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Sodium in PDB 4r5m: Crystal Structure of Vc-Aspartate Beta-Semialdehyde-Dehydrogenase with Nadp and 4-Nitro-2-Phosphono-Benzoic Acid

Enzymatic activity of Crystal Structure of Vc-Aspartate Beta-Semialdehyde-Dehydrogenase with Nadp and 4-Nitro-2-Phosphono-Benzoic Acid

All present enzymatic activity of Crystal Structure of Vc-Aspartate Beta-Semialdehyde-Dehydrogenase with Nadp and 4-Nitro-2-Phosphono-Benzoic Acid:
1.2.1.11;

Protein crystallography data

The structure of Crystal Structure of Vc-Aspartate Beta-Semialdehyde-Dehydrogenase with Nadp and 4-Nitro-2-Phosphono-Benzoic Acid, PDB code: 4r5m was solved by A.G.Pavlovsky, B.Thangavelu, P.Bhansali, R.E.Viola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.85 / 1.89
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.353, 107.353, 152.837, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Vc-Aspartate Beta-Semialdehyde-Dehydrogenase with Nadp and 4-Nitro-2-Phosphono-Benzoic Acid (pdb code 4r5m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Vc-Aspartate Beta-Semialdehyde-Dehydrogenase with Nadp and 4-Nitro-2-Phosphono-Benzoic Acid, PDB code: 4r5m:

Sodium binding site 1 out of 1 in 4r5m

Go back to Sodium Binding Sites List in 4r5m
Sodium binding site 1 out of 1 in the Crystal Structure of Vc-Aspartate Beta-Semialdehyde-Dehydrogenase with Nadp and 4-Nitro-2-Phosphono-Benzoic Acid


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 Vc-Aspartate Beta-Semialdehyde-Dehydrogenase with Nadp and 4-Nitro-2-Phosphono-Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:28.4
occ:1.00
 O A:PHE212 2.3 21.6 1.0
O A:HOH698 2.4 27.4 1.0
O A:HOH640 2.4 24.6 1.0
O A:GLY210 2.5 26.4 1.0
OG1 A:THR214 2.6 24.9 1.0
O A:HOH533 2.6 25.8 1.0
C A:PHE212 3.5 21.8 1.0
C A:GLY210 3.6 25.4 1.0
CB A:THR214 3.7 24.2 1.0
N A:THR214 3.8 24.4 1.0
CG2 A:THR214 3.9 24.2 1.0
N A:PHE212 4.0 23.0 1.0
O A:HOH593 4.0 33.4 1.0
O A:HOH728 4.2 36.5 1.0
O A:SER209 4.2 23.9 1.0
CA A:GLY210 4.3 24.7 1.0
CA A:PHE212 4.3 22.0 1.0
C A:SER211 4.3 24.8 1.0
CA A:THR214 4.3 24.8 1.0
O A:HOH622 4.3 31.4 1.0
N A:SER211 4.5 25.1 1.0
O A:HOH787 4.5 42.1 1.0
N A:PRO213 4.6 22.6 1.0
CB A:PHE212 4.6 21.0 1.0
C A:PRO213 4.6 24.1 1.0
CA A:PRO213 4.6 23.5 1.0
CA A:SER211 4.7 26.1 1.0
O A:HOH656 4.8 27.6 1.0
O A:SER211 4.8 24.9 1.0
C A:THR214 4.9 24.9 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: Tue Dec 15 07:09:34 2020

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