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Sodium in PDB 4iqw: Tdt Core in Complex with Inhibitor (2Z,5E)-6-[4-(4-Fluorobenzoyl)-1H- Pyrrol-2-Yl]-2-Hydroxy-4-Oxohexa-2,5-Dienoic Acid and Ssdna

Enzymatic activity of Tdt Core in Complex with Inhibitor (2Z,5E)-6-[4-(4-Fluorobenzoyl)-1H- Pyrrol-2-Yl]-2-Hydroxy-4-Oxohexa-2,5-Dienoic Acid and Ssdna

All present enzymatic activity of Tdt Core in Complex with Inhibitor (2Z,5E)-6-[4-(4-Fluorobenzoyl)-1H- Pyrrol-2-Yl]-2-Hydroxy-4-Oxohexa-2,5-Dienoic Acid and Ssdna:
2.7.7.31;

Protein crystallography data

The structure of Tdt Core in Complex with Inhibitor (2Z,5E)-6-[4-(4-Fluorobenzoyl)-1H- Pyrrol-2-Yl]-2-Hydroxy-4-Oxohexa-2,5-Dienoic Acid and Ssdna, PDB code: 4iqw was solved by J.Gouge, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.49 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.650, 84.670, 114.730, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.9

Other elements in 4iqw:

The structure of Tdt Core in Complex with Inhibitor (2Z,5E)-6-[4-(4-Fluorobenzoyl)-1H- Pyrrol-2-Yl]-2-Hydroxy-4-Oxohexa-2,5-Dienoic Acid and Ssdna also contains other interesting chemical elements:

Fluorine (F) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Tdt Core in Complex with Inhibitor (2Z,5E)-6-[4-(4-Fluorobenzoyl)-1H- Pyrrol-2-Yl]-2-Hydroxy-4-Oxohexa-2,5-Dienoic Acid and Ssdna (pdb code 4iqw). 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 Tdt Core in Complex with Inhibitor (2Z,5E)-6-[4-(4-Fluorobenzoyl)-1H- Pyrrol-2-Yl]-2-Hydroxy-4-Oxohexa-2,5-Dienoic Acid and Ssdna, PDB code: 4iqw:

Sodium binding site 1 out of 1 in 4iqw

Go back to Sodium Binding Sites List in 4iqw
Sodium binding site 1 out of 1 in the Tdt Core in Complex with Inhibitor (2Z,5E)-6-[4-(4-Fluorobenzoyl)-1H- Pyrrol-2-Yl]-2-Hydroxy-4-Oxohexa-2,5-Dienoic Acid and Ssdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tdt Core in Complex with Inhibitor (2Z,5E)-6-[4-(4-Fluorobenzoyl)-1H- Pyrrol-2-Yl]-2-Hydroxy-4-Oxohexa-2,5-Dienoic Acid and Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:59.7
occ:1.00
 O A:THR253 2.4 47.8 1.0
OP1 C:DC3 2.7 0.9 1.0
O A:VAL258 2.7 40.6 1.0
O A:VAL255 2.8 47.3 1.0
C A:THR253 3.4 48.3 1.0
OP2 C:DC3 3.5 0.4 1.0
P C:DC3 3.5 0.2 1.0
CG2 A:THR253 3.6 69.0 1.0
C A:VAL258 3.7 43.5 1.0
C A:VAL255 3.8 46.6 1.0
CA A:THR253 3.9 45.3 1.0
N A:VAL258 3.9 39.8 1.0
N A:GLY257 4.3 41.2 1.0
CA A:VAL258 4.3 40.1 1.0
CA A:PHE256 4.3 42.7 1.0
CB A:THR253 4.3 54.7 1.0
N A:PHE256 4.4 43.0 1.0
N A:VAL255 4.5 43.4 1.0
O A:HOH712 4.5 53.1 1.0
O5' C:DC3 4.6 0.7 1.0
N A:SER254 4.6 44.7 1.0
CB A:VAL258 4.7 43.0 1.0
C A:PHE256 4.7 45.4 1.0
C A:SER254 4.7 48.9 1.0
CA A:VAL255 4.8 42.2 1.0
O3' C:DC2 4.8 0.3 1.0
N A:GLY259 4.8 40.8 1.0
C A:GLY257 5.0 42.8 1.0
CA A:SER254 5.0 43.2 1.0

Reference:

R.Costi, G.Cuzzucoli Crucitti, L.Pescatori, A.Messore, L.Scipione, S.Tortorella, A.Amoroso, E.Crespan, P.Campiglia, B.Maresca, A.Porta, I.Granata, E.Novellino, J.Gouge, M.Delarue, G.Maga, R.Di Santo. New Nucleotide-Competitive Non-Nucleoside Inhibitors of Terminal Deoxynucleotidyl Transferase: Discovery, Characterization, and Crystal Structure in Complex with the Target. J.Med.Chem. V. 56 7431 2013.
ISSN: ISSN 0022-2623
PubMed: 23968551
DOI: 10.1021/JM4010187
Page generated: Mon Oct 7 16:05:56 2024

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