Sodium in PDB 4v2p: Ketosynthase Mxnb

The structure of Ketosynthase Mxnb, PDB code: 4v2p was solved by J.Koehnke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.05 / 1.67
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.190, 58.790, 62.820, 104.75, 105.48, 93.90
R / Rfree (%)	14.6 / 17.7

The structure of Ketosynthase Mxnb also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Ketosynthase Mxnb (pdb code 4v2p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ketosynthase Mxnb, PDB code: 4v2p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ketosynthase Mxnb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ketosynthase Mxnb within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1342 b:38.9 occ:1.00 NE2 A:GLN38 2.4 80.1 1.0 O A:HOH2375 2.7 25.2 1.0 OE1 A:GLU31 2.9 21.2 1.0 O A:HOH2038 3.4 23.2 1.0 CD A:GLN38 3.4 74.6 1.0 N A:GLY39 3.5 25.5 1.0 CB A:SER28 3.6 20.7 1.0 CA A:SER28 3.7 20.2 1.0 CD A:GLU31 3.8 19.4 1.0 CA A:GLY39 3.9 23.8 1.0 N A:SER28 3.9 19.6 1.0 OE2 A:GLU31 3.9 22.7 1.0 O A:HOH2030 4.0 20.9 1.0 CG A:GLN38 4.1 61.7 1.0 OE1 A:GLN38 4.3 71.2 1.0 C A:GLN38 4.5 33.7 1.0 C A:SER27 4.6 19.0 1.0 CA A:GLN38 4.7 37.8 1.0 OG A:SER28 4.8 26.2 1.0 O A:HOH2019 4.9 53.9 1.0 CB A:SER27 4.9 13.3 1.0 O A:SER27 5.0 20.2 1.0 C A:GLY39 5.0 20.2 1.0

Sodium binding site 2 out of 2 in the Ketosynthase Mxnb


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ketosynthase Mxnb within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1342 b:19.7 occ:1.00 O A:HOH2368 2.7 13.9 1.0 OD1 B:ASP96 2.7 14.0 1.0 O B:ALA114 2.7 10.1 1.0 CA A:ALA119 3.4 12.2 1.0 CB A:ALA119 3.5 13.8 1.0 CG B:ASP96 3.5 11.4 1.0 CD B:PRO99 3.6 11.0 1.0 CG B:PRO99 3.6 10.5 1.0 OD2 B:ASP96 3.6 12.5 1.0 O A:HOH2200 3.7 23.5 1.0 CA B:ILE115 3.8 7.8 1.0 C B:ALA114 3.8 9.9 1.0 C A:ALA119 4.0 12.7 1.0 CG2 B:ILE115 4.2 11.9 1.0 OG A:SER327 4.2 10.6 1.0 N B:ILE115 4.2 8.1 1.0 O A:ASN118 4.3 13.1 1.0 O A:ALA119 4.4 11.6 1.0 CB B:ILE115 4.5 8.7 1.0 N A:ALA119 4.6 11.0 1.0 C B:ILE115 4.7 9.7 1.0 N A:SER120 4.7 12.6 1.0 C A:ASN118 4.9 13.3 1.0 O A:HOH2198 4.9 16.2 1.0 N B:PRO99 4.9 7.9 1.0 N B:THR116 4.9 9.0 1.0 CB B:ASP96 4.9 9.4 1.0

H.Sucipto, J.H.Sahner, E.Prusov, S.C.Wenzel, R.W.Hartmann, J.Koehnke, R.Muller. In Vitro Reconstitution of Alpha-Pyrone Ring Formation in Myxopyronin Biosynthesis. Chem Sci V. 6 5076 2015.
ISSN: ISSN 2041-6520
PubMed: 29308173
DOI: 10.1039/C5SC01013F