Sodium in PDB 3ijp: Crystal Structure of Dihydrodipicolinate Reductase From Bartonella Henselae at 2.0A Resolution

All present enzymatic activity of Crystal Structure of Dihydrodipicolinate Reductase From Bartonella Henselae at 2.0A Resolution:
1.3.1.26;

The structure of Crystal Structure of Dihydrodipicolinate Reductase From Bartonella Henselae at 2.0A Resolution, PDB code: 3ijp was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.380, 109.380, 176.950, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.8

The structure of Crystal Structure of Dihydrodipicolinate Reductase From Bartonella Henselae at 2.0A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Dihydrodipicolinate Reductase From Bartonella Henselae at 2.0A Resolution (pdb code 3ijp). 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 Reductase From Bartonella Henselae at 2.0A Resolution, PDB code: 3ijp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Dihydrodipicolinate Reductase From Bartonella Henselae at 2.0A Resolution


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 Reductase From Bartonella Henselae at 2.0A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:34.6 occ:1.00 O A:HOH459 2.2 39.7 1.0 O A:VAL26 2.4 27.1 1.0 O A:ARG23 2.5 43.5 1.0 O A:ILE20 2.5 32.0 1.0 O A:HOH460 2.6 20.2 1.0 C A:ILE20 3.6 32.0 1.0 C A:VAL26 3.6 28.9 1.0 C A:ARG23 3.7 43.0 1.0 CG2 A:ILE20 3.9 26.6 1.0 CA A:GLN21 4.2 39.0 1.0 CA A:GLU27 4.2 28.8 1.0 N A:ARG23 4.3 44.8 1.0 O A:GLN21 4.3 41.9 1.0 N A:GLN21 4.3 36.0 1.0 C A:GLN21 4.3 41.4 1.0 N A:GLU27 4.4 28.4 1.0 CA A:ARG23 4.5 43.5 1.0 CG2 A:VAL26 4.6 27.6 1.0 OE1 A:GLN21 4.6 42.5 1.0 CA A:ILE20 4.6 29.2 1.0 N A:LYS24 4.7 41.6 1.0 CA A:VAL26 4.7 29.3 1.0 N A:VAL26 4.7 31.3 1.0 CA A:LYS24 4.8 40.4 1.0 CB A:ILE20 4.9 28.9 1.0 CB A:ARG23 4.9 43.3 1.0 N A:LEU28 4.9 24.9 1.0 CD A:GLN21 4.9 44.5 1.0 C A:LYS24 5.0 38.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Dihydrodipicolinate Reductase From Bartonella Henselae at 2.0A Resolution


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 Reductase From Bartonella Henselae at 2.0A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:24.2 occ:1.00 O B:HOH494 2.3 29.9 1.0 O B:HOH481 2.3 33.0 1.0 O B:VAL26 2.4 24.0 1.0 O B:ILE20 2.5 22.7 1.0 O B:ARG23 2.5 30.1 1.0 O B:HOH332 2.6 15.6 1.0 C B:VAL26 3.6 24.5 1.0 C B:ILE20 3.6 23.3 1.0 C B:ARG23 3.7 30.1 1.0 CG2 B:ILE20 3.9 17.7 1.0 CA B:GLU27 4.1 24.4 1.0 O B:HOH480 4.1 33.2 1.0 O B:GLN21 4.2 28.6 1.0 CA B:GLN21 4.2 27.7 1.0 N B:GLU27 4.2 24.6 1.0 C B:GLN21 4.3 28.9 1.0 N B:ARG23 4.3 31.4 1.0 N B:GLN21 4.3 25.5 1.0 CA B:ARG23 4.5 30.1 1.0 OE1 B:GLN21 4.5 33.7 1.0 CG2 B:VAL26 4.6 22.1 1.0 CA B:ILE20 4.6 21.7 1.0 N B:LYS24 4.7 29.7 1.0 CA B:VAL26 4.7 24.0 1.0 N B:LEU28 4.7 22.3 1.0 N B:VAL26 4.8 25.0 1.0 CA B:LYS24 4.8 30.4 1.0 CB B:ILE20 4.9 21.7 1.0 C B:GLU27 4.9 23.1 1.0 CD B:GLN21 5.0 35.3 1.0

A.R.Cala, M.T.Nadeau, J.Abendroth, B.L.Staker, A.R.Reers, A.W.Weatherhead, R.C.Dobson, P.J.Myler, A.O.Hudson. The Crystal Structure of Dihydrodipicolinate Reductase From the Human-Pathogenic Bacterium Bartonella Henselae Strain Houston-1 at 2.3 Angstrom Resolution. Acta Crystallogr F Struct V. 72 885 2016BIOL Commun.
ISSN: ISSN 2053-230X
PubMed: 27917836
DOI: 10.1107/S2053230X16018525