Sodium in PDB 2yeq: Structure of Phod

All present enzymatic activity of Structure of Phod:
3.1.3.1;

The structure of Structure of Phod, PDB code: 2yeq was solved by J.E.D.Lillington, F.Rodriguez, P.Roversi, S.J.Johnson, B.Berks, S.M.Lea, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	135.64 / 1.93
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	147.318, 147.318, 347.646, 90.00, 90.00, 90.00
R / Rfree (%)	17.842 / 20.243

The structure of Structure of Phod also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Calcium	(Ca)	4 atoms

The binding sites of Sodium atom in the Structure of Phod (pdb code 2yeq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of Phod, PDB code: 2yeq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Structure of Phod


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Phod within 5.0Å range: probe atom residue distance (Å) B Occ A:Na577 b:13.9 occ:1.00 OD1 A:ASP284 2.2 22.5 1.0 O A:HOH2129 2.3 16.9 1.0 O A:HOH2134 2.3 26.7 1.0 O A:HOH2177 2.3 28.2 1.0 O A:HOH2174 2.3 31.2 1.0 OE1 A:GLN285 2.4 18.6 1.0 CG A:ASP284 3.4 25.1 1.0 CD A:GLN285 3.6 23.2 1.0 OD2 A:ASP284 3.9 24.4 1.0 O A:HOH2173 4.1 42.8 1.0 N A:GLN285 4.1 19.7 1.0 O A:ASN216 4.2 20.8 1.0 NE2 A:GLN285 4.3 18.1 1.0 C48 A:PE5554 4.4 31.1 1.0 CB A:GLN285 4.4 19.4 1.0 O A:PRO222 4.5 20.3 1.0 OD2 A:ASP289 4.5 27.4 1.0 CG2 A:ILE221 4.5 17.1 1.0 CG A:GLN285 4.6 19.6 1.0 CB A:ASP284 4.6 22.1 1.0 CA A:GLU223 4.7 20.9 1.0 O A:GLN285 4.8 22.8 1.0 CA A:GLN285 4.8 21.9 1.0 CA A:ASP284 4.8 20.1 1.0 CB A:ALA218 4.8 17.2 1.0 O A:ILE221 4.8 20.9 1.0 O1 A:PE5554 4.9 53.9 1.0 C A:ASP284 4.9 21.5 1.0 C A:PRO222 5.0 19.5 1.0

Sodium binding site 2 out of 6 in the Structure of Phod


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Phod within 5.0Å range: probe atom residue distance (Å) B Occ A:Na582 b:14.0 occ:1.00 O A:HOH2139 2.2 32.3 1.0 OE2 A:GLU175 2.2 30.5 1.0 O A:HOH2096 2.3 27.8 1.0 O A:HOH2138 2.3 26.6 1.0 OE2 A:GLU214 2.3 21.2 1.0 OE1 A:GLN517 2.6 40.8 1.0 OE1 A:GLU175 2.9 40.4 1.0 CD A:GLU175 2.9 30.1 1.0 CD A:GLN517 3.4 46.7 1.0 CD A:GLU214 3.4 22.7 1.0 NE2 A:GLN517 3.5 44.1 1.0 CG A:GLU214 3.9 19.1 1.0 OE2 A:GLU223 4.3 28.2 1.0 NE2 A:GLN226 4.3 24.9 1.0 CG A:GLU175 4.4 25.6 1.0 OE1 A:GLN226 4.4 27.9 1.0 NH1 A:ARG234 4.4 23.6 1.0 OE1 A:GLU214 4.5 21.1 1.0 CD2 A:HIS514 4.7 42.7 1.0 OE2 A:GLU155 4.7 17.4 1.0 NH2 A:ARG234 4.7 23.4 1.0 CD A:GLN226 4.8 27.8 1.0 CG A:GLN517 4.9 39.4 1.0

Sodium binding site 3 out of 6 in the Structure of Phod


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Phod within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1585 b:23.3 occ:1.00 ND2 A:ASN300 3.1 29.8 1.0 O B:HOH2289 3.2 39.5 1.0 N B:SER227 3.3 21.0 1.0 ND2 A:ASN302 3.3 33.8 1.0 O2 B:PE5536 3.7 61.6 1.0 CB A:ASN302 3.7 24.5 1.0 CB B:SER227 3.7 21.6 1.0 CB B:GLN226 3.7 24.5 1.0 OD1 A:ASN300 4.0 25.9 1.0 CG A:ASN300 4.0 27.0 1.0 CG A:ASN302 4.0 31.1 1.0 CA B:SER227 4.1 22.1 1.0 CA B:GLN226 4.2 22.9 1.0 C B:GLN226 4.2 22.1 1.0 CG B:GLN226 4.3 24.9 1.0 NE2 B:GLN226 4.3 24.1 1.0 CB B:ALA230 4.4 18.6 1.0 O B:SER227 4.6 22.5 1.0 CD B:GLN226 4.7 28.3 1.0 C2 B:PE5536 4.8 51.2 1.0 OG B:SER227 4.8 21.1 1.0 C B:SER227 4.9 23.3 1.0 C1 B:PE5536 4.9 50.9 1.0

