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Potassium 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 (Na) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium 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 Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4pv2

Go back to Potassium Binding Sites List in 4pv2
Potassium 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 Potassium with other atoms in the K 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:K203

b:36.2
occ:0.30
 NA A:NA201 1.8 18.7 0.7
O A:HOH379 2.6 28.1 1.0
O A:PHE64 2.7 22.9 1.0
O A:LEU58 2.7 23.4 1.0
O A:SER66 2.7 21.8 1.0
O A:ASP61 2.9 21.1 1.0
OG A:SER66 3.0 29.7 1.0
C A:PHE64 3.3 23.1 1.0
N A:SER66 3.5 18.9 1.0
C A:SER66 3.6 20.8 1.0
N A:PHE64 3.6 24.3 1.0
O A:ARG68 3.7 24.6 1.0
O A:GLU59 3.8 23.8 1.0
CA A:PHE64 3.8 20.5 1.0
C A:LEU58 3.8 22.1 1.0
CB A:PHE64 3.9 18.6 1.0
CA A:SER66 3.9 18.8 1.0
CB A:SER66 4.0 21.6 1.0
CA A:GLU59 4.1 19.0 1.0
C A:ASP61 4.1 23.4 1.0
C A:GLU59 4.1 24.8 1.0
N A:ASN65 4.2 22.6 1.0
N A:GLU59 4.4 18.9 1.0
C A:ASN65 4.4 19.9 1.0
C A:PRO62 4.5 30.2 1.0
N A:LEU63 4.6 25.4 1.0
CG1 B:VAL197 4.6 23.2 1.0
C A:LEU63 4.6 30.2 1.0
CA A:ASN65 4.7 18.2 1.0
CA A:PRO62 4.7 25.0 1.0
N A:GLY67 4.7 20.4 1.0
C A:ARG68 4.8 19.9 1.0
N A:ASP61 4.9 20.9 1.0
O A:PRO62 4.9 28.8 1.0
CA A:LEU58 4.9 20.8 1.0
N A:PRO62 5.0 21.6 1.0

Potassium binding site 2 out of 4 in 4pv2

Go back to Potassium Binding Sites List in 4pv2
Potassium 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 Potassium with other atoms in the K 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:K204

b:34.5
occ:0.30
 NA A:NA202 1.3 28.1 0.7
O A:HOH420 1.9 18.7 0.7
O A:HIS117 2.4 25.8 1.0
O A:HOH422 2.8 35.4 1.0
O A:HOH423 2.8 40.7 1.0
O A:VAL111 2.9 19.2 1.0
O A:SER115 3.2 35.7 1.0
C A:HIS117 3.3 25.9 1.0
O A:MET112 3.4 20.9 1.0
O A:HOH421 3.5 48.7 1.0
O A:CYS92 3.6 18.3 1.0
CA A:SER118 3.6 24.7 1.0
CA A:MET112 3.6 21.7 1.0
C A:VAL111 3.7 15.2 1.0
N A:SER118 3.8 22.8 1.0
C A:MET112 3.9 29.4 1.0
OG A:SER118 3.9 35.7 1.0
N A:MET112 4.1 17.8 1.0
C A:SER115 4.2 34.3 1.0
N A:HIS117 4.3 36.3 1.0
CG1 A:VAL111 4.3 17.6 1.0
CB A:SER118 4.4 26.9 1.0
CA A:HIS117 4.4 30.0 1.0
C A:PRO116 4.5 40.7 1.0
CB A:SER115 4.7 22.3 1.0
O A:PRO116 4.7 43.1 1.0
C A:SER118 4.7 18.8 1.0
C A:CYS92 4.8 15.5 1.0
CA A:SER115 4.9 26.3 1.0
CB A:MET112 4.9 18.3 1.0
N A:SER115 4.9 30.0 1.0
O A:HOH302 5.0 28.1 1.0
CA A:VAL111 5.0 14.5 1.0

Potassium binding site 3 out of 4 in 4pv2

Go back to Potassium Binding Sites List in 4pv2
Potassium 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 Potassium with other atoms in the K 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:K203

b:26.8
occ:0.30
 NA C:NA201 2.0 13.2 0.7
O C:LEU58 2.5 20.5 1.0
O C:HOH304 2.6 24.5 1.0
O C:SER66 2.8 20.5 1.0
O C:PHE64 2.8 21.6 1.0
O C:ASP61 2.9 17.5 1.0
OG C:SER66 3.1 26.1 1.0
C C:PHE64 3.4 16.5 1.0
N C:SER66 3.4 13.6 1.0
C C:SER66 3.6 19.0 1.0
C C:LEU58 3.7 20.1 1.0
O C:GLU59 3.7 21.3 1.0
N C:PHE64 3.8 16.7 1.0
O C:ARG68 3.8 19.8 1.0
CA C:SER66 3.9 15.4 1.0
CB C:PHE64 3.9 18.2 1.0
CA C:PHE64 3.9 15.2 1.0
CA C:GLU59 4.0 16.6 1.0
CB C:SER66 4.0 21.1 1.0
C C:GLU59 4.1 18.6 1.0
C C:ASP61 4.2 17.6 1.0
N C:ASN65 4.3 16.9 1.0
N C:GLU59 4.3 17.3 1.0
C C:ASN65 4.3 16.4 1.0
CG1 D:VAL197 4.5 19.2 1.0
C C:PRO62 4.6 22.4 1.0
N C:GLY67 4.7 14.6 1.0
CA C:ASN65 4.7 14.2 1.0
N C:LEU63 4.7 17.2 1.0
CA C:LEU58 4.8 17.2 1.0
C C:LEU63 4.9 19.7 1.0
N C:ASP61 4.9 16.2 1.0
CA C:PRO62 4.9 19.1 1.0
O C:PRO62 4.9 22.9 1.0
C C:ARG68 5.0 18.4 1.0

Potassium binding site 4 out of 4 in 4pv2

Go back to Potassium Binding Sites List in 4pv2
Potassium 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 Potassium with other atoms in the K 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:K204

b:47.8
occ:0.30
 O C:HOH449 0.5 51.6 0.7
NA C:NA202 2.1 25.0 0.7
O C:HOH451 2.7 44.5 1.0
O C:SER115 2.7 40.1 1.0
O C:HOH450 3.0 26.1 1.0
O C:HOH452 3.2 45.4 1.0
O C:MET112 3.6 26.0 1.0
O C:HIS117 3.9 25.3 1.0
C C:SER115 3.9 31.9 1.0
C C:PRO116 4.1 31.5 1.0
O C:PRO116 4.2 42.4 1.0
CA C:PRO116 4.2 34.0 1.0
OE2 B:GLU250 4.4 55.6 1.0
O C:VAL111 4.4 18.2 1.0
N C:HIS117 4.5 32.1 1.0
N C:PRO116 4.5 32.3 1.0
C C:HIS117 4.6 26.9 1.0
C C:MET112 4.6 25.6 1.0
O C:HOH433 4.7 49.8 1.0
O B:HOH542 4.8 44.8 1.0
O C:HOH323 5.0 45.1 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 Aug 12 11:46:10 2024

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