Calcium 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
Sodium	(Na)	6 atoms

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

Calcium binding site 1 out of 4 in the Structure of Phod


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Phod within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1525 b:18.4 occ:1.00 OD2 A:ASP209 2.3 17.8 1.0 O2 A:PO41527 2.3 16.9 1.0 OD1 A:ASP380 2.4 16.5 1.0 OD1 A:ASP210 2.4 17.2 1.0 OD2 A:ASP151 2.5 16.9 1.0 O A:HOH2095 2.6 13.7 1.0 O4 A:PO41527 2.7 18.8 1.0 OD1 A:ASP151 2.9 16.6 1.0 CG A:ASP151 3.0 16.4 1.0 P A:PO41527 3.2 19.0 1.0 CG A:ASP209 3.4 15.5 1.0 CG A:ASP210 3.5 19.0 1.0 CG A:ASP380 3.5 19.9 1.0 O A:HOH2227 3.6 21.0 1.0 OD2 A:ASP210 3.9 16.9 1.0 CB A:ASP209 3.9 14.2 1.0 FE A:FE1524 3.9 17.6 1.0 CB A:ASP380 4.1 18.4 1.0 O3 A:PO41527 4.1 19.7 1.0 CA A:CA1526 4.1 20.4 1.0 CD2 A:HIS211 4.2 18.0 1.0 CA A:ASP380 4.2 18.1 1.0 N A:ASP210 4.3 15.8 1.0 O1 A:PO41527 4.3 19.1 1.0 CB A:ASP151 4.4 15.3 1.0 OD1 A:ASP209 4.5 15.9 1.0 O A:ASP380 4.5 20.6 1.0 OD2 A:ASP380 4.6 20.4 1.0 SG A:CYS124 4.6 18.0 1.0 NH2 A:ARG279 4.6 15.8 1.0 CB A:ASP210 4.7 16.0 1.0 O A:HOH2094 4.8 19.5 1.0 C A:ASP380 4.9 19.0 1.0 NE2 A:HIS211 4.9 19.7 1.0 N A:HIS211 4.9 15.5 1.0

Calcium binding site 2 out of 4 in the Structure of Phod


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Phod within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1526 b:20.4 occ:1.00 O A:HOH2303 2.2 24.2 1.0 OD2 A:ASP210 2.3 16.9 1.0 OD1 A:ASN216 2.4 20.1 1.0 OD1 A:ASN215 2.4 18.0 1.0 O A:HOH2227 2.4 21.0 1.0 O2 A:PO41527 2.4 16.9 1.0 CG A:ASP210 3.3 19.0 1.0 P A:PO41527 3.5 19.0 1.0 CG A:ASN215 3.5 18.4 1.0 CG A:ASN216 3.6 24.0 1.0 O1 A:PO41527 3.6 19.1 1.0 OD1 A:ASP210 3.7 17.2 1.0 NE2 A:HIS211 3.7 19.7 1.0 N A:ASN216 3.9 19.8 1.0 CA A:CA1525 4.1 18.4 1.0 ND2 A:ASN215 4.2 17.8 1.0 CD2 A:HIS211 4.2 18.0 1.0 NE2 A:HIS510 4.3 32.5 1.0 O A:HOH2128 4.3 33.9 1.0 OD1 A:ASP380 4.4 16.5 1.0 O3 A:PO41527 4.4 19.7 1.0 CD2 A:HIS510 4.4 32.0 1.0 ND2 A:ASN216 4.4 21.4 1.0 CA A:ASN216 4.5 19.2 1.0 CA A:ASN215 4.5 18.1 1.0 O4 A:PO41527 4.5 18.8 1.0 CB A:ASN216 4.6 19.7 1.0 CB A:ASN215 4.6 16.7 1.0 CE1 A:HIS211 4.6 19.4 1.0 CB A:ASP210 4.6 16.0 1.0 OD2 A:ASP350 4.6 20.5 1.0 C A:ASN215 4.7 20.6 1.0 CE1 A:HIS510 4.9 35.5 1.0 NH2 A:ARG279 4.9 15.8 1.0

