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Sodium in PDB 4r51: Crystal Complex Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine Dinucleotide Phosphate and Phthalic Acid

Enzymatic activity of Crystal Complex Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine Dinucleotide Phosphate and Phthalic Acid

All present enzymatic activity of Crystal Complex Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine Dinucleotide Phosphate and Phthalic Acid:
1.2.1.11;

Protein crystallography data

The structure of Crystal Complex Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine Dinucleotide Phosphate and Phthalic Acid, PDB code: 4r51 was solved by A.G.Pavlovsky, R.E.Viola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.780, 98.399, 63.973, 90.00, 102.65, 90.00
R / Rfree (%) 17.6 / 19.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Complex Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine Dinucleotide Phosphate and Phthalic Acid (pdb code 4r51). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Complex Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine Dinucleotide Phosphate and Phthalic Acid, PDB code: 4r51:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4r51

Go back to Sodium Binding Sites List in 4r51
Sodium binding site 1 out of 3 in the Crystal Complex Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine Dinucleotide Phosphate and Phthalic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Complex Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine Dinucleotide Phosphate and Phthalic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:20.3
occ:1.00
 O A:ALA279 2.3 21.7 1.0
O A:ALA274 2.3 20.5 1.0
O A:PHE276 2.4 18.3 1.0
C A:ALA274 3.2 20.4 1.0
C A:PHE276 3.2 19.6 1.0
N A:PHE276 3.4 19.9 1.0
C A:ALA279 3.5 20.3 1.0
O A:ILE273 3.5 20.0 1.0
C A:ALA275 3.8 20.6 1.0
CA A:PHE276 3.9 19.3 1.0
CA A:ALA274 4.0 20.5 1.0
N A:ALA275 4.0 20.8 1.0
O A:HOH624 4.1 26.9 1.0
N A:ALA279 4.1 18.8 1.0
O A:HOH606 4.1 26.5 1.0
N A:PRO277 4.1 21.2 1.0
CA A:ALA279 4.2 19.0 1.0
CA A:ALA275 4.3 21.2 1.0
CA A:PRO277 4.3 21.7 1.0
O A:ALA275 4.3 21.9 1.0
CB A:ALA279 4.4 19.0 1.0
N A:VAL280 4.5 19.4 1.0
C A:ILE273 4.5 20.4 1.0
N A:GLY278 4.7 20.7 1.0
C A:PRO277 4.7 21.1 1.0
CA A:VAL280 4.7 20.0 1.0
CB A:PHE276 4.7 19.7 1.0
N A:ALA274 4.7 20.5 1.0

Sodium binding site 2 out of 3 in 4r51

Go back to Sodium Binding Sites List in 4r51
Sodium binding site 2 out of 3 in the Crystal Complex Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine Dinucleotide Phosphate and Phthalic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Complex Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine Dinucleotide Phosphate and Phthalic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:20.0
occ:1.00
 O A:GLU343 2.3 22.2 1.0
C A:GLU343 3.4 22.1 1.0
N A:ARG344 4.3 21.7 1.0
CA A:GLU343 4.3 22.0 1.0
CA A:ARG344 4.4 22.9 1.0
N A:GLY345 4.4 21.2 1.0
O A:HIS342 4.6 19.6 1.0
C A:ARG344 4.6 22.2 1.0

Sodium binding site 3 out of 3 in 4r51

Go back to Sodium Binding Sites List in 4r51
Sodium binding site 3 out of 3 in the Crystal Complex Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine Dinucleotide Phosphate and Phthalic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Complex Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine Dinucleotide Phosphate and Phthalic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:31.3
occ:1.00
 O B:HOH561 2.2 33.4 1.0
O B:SER236 2.3 29.0 1.0
O B:HOH612 2.4 36.7 1.0
O B:ASP147 2.6 23.3 1.0
OD1 B:ASP147 2.6 33.7 1.0
O B:HOH551 2.6 27.1 1.0
C B:SER236 3.5 29.0 1.0
C B:ASP147 3.5 23.9 1.0
CA B:ASP147 3.7 25.7 1.0
CG B:ASP147 3.7 32.3 1.0
N B:ALA238 4.0 22.8 1.0
CA B:ILE237 4.1 26.0 1.0
N B:ILE237 4.2 27.0 1.0
OG B:SER236 4.3 32.4 1.0
CB B:ASP147 4.3 27.6 1.0
NZ B:LYS261 4.4 36.5 1.0
CB B:SER236 4.4 31.0 1.0
CA B:SER236 4.5 30.9 1.0
C B:ILE237 4.5 24.1 1.0
O B:LEU146 4.6 26.9 1.0
O1 B:EDO403 4.6 48.8 1.0
OD2 B:ASP147 4.7 38.5 1.0
N B:ARG148 4.7 21.5 1.0
CB B:ALA238 4.8 22.6 1.0
N B:ASP147 4.9 24.9 1.0
CA B:ALA238 5.0 22.2 1.0

Reference:

A.G.Pavlovsky, B.Thangavelu, P.Bhansali, R.E.Viola. A Cautionary Tale of Structure-Guided Inhibitor Development Against An Essential Enzyme in the Aspartate-Biosynthetic Pathway Acta Crystallogr.,Sect.D V. 70 3244 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004714023979
Page generated: Mon Oct 7 18:11:43 2024

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