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Sodium in PDB 8bj4: Crystal Structure of Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form

Enzymatic activity of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form

All present enzymatic activity of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form:
2.6.1.9;

Protein crystallography data

The structure of Crystal Structure of Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form, PDB code: 8bj4 was solved by M.Rutkiewicz, W.Witek, M.Ruszkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.43 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.039, 93.082, 110.518, 90, 106.57, 90
R / Rfree (%) 14.8 / 18.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form (pdb code 8bj4). 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 Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form, PDB code: 8bj4:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8bj4

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Sodium binding site 1 out of 4 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form


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 Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na413

b:81.3
occ:1.00
 O A:LEU317 2.5 40.6 1.0
O A:LYS312 2.5 33.8 0.5
O A:LYS312 2.6 33.8 0.5
O A:VAL314 2.6 38.5 1.0
C A:LYS312 3.5 33.9 0.5
C A:LYS312 3.5 34.0 0.5
C A:LEU317 3.6 39.5 1.0
C A:VAL314 3.7 40.0 1.0
O A:PRO315 4.1 40.6 1.0
CA A:LYS312 4.1 33.5 0.5
CA A:LYS312 4.2 33.6 0.5
C A:PRO315 4.2 40.1 1.0
N A:LEU317 4.2 38.3 1.0
O A:LEU311 4.3 32.7 1.0
CA A:PRO315 4.3 40.7 1.0
N A:VAL314 4.4 38.9 1.0
C A:ALA313 4.5 37.8 1.0
N A:PRO315 4.5 40.1 1.0
N A:LYS318 4.5 37.3 1.0
CA A:LEU317 4.5 39.3 1.0
N A:ALA313 4.5 34.2 1.0
CA A:LYS318 4.6 37.9 1.0
CA A:VAL314 4.7 40.1 1.0
CD A:PRO319 4.8 32.0 1.0
CA A:ALA313 4.8 35.5 1.0
O A:ALA313 4.8 38.0 1.0
CG A:LYS312 4.8 36.0 0.5
CG A:LYS312 4.8 36.3 0.5
N A:PHE316 4.9 38.9 1.0

Sodium binding site 2 out of 4 in 8bj4

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Sodium binding site 2 out of 4 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form


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 Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na407

b:51.2
occ:1.00
 O B:LEU317 2.3 22.1 1.0
O B:LYS312 2.4 25.0 1.0
O B:HOH802 2.5 36.4 1.0
O B:VAL314 2.5 22.7 1.0
C B:LYS312 3.3 23.8 1.0
C B:LEU317 3.5 20.7 1.0
C B:VAL314 3.7 23.1 1.0
CA B:LYS312 3.9 24.2 1.0
O B:LEU311 4.0 20.8 1.0
N B:VAL314 4.1 24.7 1.0
O B:HOH777 4.2 46.1 1.0
N B:LEU317 4.2 20.3 1.0
N B:ALA313 4.3 24.1 1.0
C B:ALA313 4.4 25.9 1.0
CA B:PRO315 4.4 25.8 1.0
C B:PRO315 4.4 25.1 1.0
CA B:LEU317 4.4 20.2 1.0
O B:PRO315 4.4 27.5 1.0
N B:PRO315 4.5 24.6 1.0
N B:LYS318 4.5 20.7 1.0
CA B:VAL314 4.5 22.9 1.0
CA B:LYS318 4.6 22.5 1.0
CD B:PRO319 4.6 21.0 1.0
CA B:ALA313 4.6 25.3 1.0
CG B:LYS312 4.7 33.0 1.0
C B:LEU311 4.9 21.9 1.0
O B:ALA313 4.9 27.2 1.0
CB B:LYS312 4.9 28.1 1.0
CB B:LEU317 4.9 20.5 1.0
N B:LYS312 4.9 22.6 1.0
N B:PHE316 4.9 23.1 1.0

Sodium binding site 3 out of 4 in 8bj4

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Sodium binding site 3 out of 4 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form


