Calcium in PDB 4lj3: Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Substrate C-Di-Gmp and Ca++

The structure of Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Substrate C-Di-Gmp and Ca++, PDB code: 4lj3 was solved by A.Sundriyal, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.63 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.693, 70.300, 66.636, 90.00, 98.68, 90.00
R / Rfree (%)	22.1 / 25.4

The binding sites of Calcium atom in the Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Substrate C-Di-Gmp and Ca++ (pdb code 4lj3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Substrate C-Di-Gmp and Ca++, PDB code: 4lj3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Substrate C-Di-Gmp and Ca++


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Substrate C-Di-Gmp and Ca++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:4.6 occ:1.00 O2P A:C2E401 2.3 5.7 1.0 OE1 A:GLU232 2.3 8.8 1.0 O A:HOH505 2.4 5.3 1.0 OD1 A:ASP262 2.4 8.1 1.0 OE1 A:GLU141 2.4 7.0 1.0 OD1 A:ASN200 2.5 7.8 1.0 OD2 A:ASP262 2.6 8.2 1.0 CG A:ASP262 2.8 8.3 1.0 CD A:GLU141 3.3 7.3 1.0 P1 A:C2E401 3.5 6.3 1.0 CG A:ASN200 3.5 8.3 1.0 CD A:GLU232 3.5 8.0 1.0 OE2 A:GLU141 3.7 7.6 1.0 O5' A:C2E401 3.8 6.5 1.0 ND2 A:ASN200 3.9 8.2 1.0 CB A:GLU232 4.1 7.8 1.0 O1P A:C2E401 4.1 5.4 1.0 NZ A:LYS283 4.2 7.4 1.0 CB A:ASP262 4.3 8.0 1.0 OE2 A:GLU232 4.4 8.2 1.0 O A:HOH521 4.4 14.2 1.0 CG A:GLU232 4.4 7.9 1.0 O A:HOH506 4.4 14.0 1.0 N3 A:IMD404 4.4 6.2 1.0 CG A:GLU141 4.5 7.6 1.0 CD A:LYS283 4.6 7.1 1.0 O3A A:C2E401 4.8 6.2 1.0 CB A:ASN200 4.9 8.4 1.0 C5' A:C2E401 4.9 6.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Substrate C-Di-Gmp and Ca++


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Substrate C-Di-Gmp and Ca++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:17.8 occ:1.00 OD1 A:ASP263 2.1 15.1 1.0 O1P A:C2E401 2.3 5.4 1.0 O A:HOH520 2.3 12.0 1.0 OE2 A:GLU319 2.3 9.1 0.5 O A:HOH506 2.5 14.0 1.0 O A:HOH586 2.6 19.6 1.0 OE1 A:GLU319 2.6 9.8 0.5 OE1 A:GLU319 2.6 8.5 0.5 CD A:GLU319 2.8 9.4 0.5 CG A:ASP263 3.3 12.1 1.0 CD A:GLU319 3.7 8.7 0.5 P1 A:C2E401 3.8 6.3 1.0 OD2 A:ASP263 3.8 15.3 1.0 OE2 A:GLU319 4.2 8.9 0.5 C5' A:C2E401 4.2 6.8 1.0 CG A:GLU319 4.3 9.5 0.5 OD1 A:ASP285 4.3 11.6 1.0 O5' A:C2E401 4.4 6.5 1.0 O A:HOH505 4.4 5.3 1.0 N A:ASP263 4.5 8.4 1.0 O A:HOH716 4.5 19.1 1.0 O3A A:C2E401 4.5 6.2 1.0 CB A:ASP263 4.5 11.0 1.0 N A:LYS286 4.5 9.4 1.0 O2P A:C2E401 4.6 5.7 1.0 OD1 A:ASP262 4.6 8.1 1.0 CA A:ASP263 4.6 9.2 1.0 O A:HOH715 4.6 28.0 1.0 CA A:ASP285 4.8 9.1 1.0 O A:HOH521 4.8 14.2 1.0 C4' A:C2E401 4.9 7.0 1.0 CB A:LYS286 4.9 11.0 1.0 CG A:ASP285 4.9 10.6 1.0 CG A:GLU319 4.9 8.7 0.5 O4' A:C2E401 4.9 7.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Substrate C-Di-Gmp and Ca++


