Sodium in PDB 4e0t: Crystal Structure of Cdpnpt in Its Unbound State

The structure of Crystal Structure of Cdpnpt in Its Unbound State, PDB code: 4e0t 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 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.510, 137.020, 172.630, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.3

The structure of Crystal Structure of Cdpnpt in Its Unbound State also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

The binding sites of Sodium atom in the Crystal Structure of Cdpnpt in Its Unbound State (pdb code 4e0t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Cdpnpt in Its Unbound State, PDB code: 4e0t:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Cdpnpt in Its Unbound State


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 Its Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na609 b:40.5 occ:1.00 O A:THR414 2.7 48.7 1.0 O A:GLN417 2.7 38.8 1.0 OE2 A:GLU374 2.8 47.0 1.0 O A:ILE372 2.8 51.4 1.0 O A:LEU369 2.8 50.4 1.0 CD1 A:ILE377 3.0 47.7 1.0 OE1 A:GLU374 3.1 55.8 1.0 CD A:GLU374 3.2 49.5 1.0 C A:THR414 3.3 49.4 1.0 C A:LEU369 3.7 49.8 1.0 C A:GLN417 3.9 37.9 1.0 CA A:THR414 3.9 46.6 1.0 C A:ILE372 4.0 52.7 1.0 CB A:LEU369 4.0 40.9 1.0 N A:ARG415 4.2 44.8 1.0 N A:GLN417 4.2 35.5 1.0 N A:ILE372 4.3 49.7 1.0 N A:THR370 4.3 49.9 1.0 CA A:THR370 4.4 51.1 1.0 N A:TYR416 4.4 38.9 1.0 CA A:GLN417 4.4 33.6 1.0 CA A:LEU369 4.5 41.7 1.0 CB A:GLN417 4.5 34.9 1.0 CG1 A:ILE377 4.5 41.5 1.0 CA A:ILE372 4.5 49.4 1.0 CA A:ARG415 4.6 43.3 1.0 CG A:GLU374 4.6 42.5 1.0 CB A:ILE372 4.7 51.4 1.0 N A:GLY371 4.7 53.8 1.0 CB A:THR414 4.8 51.4 1.0 N A:GLU374 4.9 45.1 1.0 C A:PRO373 4.9 50.1 1.0 C A:ARG415 4.9 43.8 1.0 C A:THR370 4.9 57.6 1.0 N A:ALA418 5.0 34.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Cdpnpt in Its Unbound State


