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Sodium in PDB 4r41: Complex Crystal Structure of 4-Nitro-2-Phosphono-Benzoic Acid with Sp- Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-Dinucleotide

Enzymatic activity of Complex Crystal Structure of 4-Nitro-2-Phosphono-Benzoic Acid with Sp- Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-Dinucleotide

All present enzymatic activity of Complex Crystal Structure of 4-Nitro-2-Phosphono-Benzoic Acid with Sp- Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-Dinucleotide:
1.2.1.11;

Protein crystallography data

The structure of Complex Crystal Structure of 4-Nitro-2-Phosphono-Benzoic Acid with Sp- Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-Dinucleotide, PDB code: 4r41 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 / 1.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.595, 97.733, 63.943, 90.00, 102.52, 90.00
R / Rfree (%) 18.8 / 21.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Complex Crystal Structure of 4-Nitro-2-Phosphono-Benzoic Acid with Sp- Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-Dinucleotide (pdb code 4r41). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Complex Crystal Structure of 4-Nitro-2-Phosphono-Benzoic Acid with Sp- Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-Dinucleotide, PDB code: 4r41:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4r41

Go back to Sodium Binding Sites List in 4r41
Sodium binding site 1 out of 3 in the Complex Crystal Structure of 4-Nitro-2-Phosphono-Benzoic Acid with Sp- Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-Dinucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex Crystal Structure of 4-Nitro-2-Phosphono-Benzoic Acid with Sp- Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:14.5
occ:1.00
 O A:PHE276 2.2 12.7 1.0
O A:ALA279 2.3 13.8 1.0
O A:ALA274 2.4 17.8 1.0
O A:HOH614 2.6 24.6 1.0
C A:PHE276 3.1 13.6 1.0
C A:ALA274 3.3 16.0 1.0
N A:PHE276 3.3 14.3 1.0
C A:ALA279 3.4 13.2 1.0
O A:ILE273 3.4 14.5 1.0
C A:ALA275 3.8 15.3 1.0
CA A:PHE276 3.8 13.6 1.0
O A:HOH639 3.9 19.9 1.0
N A:ALA279 4.0 12.3 1.0
N A:ALA275 4.1 15.2 1.0
N A:PRO277 4.1 15.2 1.0
CA A:ALA279 4.1 12.1 1.0
CA A:ALA274 4.1 16.6 1.0
O A:HOH621 4.2 22.2 1.0
CA A:PRO277 4.3 15.1 1.0
CA A:ALA275 4.3 15.8 1.0
CB A:ALA279 4.3 11.7 1.0
O A:ALA275 4.4 16.1 1.0
N A:VAL280 4.5 12.5 1.0
C A:ILE273 4.5 15.6 1.0
N A:GLY278 4.5 14.4 1.0
C A:PRO277 4.6 14.8 1.0
CB A:PHE276 4.6 13.0 1.0
CA A:VAL280 4.7 12.6 1.0
N A:ALA274 4.8 15.5 1.0

Sodium binding site 2 out of 3 in 4r41

Go back to Sodium Binding Sites List in 4r41
Sodium binding site 2 out of 3 in the Complex Crystal Structure of 4-Nitro-2-Phosphono-Benzoic Acid with Sp- Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-Dinucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex Crystal Structure of 4-Nitro-2-Phosphono-Benzoic Acid with Sp- Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:15.4
occ:1.00
 O A:GLU343 2.3 15.0 1.0
O A:HOH632 2.5 25.5 1.0
C A:GLU343 3.4 15.1 1.0
N A:ARG344 4.2 14.6 1.0
CA A:GLU343 4.3 16.0 1.0
CA A:ARG344 4.3 15.4 1.0
N A:GLY345 4.5 15.2 1.0
C A:ARG344 4.6 14.8 1.0
O A:HIS342 4.6 15.3 1.0

Sodium binding site 3 out of 3 in 4r41

Go back to Sodium Binding Sites List in 4r41
Sodium binding site 3 out of 3 in the Complex Crystal Structure of 4-Nitro-2-Phosphono-Benzoic Acid with Sp- Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-Dinucleotide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Complex Crystal Structure of 4-Nitro-2-Phosphono-Benzoic Acid with Sp- Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:23.3
occ:1.00
 O B:HOH567 2.3 29.1 1.0
O B:SER236 2.3 24.0 1.0
O B:HOH619 2.4 30.7 1.0
O B:HOH558 2.4 24.7 1.0
OD1 B:ASP147 2.5 27.3 1.0
O B:ASP147 2.5 17.4 1.0
C B:ASP147 3.4 18.6 1.0
C B:SER236 3.4 23.4 1.0
CG B:ASP147 3.5 26.6 1.0
CA B:ASP147 3.6 19.4 1.0
N B:ALA238 4.0 19.4 1.0
CA B:ILE237 4.0 21.0 1.0
N B:ILE237 4.1 21.8 1.0
CB B:ASP147 4.2 22.1 1.0
OG B:SER236 4.2 25.3 1.0
NZ B:LYS261 4.3 29.8 1.0
CB B:SER236 4.4 24.8 1.0
OD2 B:ASP147 4.5 30.2 1.0
C B:ILE237 4.5 19.7 1.0
CA B:SER236 4.5 24.2 1.0
O B:LEU146 4.5 19.3 1.0
O1 B:EDO406 4.6 44.3 1.0
N B:ARG148 4.6 16.9 1.0
CB B:ALA238 4.8 18.3 1.0
N B:ASP147 4.8 18.6 1.0
CE B:LYS261 5.0 29.4 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 18:11:14 2024

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