Sodium in PDB 7zi3: Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor

Enzymatic activity of Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor

All present enzymatic activity of Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor:
2.7.1.113; 2.7.1.74; 2.7.1.76;

Protein crystallography data

The structure of Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor, PDB code: 7zi3 was solved by K.Ben-Yaala, M.Saez-Ayala, S.Betzi, E.Rebuffet, X.Morelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.75 / 1.90
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 68.94, 68.94, 120.763, 90, 90, 90
R / Rfree (%) 19 / 23

Other elements in 7zi3:

The structure of Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor (pdb code 7zi3). 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 Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor, PDB code: 7zi3:

Sodium binding site 1 out of 1 in 7zi3

Go back to Sodium Binding Sites List in 7zi3
Sodium binding site 1 out of 1 in the Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor


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 Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:51.2
occ:1.00
 O A:LYS42 2.2 47.3 1.0
O A:SER45 2.3 52.9 1.0
O A:TRP48 2.3 51.0 1.0
O A:HOH463 2.3 54.9 1.0
C A:SER45 3.4 61.1 1.0
C A:LYS42 3.4 46.5 1.0
C A:TRP48 3.4 43.7 1.0
CA A:LYS42 4.0 50.0 1.0
CA A:GLU46 4.0 56.5 1.0
N A:GLU46 4.1 51.3 1.0
N A:TRP48 4.1 48.2 1.0
CA A:TRP48 4.1 44.5 1.0
CB A:TRP48 4.2 46.4 1.0
C A:GLU46 4.4 51.2 1.0
N A:SER45 4.4 48.9 1.0
CB A:LYS42 4.5 55.7 1.0
N A:GLN43 4.5 49.3 1.0
CA A:SER45 4.5 50.0 1.0
N A:GLU49 4.5 44.7 1.0
O A:GLU46 4.6 55.1 1.0
OE1 A:GLU49 4.6 63.1 1.0
OE2 A:GLU49 4.7 79.8 1.0
CD A:GLU49 4.8 67.0 1.0
CA A:GLU49 4.8 51.1 1.0
CA A:GLN43 4.9 57.6 1.0
N A:ASP47 4.9 47.4 1.0

Reference:

M.Saez-Ayala, L.Hoffer, S.Abel, K.Ben Yaala, B.Sicard, G.P.Andrieu, M.Latiri, E.K.Davison, M.A.Ciufolini, P.Bremond, E.Rebuffet, P.Roche, C.Derviaux, E.Voisset, C.Montersino, R.Castellano, Y.Collette, V.Asnafi, S.Betzi, P.Dubreuil, S.Combes, X.Morelli. From A Drug Repositioning to A Structure-Based Drug Design Approach to Tackle Acute Lymphoblastic Leukemia. Nat Commun V. 14 3079 2023.
ISSN: ESSN 2041-1723
PubMed: 37248212
DOI: 10.1038/S41467-023-38668-2
Page generated: Wed Oct 9 10:16:38 2024

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