Sodium in PDB 2dua: Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++

The structure of Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++, PDB code: 2dua was solved by O.Herzberg, C.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.78 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.890, 79.180, 93.430, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 21.9

The structure of Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++ also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++ (pdb code 2dua). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++, PDB code: 2dua:

Sodium binding site 1 out of 1 in the Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++


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 Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na314 b:19.8 occ:1.00 CL A:CL549 2.8 13.2 0.5 OG A:SER49 2.8 9.2 1.0 O A:HIS23 2.8 11.8 1.0 CL A:CL548 2.8 14.6 0.5 CB A:SER49 3.4 10.1 1.0 CD1 A:LEU46 3.6 6.8 1.0 C A:HIS23 3.8 12.1 1.0 CE A:MET66 4.1 13.2 1.0 CB A:HIS23 4.3 10.9 1.0 CB A:ASN24 4.3 9.8 1.0 CE2 A:TYR50 4.4 10.7 1.0 CD2 A:HIS23 4.5 12.3 1.0 CA A:HIS23 4.6 11.3 1.0 N A:ASN24 4.7 10.8 1.0 O A:HOH391 4.8 19.0 1.0 CD2 A:TYR50 4.8 10.0 1.0 CG A:HIS23 4.8 14.0 1.0 CA A:ASN24 4.8 10.7 1.0 CA A:SER49 4.9 8.8 1.0 ND2 A:ASN24 4.9 8.0 1.0 CG A:LEU46 5.0 5.6 1.0

C.C.H.Chen, Y.Han, W.Niu, A.N.Kulakova, A.Howard, J.P.Quinn, D.Dunaway-Mariano, O.Herzberg. Structure and Kinetics of Phosphonopyruvate Hydrolase From Voriovorax Sp. PAL2: New Insight Into the Divergence of Catalysis Within the Pep Mutase/Isocitrate Lyase Superfamily Biochemistry V. 45 11491 2006.
ISSN: ISSN 0006-2960
PubMed: 16981709
DOI: 10.1021/BI061208L