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 Cdpnpt in Its Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na508 b:63.7 occ:1.00 OE2 B:GLU374 2.5 63.7 1.0 O B:THR414 2.6 67.7 1.0 O B:ILE372 2.8 64.8 1.0 O B:GLN417 2.8 57.5 1.0 O B:LEU369 2.9 70.8 1.0 OE1 B:GLU374 3.0 70.9 1.0 CD B:GLU374 3.0 71.5 1.0 CD1 B:ILE377 3.1 64.6 1.0 C B:THR414 3.2 68.6 1.0 CA B:THR414 3.8 66.7 1.0 C B:LEU369 3.8 70.5 1.0 C B:GLN417 3.9 57.9 1.0 C B:ILE372 4.0 68.0 1.0 N B:ARG415 4.0 64.4 1.0 N B:GLN417 4.1 56.8 1.0 N B:TYR416 4.2 59.7 1.0 CB B:LEU369 4.3 62.4 1.0 N B:ILE372 4.4 67.2 1.0 CG B:GLU374 4.4 59.5 1.0 CA B:GLN417 4.4 55.4 1.0 CA B:ARG415 4.4 62.4 1.0 CA B:THR370 4.5 68.0 1.0 N B:THR370 4.5 67.9 1.0 CB B:GLN417 4.5 58.1 1.0 CA B:ILE372 4.6 67.7 1.0 CG1 B:ILE377 4.6 64.7 1.0 CA B:LEU369 4.7 64.3 1.0 CB B:THR414 4.7 74.5 1.0 N B:GLY371 4.7 69.9 1.0 N B:GLU374 4.7 60.5 1.0 C B:ARG415 4.8 63.5 1.0 CB B:ILE372 4.8 70.6 1.0 C B:PRO373 4.8 66.8 1.0 N B:THR414 4.8 67.0 1.0 CA B:GLU374 4.9 58.8 1.0 C B:TYR416 5.0 60.6 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Cdpnpt in Its Unbound State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Cdpnpt in Its Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na708 b:57.5 occ:1.00 O C:THR414 2.5 60.8 1.0 O C:GLN417 2.8 51.3 1.0 O C:ILE372 2.8 63.6 1.0 OE2 C:GLU374 2.8 57.5 1.0 O C:LEU369 3.0 69.4 1.0 CD1 C:ILE377 3.2 73.0 1.0 C C:THR414 3.2 62.3 1.0 OE1 C:GLU374 3.3 58.9 1.0 CD C:GLU374 3.3 64.1 1.0 C C:LEU369 3.6 67.4 1.0 CA C:THR414 3.8 62.3 1.0 C C:GLN417 3.9 51.7 1.0 C C:ILE372 4.0 66.2 1.0 CB C:LEU369 4.1 58.8 1.0 N C:ARG415 4.1 57.4 1.0 CA C:THR370 4.1 65.3 1.0 N C:THR370 4.1 64.4 1.0 N C:ILE372 4.2 66.2 1.0 N C:GLN417 4.2 49.5 1.0 N C:TYR416 4.4 52.5 1.0 CA C:ILE372 4.5 65.6 1.0 CA C:LEU369 4.5 60.2 1.0 CA C:ARG415 4.5 55.3 1.0 N C:GLY371 4.5 68.6 1.0 CA C:GLN417 4.5 48.0 1.0 CB C:GLN417 4.6 49.5 1.0 CB C:ILE372 4.6 68.3 1.0 CG1 C:ILE377 4.6 64.3 1.0 CB C:THR414 4.7 70.4 1.0 C C:THR370 4.7 71.7 1.0 CG C:GLU374 4.7 59.4 1.0 C C:ARG415 4.9 56.7 1.0 N C:THR414 5.0 62.7 1.0 N C:GLU374 5.0 58.9 1.0 C C:PRO373 5.0 63.5 1.0 N C:ALA418 5.0 47.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Cdpnpt in Its Unbound State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Cdpnpt in Its Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ D:Na506 b:34.0 occ:1.00 O D:THR414 2.6 36.8 1.0 O D:LEU369 2.7 46.0 1.0 OE2 D:GLU374 2.8 42.5 1.0 O D:GLN417 2.8 38.0 1.0 O D:ILE372 2.9 37.6 1.0 CD1 D:ILE377 3.1 45.1 1.0 OE1 D:GLU374 3.2 45.1 1.0 C D:THR414 3.3 37.7 1.0 CD D:GLU374 3.3 47.1 1.0 C D:LEU369 3.6 44.5 1.0 CA D:THR414 3.9 33.8 1.0 C D:GLN417 3.9 38.8 1.0 C D:ILE372 4.0 41.8 1.0 N D:ARG415 4.0 35.0 1.0 CB D:LEU369 4.1 35.9 1.0 N D:GLN417 4.2 33.7 1.0 CA D:THR370 4.2 42.3 1.0 N D:THR370 4.3 42.2 1.0 N D:ILE372 4.3 41.3 1.0 N D:TYR416 4.4 36.0 1.0 CA D:ARG415 4.4 35.2 1.0 CA D:GLN417 4.5 33.4 1.0 CA D:LEU369 4.5 37.6 1.0 CA D:ILE372 4.5 41.2 1.0 CB D:GLN417 4.6 34.6 1.0 CG1 D:ILE377 4.6 41.1 1.0 N D:GLY371 4.7 42.5 1.0 CG D:GLU374 4.7 43.3 1.0 CB D:ILE372 4.7 43.9 1.0 C D:THR370 4.8 47.6 1.0 C D:ARG415 4.8 39.8 1.0 CB D:THR414 4.8 41.9 1.0 N D:GLU374 4.9 39.7 1.0 C D:PRO373 5.0 42.8 1.0 N D:THR414 5.0 34.6 1.0 N D:ALA418 5.0 35.2 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