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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:

Potassium (K) 4 atoms

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

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