Sodium in PDB 4e0u: Crystal Structure of Cdpnpt in Complex with Thiolodiphosphate and (S)- Benzodiazependione

The structure of Crystal Structure of Cdpnpt in Complex with Thiolodiphosphate and (S)- Benzodiazependione, PDB code: 4e0u was solved by J.M.Schuller, G.Zocher, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.83 / 2.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	137.730, 137.730, 170.510, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.9

The binding sites of Sodium atom in the Crystal Structure of Cdpnpt in Complex with Thiolodiphosphate and (S)- Benzodiazependione (pdb code 4e0u). 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 Cdpnpt in Complex with Thiolodiphosphate and (S)- Benzodiazependione, PDB code: 4e0u:

Sodium binding site 1 out of 1 in the Crystal Structure of Cdpnpt in Complex with Thiolodiphosphate and (S)- Benzodiazependione


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 Cdpnpt in Complex with Thiolodiphosphate and (S)- Benzodiazependione within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:57.4 occ:1.00 OE2 A:GLU374 2.3 76.4 1.0 O A:THR414 2.3 76.7 1.0 O A:LEU369 2.3 76.8 1.0 O A:ILE372 2.3 74.3 1.0 O A:GLN417 2.3 76.2 1.0 CD A:GLU374 3.2 74.2 1.0 C A:THR414 3.3 70.8 1.0 C A:LEU369 3.4 73.3 1.0 CD1 A:ILE377 3.4 70.6 1.0 OE1 A:GLU374 3.5 75.4 1.0 C A:ILE372 3.6 72.3 1.0 C A:GLN417 3.6 66.9 1.0 CA A:THR414 3.9 71.7 1.0 CB A:LEU369 4.0 69.4 1.0 CA A:THR370 4.1 74.9 1.0 N A:ILE372 4.1 75.0 1.0 N A:THR370 4.1 74.1 1.0 N A:ARG415 4.2 70.5 1.0 N A:GLN417 4.2 65.0 1.0 CA A:ILE372 4.3 73.7 1.0 CA A:GLN417 4.3 64.1 1.0 CA A:LEU369 4.3 71.8 1.0 CB A:ILE372 4.4 73.3 1.0 N A:TYR416 4.5 67.7 1.0 CB A:GLN417 4.5 63.6 1.0 CG A:GLU374 4.5 72.0 1.0 N A:GLY371 4.5 74.6 1.0 CA A:ARG415 4.5 70.5 1.0 N A:PRO373 4.7 73.8 1.0 N A:ALA418 4.7 65.6 1.0 C A:THR370 4.7 75.8 1.0 CB A:THR414 4.7 74.5 1.0 CG1 A:ILE377 4.8 74.1 1.0 C A:PRO373 4.9 71.9 1.0 C A:ARG415 5.0 68.5 1.0 N A:GLU374 5.0 71.1 1.0

J.M.Schuller, G.Zocher, M.Liebhold, X.Xie, M.Stahl, S.M.Li, T.Stehle. Structure and Catalytic Mechanism of A Cyclic Dipeptide Prenyltransferase with Broad Substrate Promiscuity. J.Mol.Biol. V. 422 87 2012.
ISSN: ISSN 0022-2836
PubMed: 22683356
DOI: 10.1016/J.JMB.2012.05.033