Sodium in PDB 6ef6: Structure of the Microcompartment-Associated Aminopropanol Kinase

The structure of Structure of the Microcompartment-Associated Aminopropanol Kinase, PDB code: 6ef6 was solved by E.Mallette, M.S.Kimber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.83 / 1.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.010, 70.050, 60.720, 90.00, 95.12, 90.00
R / Rfree (%)	14.9 / 16.8

The binding sites of Sodium atom in the Structure of the Microcompartment-Associated Aminopropanol Kinase (pdb code 6ef6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Microcompartment-Associated Aminopropanol Kinase, PDB code: 6ef6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Microcompartment-Associated Aminopropanol Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Microcompartment-Associated Aminopropanol Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:44.0 occ:1.00 O A:HOH557 2.0 45.1 1.0 O A:HOH661 2.2 24.4 1.0 OD2 A:ASP211 2.2 19.7 1.0 O A:HOH658 2.5 30.4 1.0 OD2 A:ASP232 2.6 27.0 1.0 HH21 A:ARG213 3.0 30.6 0.5 CG A:ASP211 3.3 17.7 1.0 CG A:ASP232 3.4 25.9 1.0 OD1 A:ASP232 3.6 24.5 1.0 HD21 A:ASN216 3.7 23.5 1.0 HB3 A:ASP211 3.7 19.3 1.0 NH2 A:ARG213 3.8 25.6 0.5 HB2 A:ASP211 3.8 19.3 1.0 OD2 A:ASP235 3.8 23.3 1.0 H A:GLU33 3.8 44.1 1.0 CB A:ASP211 3.9 16.2 1.0 HH22 A:ARG213 3.9 30.6 0.5 H151 A:JFN402 4.0 58.6 1.0 HA A:SER32 4.0 40.9 1.0 HH21 A:ARG213 4.1 29.4 0.5 O A:HOH572 4.1 31.7 1.0 OD1 A:ASP211 4.3 19.6 1.0 O A:HOH522 4.3 34.3 1.0 NH2 A:ARG213 4.4 24.6 0.5 HB2 A:GLU33 4.4 70.9 1.0 ND2 A:ASN216 4.5 19.6 1.0 CG A:ASP235 4.5 25.1 1.0 HH22 A:ARG213 4.5 29.4 0.5 HB2 A:ASP235 4.5 25.4 1.0 HG3 A:GLU33 4.5 85.4 1.0 H091 A:JFN402 4.6 68.8 1.0 N A:GLU33 4.6 36.8 1.0 HB3 A:ASP232 4.7 25.4 1.0 HE A:ARG213 4.7 25.7 0.5 HD22 A:ASN216 4.7 23.5 1.0 H153 A:JFN402 4.7 58.6 1.0 CB A:ASP232 4.7 21.2 1.0 HB3 A:ASP234 4.7 26.3 1.0 N04 A:JFN402 4.8 57.5 1.0 H1 A:JFN402 4.8 68.9 1.0 O A:ASP232 4.8 16.9 1.0 C15 A:JFN402 4.8 48.9 1.0 H A:ASP235 4.9 21.8 1.0 CZ A:ARG213 5.0 21.9 0.5 O A:HOH575 5.0 17.0 1.0 CA A:SER32 5.0 34.2 1.0 OD1 A:ASP235 5.0 23.8 1.0

Sodium binding site 2 out of 2 in the Structure of the Microcompartment-Associated Aminopropanol Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Microcompartment-Associated Aminopropanol Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:23.1 occ:1.00 O A:GLN171 2.2 18.4 1.0 O A:HOH573 2.3 21.1 1.0 O A:VAL176 2.3 20.3 1.0 O A:HOH598 2.3 24.3 1.0 O A:HOH686 2.8 45.6 1.0 HB A:VAL176 3.4 15.8 1.0 C A:GLN171 3.5 15.9 1.0 C A:VAL176 3.5 17.0 1.0 HA A:ASP172 3.6 23.2 1.0 HG12 A:VAL176 3.6 20.7 1.0 O A:HOH710 3.9 32.9 1.0 HA2 A:GLY177 4.0 19.3 1.0 CB A:VAL176 4.1 13.2 1.0 O A:HOH719 4.2 31.4 1.0 HB3 A:GLN171 4.2 19.8 1.0 HA A:GLN171 4.2 19.3 1.0 OG1 A:THR181 4.2 15.9 1.0 HG1 A:THR181 4.3 19.0 1.0 CG1 A:VAL176 4.3 17.3 1.0 O A:HOH645 4.3 39.2 1.0 CA A:ASP172 4.3 19.4 1.0 N A:ASP172 4.3 16.1 1.0 CA A:VAL176 4.3 15.2 1.0 O A:ALA173 4.4 18.9 1.0 CA A:GLN171 4.4 16.1 1.0 HG11 A:VAL176 4.5 20.7 1.0 N A:GLY177 4.5 16.0 1.0 H A:VAL176 4.6 18.4 1.0 CA A:GLY177 4.7 16.1 1.0 C A:ASP172 4.7 20.0 1.0 CB A:GLN171 4.8 16.6 1.0 H A:ALA173 4.9 21.7 1.0 N A:VAL176 4.9 15.4 1.0 N A:ALA173 5.0 18.1 1.0

E.Mallette, M.S.Kimber. Structural and Kinetic Characterization of (S)-1-Amino-2-Propanol Kinase From the Aminoacetone Utilization Microcompartment Ofmycobacterium Smegmatis. J.Biol.Chem. V. 293 19909 2018.
ISSN: ESSN 1083-351X
PubMed: 30361441
DOI: 10.1074/JBC.RA118.005485