Sodium binding site 4 out of 6 in the Structure of Phod


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Phod within 5.0Å range: probe atom residue distance (Å) B Occ B:Na577 b:19.0 occ:1.00 O B:HOH2130 2.2 20.6 1.0 OD1 B:ASP284 2.3 28.3 1.0 O B:HOH2176 2.3 37.6 1.0 O B:HOH2178 2.3 31.7 1.0 OE1 B:GLN285 2.4 26.7 1.0 O B:HOH2136 2.4 27.4 1.0 CG B:ASP284 3.5 32.4 1.0 CD B:GLN285 3.6 29.8 1.0 O B:HOH2174 3.9 35.6 1.0 OD2 B:ASP284 3.9 33.0 1.0 N B:GLN285 4.1 26.7 1.0 O B:ASN216 4.1 24.8 1.0 NE2 B:GLN285 4.3 24.8 1.0 CB B:GLN285 4.4 28.0 1.0 C48 B:PE5554 4.5 43.3 1.0 O B:PRO222 4.5 21.7 1.0 OD2 B:ASP289 4.5 31.4 1.0 CG2 B:ILE221 4.6 19.5 1.0 CG B:GLN285 4.6 26.4 1.0 CA B:GLU223 4.7 22.7 1.0 CB B:ASP284 4.7 28.2 1.0 O B:GLN285 4.8 30.1 1.0 CA B:GLN285 4.8 28.4 1.0 CB B:ALA218 4.8 20.9 1.0 O B:ILE221 4.8 23.7 1.0 CA B:ASP284 4.8 26.5 1.0 C B:PRO222 4.9 22.2 1.0 C B:ASP284 4.9 28.4 1.0

Sodium binding site 5 out of 6 in the Structure of Phod


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Phod within 5.0Å range: probe atom residue distance (Å) B Occ B:Na582 b:16.2 occ:1.00 OE2 B:GLU175 2.2 27.2 1.0 O B:HOH2138 2.2 28.9 1.0 O B:HOH2141 2.3 36.0 1.0 OE2 B:GLU214 2.3 23.4 1.0 O B:HOH2093 2.4 29.0 1.0 OE1 B:GLN517 2.6 36.4 1.0 CD B:GLU175 2.9 30.9 1.0 OE1 B:GLU175 2.9 35.7 1.0 CD B:GLN517 3.4 49.3 1.0 CD B:GLU214 3.5 25.2 1.0 NE2 B:GLN517 3.5 44.3 1.0 CG B:GLU214 3.9 19.8 1.0 OE2 B:GLU223 4.2 31.7 1.0 NE2 B:GLN226 4.2 24.1 1.0 OE1 B:GLN226 4.3 28.7 1.0 CG B:GLU175 4.4 27.2 1.0 NH1 B:ARG234 4.4 23.8 1.0 OE1 B:GLU214 4.6 25.0 1.0 CD2 B:HIS514 4.7 44.2 1.0 CD B:GLN226 4.7 28.3 1.0 NH2 B:ARG234 4.8 24.9 1.0 OE2 B:GLU155 4.8 22.0 1.0 CG B:GLN517 4.8 40.6 1.0

Sodium binding site 6 out of 6 in the Structure of Phod


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Phod within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1585 b:26.7 occ:1.00 ND2 B:ASN302 3.2 42.4 1.0 N A:SER227 3.3 23.1 1.0 ND2 B:ASN300 3.3 32.8 1.0 CB B:ASN302 3.5 35.8 1.0 O A:HOH2309 3.6 45.5 1.0 CB A:GLN226 3.6 23.2 1.0 CG B:ASN302 3.8 41.7 1.0 CB A:SER227 3.9 24.1 1.0 O2 A:PE5536 3.9 76.5 1.0 CA A:GLN226 3.9 24.1 1.0 OD1 B:ASN300 4.0 34.4 1.0 CG A:GLN226 4.0 23.7 1.0 CG B:ASN300 4.1 33.8 1.0 C A:GLN226 4.1 24.6 1.0 CA A:SER227 4.2 25.6 1.0 NE2 A:GLN226 4.2 24.9 1.0 CD A:GLN226 4.5 27.8 1.0 O A:SER227 4.8 20.5 1.0 CA B:ASN302 4.8 28.8 1.0 C2 A:PE5536 4.9 59.8 1.0 CB A:ALA230 5.0 22.2 1.0 OG A:SER227 5.0 26.9 1.0

F.Rodriguez, J.Lillington, S.Johnson, C.R.Timmel, S.M.Lea, B.C.Berks. Crystal Structure of the Bacillus Subtilis Phosphodiesterase Phod Reveals An Iron and Calcium- Containing Active Site. J.Biol.Chem. V. 289 30889 2014.
ISSN: ISSN 0021-9258
PubMed: 25217636
DOI: 10.1074/JBC.M114.604892