Sodium in PDB 3drw: Crystal Structure of A Phosphofructokinase From Pyrococcus Horikoshii OT3 with Amp

All present enzymatic activity of Crystal Structure of A Phosphofructokinase From Pyrococcus Horikoshii OT3 with Amp:
2.7.1.146;

The structure of Crystal Structure of A Phosphofructokinase From Pyrococcus Horikoshii OT3 with Amp, PDB code: 3drw was solved by A.U.Singer, T.Skarina, S.Kochinyan, G.Brown, M.E.Cuff, A.M.Edwards, A.Joachimiak, A.Savchenko, A.F.Yakunin, Z.Jia, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.45 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.464, 104.190, 70.844, 90.00, 105.09, 90.00
R / Rfree (%)	17.2 / 22.4

The binding sites of Sodium atom in the Crystal Structure of A Phosphofructokinase From Pyrococcus Horikoshii OT3 with Amp (pdb code 3drw). 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 A Phosphofructokinase From Pyrococcus Horikoshii OT3 with Amp, PDB code: 3drw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Phosphofructokinase From Pyrococcus Horikoshii OT3 with Amp


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 A Phosphofructokinase From Pyrococcus Horikoshii OT3 with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1485 b:17.8 occ:1.00 OG1 A:THR104 3.0 20.9 1.0 O A:HOH1650 3.2 28.0 1.0 O A:HOH1506 3.2 22.5 1.0 N A:ILE375 3.3 22.9 1.0 NE A:ARG369 3.3 23.9 1.0 CD A:ARG369 3.6 21.3 1.0 CG1 A:ILE375 3.7 20.0 1.0 O A:HOH1531 3.7 23.6 1.0 CB A:ILE375 3.8 21.7 1.0 CA A:THR104 3.8 21.1 1.0 CG A:ARG369 3.9 24.1 1.0 CB A:THR104 3.9 22.9 1.0 CA A:ASP374 3.9 24.8 1.0 O A:HOH1570 4.1 28.6 1.0 C A:ASP374 4.1 24.5 1.0 CA A:ILE375 4.2 21.1 1.0 N A:THR104 4.2 21.1 1.0 CG2 A:THR104 4.2 21.2 1.0 CZ A:ARG369 4.4 24.8 1.0 CB A:ASP374 4.4 26.2 1.0 O A:ILE375 4.6 22.7 1.0 NH2 A:ARG369 4.7 25.7 1.0 C A:ASN103 4.7 21.2 1.0 O A:HOH1524 4.9 26.3 1.0 C A:ILE375 4.9 22.3 1.0 O A:ASN103 4.9 22.3 1.0 O A:GLY373 5.0 24.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Phosphofructokinase From Pyrococcus Horikoshii OT3 with Amp


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 A Phosphofructokinase From Pyrococcus Horikoshii OT3 with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1486 b:43.8 occ:1.00 O2P A:AMP1484 2.5 56.4 1.0 N A:GLY432 3.0 23.6 1.0 O A:HOH1591 3.4 36.2 1.0 O A:HOH1762 3.5 38.6 1.0 CA A:GLY432 3.6 23.3 1.0 N A:LEU431 3.6 25.5 1.0 O A:HOH1641 3.7 57.8 1.0 C5' A:AMP1484 3.7 35.3 1.0 P A:AMP1484 3.8 57.3 1.0 C A:GLY430 3.8 27.4 1.0 O5' A:AMP1484 3.9 46.5 1.0 CA A:GLY430 4.0 29.0 1.0 N A:GLY430 4.0 28.9 1.0 C A:LEU431 4.1 23.9 1.0 CA A:LEU431 4.3 24.5 1.0 O3P A:AMP1484 4.4 58.3 1.0 N A:ASP433 4.4 23.8 1.0 O A:GLY430 4.5 27.0 1.0 C A:GLY432 4.5 24.9 1.0 O A:HOH1730 4.8 52.6 1.0 CB A:LEU431 4.8 22.2 1.0 C4' A:AMP1484 4.9 30.3 1.0

M.A.Currie, F.Merino, T.Skarina, A.H.Wong, A.Singer, G.Brown, A.Savchenko, A.Caniuguir, V.Guixe, A.F.Yakunin, Z.Jia. Adp-Dependent 6-Phosphofructokinase From Pyrococcus Horikoshii OT3: Structure Determination and Biochemical Characterization of PH1645. J.Biol.Chem. V. 284 22664 2009.
ISSN: ISSN 0021-9258
PubMed: 19553681
DOI: 10.1074/JBC.M109.012401