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Substrate C-Di-Gmp and Ca++ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:4.9 occ:1.00 OE1 B:GLU232 2.3 8.8 1.0 OE1 B:GLU141 2.4 9.0 1.0 O2P B:C2E401 2.4 7.3 1.0 O B:HOH503 2.4 10.2 1.0 OD1 B:ASN200 2.4 8.0 1.0 OD1 B:ASP262 2.5 8.8 1.0 OD2 B:ASP262 2.6 8.7 1.0 CG B:ASP262 2.9 8.9 1.0 CD B:GLU141 3.3 9.1 1.0 CG B:ASN200 3.5 8.1 1.0 CD B:GLU232 3.5 8.4 1.0 P1 B:C2E401 3.5 7.4 1.0 OE2 B:GLU141 3.7 9.8 1.0 ND2 B:ASN200 3.8 8.2 1.0 O5' B:C2E401 3.9 7.9 1.0 CB B:GLU232 4.1 7.8 1.0 NZ B:LYS283 4.3 8.5 1.0 O1P B:C2E401 4.3 6.7 1.0 CB B:ASP262 4.4 8.4 1.0 CG B:GLU232 4.4 8.1 1.0 OE2 B:GLU232 4.4 9.1 1.0 O B:HOH514 4.4 21.6 1.0 CG B:GLU141 4.4 9.5 1.0 O B:HOH505 4.5 7.9 1.0 N3 B:IMD404 4.5 8.3 1.0 C4 B:IMD404 4.7 8.1 1.0 CD B:LYS283 4.7 8.3 1.0 CB B:ASN200 4.8 8.2 1.0 O3A B:C2E401 4.8 7.2 1.0 OE1 B:GLU319 5.0 18.1 1.0 C5' B:C2E401 5.0 8.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Substrate C-Di-Gmp and Ca++


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Substrate C-Di-Gmp and Ca++ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:16.2 occ:1.00 OD1 B:ASP263 2.1 13.7 1.0 OE2 B:GLU319 2.3 15.5 1.0 O B:HOH553 2.3 20.3 1.0 O1P B:C2E401 2.4 6.7 1.0 O B:HOH505 2.5 7.9 1.0 OD1 B:ASP285 2.7 15.8 1.0 CD B:GLU319 3.2 15.3 1.0 CG B:ASP263 3.4 12.6 1.0 OE1 B:GLU319 3.5 18.1 1.0 P1 B:C2E401 3.8 7.4 1.0 CG B:ASP285 3.9 13.5 1.0 CA B:ASP263 4.0 10.1 1.0 N B:ASP263 4.1 9.2 1.0 CB B:ASP263 4.2 11.1 1.0 O B:HOH514 4.2 21.6 1.0 OD2 B:ASP263 4.3 13.4 1.0 CG B:LYS286 4.4 14.9 1.0 CA B:ASP285 4.5 11.3 1.0 N B:LYS286 4.6 11.5 1.0 O3A B:C2E401 4.6 7.2 1.0 CG B:GLU319 4.6 14.5 1.0 O2P B:C2E401 4.6 7.3 1.0 CB B:ASP285 4.7 12.0 1.0 C5' B:C2E401 4.7 8.3 1.0 OD1 B:ASP262 4.7 8.8 1.0 O5' B:C2E401 4.8 7.9 1.0 CD B:LYS286 4.8 16.3 1.0 OD2 B:ASP285 4.8 14.2 1.0 O B:HOH503 4.9 10.2 1.0

A.Sundriyal, C.Massa, D.Samoray, F.Zehender, T.Sharpe, U.Jenal, T.Schirmer. Inherent Regulation of Eal Domain-Catalyzed Hydrolysis of Second Messenger Cyclic Di-Gmp. J.Biol.Chem. V. 289 6978 2014.
ISSN: ISSN 0021-9258
PubMed: 24451384
DOI: 10.1074/JBC.M113.516195