 35.1 1.0
N C:THR60 4.2 36.7 1.0
N C:GLU59 4.3 34.1 1.0
CA C:SER66 4.3 32.1 1.0
N C:GLY67 4.3 29.9 1.0
C C:THR60 4.3 36.7 1.0
CA C:ARG68 4.3 31.7 1.0
CA C:GLY67 4.4 30.4 1.0
C C:PRO62 4.4 37.1 1.0
CA C:ASP61 4.4 34.5 1.0
N C:PHE64 4.5 34.7 1.0
N C:GLY69 4.5 32.6 1.0
N C:LEU63 4.6 35.5 1.0
CA C:GLY69 4.7 32.4 1.0
O C:GLY67 4.7 33.9 1.0
CB C:SER66 4.7 36.6 1.0
O C:THR60 4.7 36.2 1.0
CA C:THR60 4.8 36.1 1.0
O C:PRO62 4.8 39.4 1.0
CA C:PHE64 4.9 35.4 1.0
CB C:ARG68 5.0 34.8 0.5
C C:GLY69 5.0 34.0 1.0

Sodium binding site 4 out of 4 in 4pv3

Go back to Sodium Binding Sites List in 4pv3
Sodium binding site 4 out of 4 in the Crystal Structure of Potassium-Dependent Plant-Type L-Asparaginase From Phaseolus Vulgaris in Complex with 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 Na+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:43.9
occ:1.00
 O C:HOH353 2.3 35.1 1.0
O C:SER115 2.4 42.9 1.0
O C:HIS117 2.6 37.4 1.0
O C:VAL111 2.7 32.3 1.0
O C:MET112 3.1 42.8 1.0
O B:HOH429 3.2 49.4 1.0
C C:SER115 3.4 46.4 1.0
C C:HIS117 3.6 38.7 1.0
C C:VAL111 3.7 31.9 1.0
C C:MET112 3.7 39.2 1.0
CA C:MET112 3.9 35.7 1.0
CA C:SER115 4.1 45.3 1.0
N C:SER115 4.1 44.2 1.0
CB C:SER115 4.1 36.9 1.0
N C:MET112 4.2 32.8 1.0
N C:SER118 4.2 32.2 1.0
CA C:SER118 4.2 33.4 1.0
N C:HIS117 4.2 48.0 1.0
O C:CYS92 4.3 26.8 1.0
C C:PRO116 4.3 50.4 1.0
OG C:SER118 4.5 37.7 1.0
N C:PRO116 4.5 46.2 1.0
CA C:HIS117 4.5 42.4 1.0
CG1 C:VAL111 4.6 31.3 1.0
CA C:PRO116 4.6 48.1 1.0
OG C:SER115 4.7 39.6 1.0
O C:PRO116 4.7 48.0 1.0
N C:ASP113 4.8 37.1 1.0
OE2 B:GLU250 4.9 76.6 1.0
CA C:VAL111 4.9 31.2 1.0
CB C:SER118 4.9 33.7 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 17:49:03 2024

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