Sodium in PDB 5ld8: GSK3011724A Cocrystallised with Mycobacterium Tuberculosis H37RV Kasa

All present enzymatic activity of GSK3011724A Cocrystallised with Mycobacterium Tuberculosis H37RV Kasa:
2.3.1.41;

The structure of GSK3011724A Cocrystallised with Mycobacterium Tuberculosis H37RV Kasa, PDB code: 5ld8 was solved by C.W.Chung, M.Neu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.99 / 2.13
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	77.338, 77.338, 147.675, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 18.6

The binding sites of Sodium atom in the GSK3011724A Cocrystallised with Mycobacterium Tuberculosis H37RV Kasa (pdb code 5ld8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the GSK3011724A Cocrystallised with Mycobacterium Tuberculosis H37RV Kasa, PDB code: 5ld8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the GSK3011724A Cocrystallised with Mycobacterium Tuberculosis H37RV Kasa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of GSK3011724A Cocrystallised with Mycobacterium Tuberculosis H37RV Kasa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:33.9 occ:1.00 OD1 A:ASN399 2.4 32.3 1.0 OE1 A:GLU354 2.4 36.5 1.0 O A:ASN400 2.7 37.4 1.0 OD1 A:ASN309 2.8 35.4 1.0 O A:ASN309 2.9 38.2 1.0 O A:ALA310 3.0 36.7 1.0 C A:ALA310 3.4 36.2 1.0 CG A:ASN399 3.6 34.9 1.0 C A:ASN309 3.6 36.4 1.0 CD A:GLU354 3.6 35.9 1.0 N A:ASN400 3.7 35.6 1.0 CB A:GLU354 3.7 35.2 1.0 CG A:ASN309 3.7 35.0 1.0 C A:ASN400 3.8 37.3 1.0 N A:HIS311 3.8 35.6 1.0 CA A:HIS311 4.0 36.0 1.0 N A:ALA310 4.1 35.8 1.0 O A:HOH613 4.1 35.8 1.0 CB A:ASN309 4.2 35.6 1.0 CA A:ALA310 4.2 36.0 1.0 CG A:GLU354 4.2 35.7 1.0 ND2 A:ASN399 4.3 34.3 1.0 CA A:ASN400 4.3 36.3 1.0 C A:ASN399 4.4 35.4 1.0 CA A:ASN309 4.5 35.4 1.0 CA A:ASN399 4.6 35.0 1.0 OE2 A:GLU354 4.6 35.7 1.0 CB A:ASN399 4.7 35.3 1.0 OG A:SER401 4.7 39.7 1.0 CB A:ASN400 4.8 34.8 1.0 ND2 A:ASN309 4.8 35.8 1.0 N A:SER401 4.9 36.9 1.0 C A:HIS311 5.0 34.5 1.0

Sodium binding site 2 out of 2 in the GSK3011724A Cocrystallised with Mycobacterium Tuberculosis H37RV Kasa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of GSK3011724A Cocrystallised with Mycobacterium Tuberculosis H37RV Kasa within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:25.8 occ:1.00 OE1 B:GLU354 2.2 28.9 1.0 OD1 B:ASN399 2.5 29.8 1.0 O B:ASN400 2.6 30.3 1.0 O B:ASN309 2.8 30.8 1.0 OD1 B:ASN309 2.8 32.7 1.0 O B:ALA310 2.9 33.2 1.0 C B:ALA310 3.3 32.6 1.0 CD B:GLU354 3.4 29.3 1.0 C B:ASN309 3.5 31.4 1.0 N B:HIS311 3.7 32.6 1.0 CG B:ASN399 3.7 30.1 1.0 CG B:ASN309 3.7 31.8 1.0 C B:ASN400 3.7 30.9 1.0 CB B:GLU354 3.7 27.7 1.0 O B:HOH623 3.8 39.0 1.0 N B:ASN400 3.8 30.0 1.0 CA B:HIS311 3.9 32.8 1.0 N B:ALA310 4.0 32.4 1.0 CA B:ALA310 4.1 32.1 1.0 CB B:ASN309 4.1 30.9 1.0 CG B:GLU354 4.1 28.7 1.0 CA B:ASN400 4.3 29.9 1.0 OE2 B:GLU354 4.4 31.8 1.0 CA B:ASN309 4.4 31.4 1.0 ND2 B:ASN399 4.5 29.4 1.0 C B:ASN399 4.5 29.1 1.0 CA B:ASN399 4.7 28.8 1.0 CB B:ASN399 4.8 28.8 1.0 CB B:ASN400 4.8 28.9 1.0 ND2 B:ASN309 4.9 32.2 1.0 N B:SER401 4.9 32.9 1.0 C B:HIS311 4.9 32.2 1.0 CB B:HIS311 5.0 33.8 1.0

K.A.Abrahams, C.W.Chung, S.Ghidelli-Disse, J.Rullas, M.J.Rebollo-Lopez, S.S.Gurcha, J.A.Cox, A.Mendoza, E.Jimenez-Navarro, M.S.Martinez-Martinez, M.Neu, A.Shillings, P.Homes, A.Argyrou, R.Casanueva, N.J.Loman, P.J.Moynihan, J.Lelievre, C.Selenski, M.Axtman, L.Kremer, M.Bantscheff, I.Angulo-Barturen, M.C.Izquierdo, N.C.Cammack, G.Drewes, L.Ballell, D.Barros, G.S.Besra, R.H.Bates. Identification of Kasa As the Cellular Target of An Anti-Tubercular Scaffold. Nat Commun V. 7 12581 2016.
ISSN: ESSN 2041-1723
PubMed: 27581223
DOI: 10.1038/NCOMMS12581