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 Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na413

b:76.2
occ:1.00
 O C:LEU317 2.3 25.8 1.0
O C:LYS312 2.5 27.8 1.0
O C:HOH807 2.6 90.7 1.0
O C:VAL314 2.7 29.5 1.0
C C:LYS312 3.4 27.1 1.0
C C:LEU317 3.5 25.6 1.0
C C:VAL314 3.8 29.9 1.0
O C:HOH869 3.9 51.5 1.0
CA C:LYS312 4.0 27.8 1.0
O C:LEU311 4.0 23.2 1.0
N C:LEU317 4.2 25.2 1.0
N C:VAL314 4.3 28.4 1.0
O C:PRO315 4.3 32.9 1.0
N C:LYS318 4.4 26.1 1.0
CA C:LEU317 4.4 24.5 1.0
C C:PRO315 4.4 31.8 1.0
O C:HOH776 4.4 58.4 1.0
N C:ALA313 4.4 26.4 1.0
CA C:PRO315 4.5 33.1 1.0
CA C:LYS318 4.5 28.2 1.0
C C:ALA313 4.5 27.6 1.0
N C:PRO315 4.6 32.5 1.0
CD C:PRO319 4.6 23.1 1.0
CA C:VAL314 4.6 28.9 1.0
CG C:LYS312 4.7 36.6 1.0
CA C:ALA313 4.8 27.4 1.0
C C:LEU311 4.9 23.6 1.0
CB C:LEU317 5.0 24.1 1.0
CB C:LYS312 5.0 31.3 1.0
N C:LYS312 5.0 25.2 1.0

Sodium binding site 4 out of 4 in 8bj4

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Sodium binding site 4 out of 4 in the Crystal Structure of Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form


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 Medicago Truncatula Histidinol-Phosphate Aminotransferase (HISN6) in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na411

b:66.3
occ:1.00
 O D:LEU317 2.3 29.6 1.0
O D:LYS312 2.4 30.9 1.0
O D:VAL314 2.5 30.3 1.0
O D:HOH845 2.9 44.8 1.0
C D:LYS312 3.3 30.7 1.0
C D:LEU317 3.5 28.9 1.0
C D:VAL314 3.6 30.9 1.0
O D:LEU311 3.9 24.4 1.0
CA D:LYS312 3.9 30.5 1.0
N D:VAL314 4.0 30.4 1.0
N D:ALA313 4.3 30.2 1.0
C D:ALA313 4.3 31.6 1.0
N D:LEU317 4.4 30.4 1.0
CD D:PRO319 4.4 25.3 1.0
CA D:VAL314 4.4 30.0 1.0
CA D:LYS318 4.4 27.7 1.0
N D:LYS318 4.4 28.0 1.0
CA D:PRO315 4.4 33.8 1.0
O D:PRO315 4.4 33.6 1.0
N D:PRO315 4.5 33.2 1.0
C D:PRO315 4.5 32.8 1.0
CA D:LEU317 4.5 29.5 1.0
CA D:ALA313 4.6 31.2 1.0
O D:HOH748 4.7 53.9 1.0
C D:LEU311 4.8 25.6 1.0
N D:LYS312 4.9 27.8 1.0
CB D:LEU317 4.9 29.5 1.0
O D:ALA313 4.9 33.4 1.0
CG D:LYS312 5.0 42.1 1.0

Reference:

M.Rutkiewicz, I.Nogues, W.Witek, S.Angelaccio, R.Contestabile, M.Ruszkowski. Insights Into the Substrate Specificity, Structure, and Dynamics of Plant Histidinol-Phosphate Aminotransferase (HISN6). Plant Physiol Biochem. V. 196 759 2023.
ISSN: ESSN 1873-2690
PubMed: 36842242
DOI: 10.1016/J.PLAPHY.2023.02.017
Page generated: Wed Oct 9 10:46:33 2024

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