Calcium binding site 3 out of 4 in the Structure of Phod


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Phod within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1525 b:20.6 occ:1.00 OD1 B:ASP380 2.3 20.0 1.0 O2 B:PO41527 2.4 20.1 1.0 OD2 B:ASP209 2.4 19.3 1.0 OD1 B:ASP210 2.4 18.0 1.0 OD2 B:ASP151 2.5 18.9 1.0 O B:HOH2092 2.5 13.9 1.0 O4 B:PO41527 2.7 22.8 1.0 OD1 B:ASP151 2.9 18.1 1.0 CG B:ASP151 3.0 19.7 1.0 P B:PO41527 3.3 21.9 1.0 CG B:ASP209 3.4 18.0 1.0 CG B:ASP380 3.5 23.5 1.0 CG B:ASP210 3.5 20.4 1.0 O B:HOH2216 3.8 23.4 1.0 CB B:ASP209 3.9 17.5 1.0 FE B:FE1524 3.9 19.7 1.0 CB B:ASP380 4.0 22.5 1.0 OD2 B:ASP210 4.0 21.5 1.0 O3 B:PO41527 4.1 21.4 1.0 CA B:ASP380 4.1 21.2 1.0 CD2 B:HIS211 4.2 17.7 1.0 CA B:CA1526 4.2 23.1 1.0 N B:ASP210 4.3 17.9 1.0 O1 B:PO41527 4.4 21.8 1.0 CB B:ASP151 4.4 18.0 1.0 OD1 B:ASP209 4.5 19.1 1.0 OD2 B:ASP380 4.5 24.2 1.0 O B:ASP380 4.6 21.9 1.0 SG B:CYS124 4.6 20.3 1.0 NH2 B:ARG279 4.7 20.1 1.0 O B:HOH2091 4.7 23.5 1.0 CB B:ASP210 4.8 18.6 1.0 C B:ASP380 4.9 20.7 1.0 NE2 B:HIS211 4.9 17.6 1.0 N B:HIS211 5.0 19.5 1.0

Calcium binding site 4 out of 4 in the Structure of Phod


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Phod within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1526 b:23.1 occ:1.00 OD1 B:ASN215 2.3 21.7 1.0 OD2 B:ASP210 2.3 21.5 1.0 O B:HOH2285 2.3 24.4 1.0 OD1 B:ASN216 2.3 21.2 1.0 O B:HOH2216 2.4 23.4 1.0 O2 B:PO41527 2.4 20.1 1.0 CG B:ASP210 3.3 20.4 1.0 CG B:ASN215 3.4 23.7 1.0 P B:PO41527 3.5 21.9 1.0 CG B:ASN216 3.6 26.1 1.0 O1 B:PO41527 3.6 21.8 1.0 OD1 B:ASP210 3.7 18.0 1.0 NE2 B:HIS211 3.7 17.6 1.0 N B:ASN216 4.0 20.2 1.0 ND2 B:ASN215 4.1 19.6 1.0 CD2 B:HIS211 4.1 17.7 1.0 CA B:CA1525 4.2 20.6 1.0 NE2 B:HIS510 4.3 35.7 1.0 OD1 B:ASP380 4.3 20.0 1.0 ND2 B:ASN216 4.4 23.6 1.0 O3 B:PO41527 4.4 21.4 1.0 CD2 B:HIS510 4.4 35.1 1.0 O B:HOH2131 4.4 50.0 1.0 CE1 B:HIS211 4.5 17.4 1.0 CA B:ASN215 4.5 20.0 1.0 CB B:ASN215 4.5 19.4 1.0 CA B:ASN216 4.5 20.7 1.0 O4 B:PO41527 4.5 22.8 1.0 CB B:ASN216 4.6 22.2 1.0 CB B:ASP210 4.7 18.6 1.0 C B:ASN215 4.7 22.3 1.0 OD2 B:ASP350 4.7 24.9 1.0 CE1 B:HIS510 4.9 35.0 1.0 O B:HOH2129 4.9 44.1 1.0 NH2 B:ARG279 4.9 20.1 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