Sodium in PDB 5j5d: Crystal Structure of Dihydrodipicolinate Synthase From Mycobacterium Tuberculosis in Complex with Alpha-Ketopimelic Acid

All present enzymatic activity of Crystal Structure of Dihydrodipicolinate Synthase From Mycobacterium Tuberculosis in Complex with Alpha-Ketopimelic Acid:
4.3.3.7;

The structure of Crystal Structure of Dihydrodipicolinate Synthase From Mycobacterium Tuberculosis in Complex with Alpha-Ketopimelic Acid, PDB code: 5j5d was solved by V.Navratna, B.Gopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.78 / 2.40
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.780, 84.780, 83.920, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 25.1

The binding sites of Sodium atom in the Crystal Structure of Dihydrodipicolinate Synthase From Mycobacterium Tuberculosis in Complex with Alpha-Ketopimelic Acid (pdb code 5j5d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Dihydrodipicolinate Synthase From Mycobacterium Tuberculosis in Complex with Alpha-Ketopimelic Acid, PDB code: 5j5d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Dihydrodipicolinate Synthase From Mycobacterium Tuberculosis in Complex with Alpha-Ketopimelic 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 Dihydrodipicolinate Synthase From Mycobacterium Tuberculosis in Complex with Alpha-Ketopimelic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:15.6 occ:1.00 OE2 A:GLU154 2.8 54.9 1.0 NZ A:LYS174 3.2 19.1 1.0 O A:HOH566 3.2 36.8 1.0 O A:HOH567 3.6 36.1 1.0 CB A:PRO152 3.6 16.6 1.0 CA A:GLU154 3.7 21.1 1.0 CD A:PRO155 3.7 20.9 1.0 CE A:LYS174 3.9 18.2 1.0 O A:ILE153 3.9 21.1 1.0 CG A:PRO152 3.9 16.1 1.0 CD A:GLU154 3.9 46.7 1.0 CD A:LYS174 4.0 17.0 1.0 N A:GLU154 4.2 21.2 1.0 C A:ILE153 4.2 21.2 1.0 N A:PRO155 4.4 22.3 1.0 CB A:GLU154 4.5 31.1 1.0 C A:GLU154 4.5 22.5 1.0 O A:HOH532 4.6 17.9 1.0 CG A:GLU154 4.6 39.4 1.0 OE1 A:GLU154 4.8 44.9 1.0 CA A:PRO152 4.9 28.4 1.0 CG A:PRO155 5.0 21.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Dihydrodipicolinate Synthase From Mycobacterium Tuberculosis in Complex with Alpha-Ketopimelic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Dihydrodipicolinate Synthase From Mycobacterium Tuberculosis in Complex with Alpha-Ketopimelic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:31.7 occ:1.00 OD2 A:ASP156 3.0 31.1 1.0 CB A:GLU154 3.2 31.1 1.0 CG A:ASP156 3.2 32.4 1.0 N A:ASP156 3.2 33.0 1.0 CB A:ASP156 3.2 32.4 1.0 CD A:PRO155 3.7 20.9 1.0 CG A:PRO155 3.8 21.7 1.0 CA A:ASP156 3.8 27.1 1.0 N A:PRO155 3.8 22.3 1.0 OD1 A:ASP156 4.0 36.9 1.0 CG A:GLU154 4.1 39.4 1.0 C A:GLU154 4.1 22.5 1.0 CA A:GLU154 4.2 21.1 1.0 C A:PRO155 4.3 39.5 1.0 CA A:PRO155 4.5 23.7 1.0 CD A:GLU154 4.5 46.7 1.0 OE2 A:GLU154 4.6 54.9 1.0 CB A:PRO155 4.6 28.6 1.0 O A:GLU154 4.8 40.4 1.0 N A:THR157 4.8 26.9 1.0 C A:ASP156 4.8 28.0 1.0

P.Shrivastava, V.Navratna, Y.Silla, R.P.Dewangan, A.Pramanik, S.Chaudhary, G.Rayasam, A.Kumar, B.Gopal, S.Ramachandran. Inhibition of Mycobacterium Tuberculosis Dihydrodipicolinate Synthase By Alpha-Ketopimelic Acid and Its Other Structural Analogues Sci Rep V. 6 30827 2016.
ISSN: ESSN 2045-2322
PubMed: 27501775
DOI: 10.1038/SREP30827