Calcium in PDB 4hjf: Eal Domain of Phosphodiesterase Pdea in Complex with C-Di-Gmp and Ca++

The structure of Eal Domain of Phosphodiesterase Pdea in Complex with C-Di-Gmp and Ca++, PDB code: 4hjf was solved by E.V.Filippova, G.Minasov, L.Shuvalova, O.Kiryukhina, C.Massa, T.Schirmer, A.Joachimiak, W.F.Anderson, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.22 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.202, 63.186, 66.190, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 21.4

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

Calcium binding site 1 out of 3 in the Eal Domain of Phosphodiesterase Pdea in Complex with 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 Eal Domain of Phosphodiesterase Pdea in Complex with C-Di-Gmp and Ca++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:19.6 occ:1.00 O11 A:C2E603 2.2 22.4 1.0 OD2 A:ASP446 2.2 33.0 1.0 OE2 A:GLU323 2.2 19.2 1.0 OE1 A:GLU416 2.3 21.8 1.0 O A:HOH712 2.4 24.6 1.0 OD1 A:ASN384 2.4 21.0 1.0 CG A:ASP446 3.2 30.8 1.0 CD A:GLU323 3.2 22.0 1.0 CG A:ASN384 3.3 18.2 1.0 P11 A:C2E603 3.4 20.3 1.0 CD A:GLU416 3.4 19.7 1.0 OE1 A:GLU323 3.6 24.3 1.0 OD1 A:ASP446 3.6 40.3 1.0 ND2 A:ASN384 3.6 20.1 1.0 O5A A:C2E603 3.9 20.1 1.0 O21 A:C2E603 4.1 20.6 1.0 CA A:CA602 4.1 23.4 0.5 CB A:GLU416 4.2 19.6 1.0 O A:HOH825 4.2 31.8 1.0 OE2 A:GLU416 4.3 25.1 1.0 OE2 A:GLU503 4.3 35.6 1.0 CG A:GLU416 4.3 20.1 1.0 NZ A:LYS467 4.3 21.5 1.0 CB A:ASP446 4.4 26.3 1.0 O A:HOH719 4.4 32.1 1.0 CG A:GLU323 4.5 19.5 1.0 CB A:ASN384 4.7 19.2 1.0 O3' A:C2E603 4.8 20.0 1.0 C5A A:C2E603 4.9 22.8 1.0

Calcium binding site 2 out of 3 in the Eal Domain of Phosphodiesterase Pdea in Complex with 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 Eal Domain of Phosphodiesterase Pdea in Complex with C-Di-Gmp and Ca++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:23.4 occ:0.50 CA A:CA602 0.0 23.4 0.5 CA A:CA602 1.7 48.3 0.5 OD1 A:ASP446 2.2 40.3 1.0 O21 A:C2E603 2.4 20.6 1.0 OE1 A:GLU503 2.4 37.4 1.0 OE2 A:GLU503 2.7 35.6 1.0 CD A:GLU503 2.9 31.0 1.0 CG A:ASP446 3.2 30.8 1.0 O A:HOH712 3.3 24.6 1.0 OD1 A:ASP447 3.4 50.4 1.0 P11 A:C2E603 3.5 20.3 1.0 OD2 A:ASP446 3.6 33.0 1.0 O A:HOH735 3.8 31.7 1.0 O11 A:C2E603 3.8 22.4 1.0 O A:HOH829 4.1 36.5 1.0 CA A:CA601 4.1 19.6 1.0 OD2 A:ASP469 4.2 31.3 1.0 N A:ASP447 4.2 28.7 1.0 CG A:ASP447 4.3 44.3 1.0 O5A A:C2E603 4.3 20.1 1.0 O A:HOH825 4.4 31.8 1.0 CG A:GLU503 4.4 25.7 1.0 C5A A:C2E603 4.5 22.8 1.0 CB A:ASP446 4.5 26.3 1.0 O A:HOH851 4.6 44.0 1.0 O3' A:C2E603 4.6 20.0 1.0 CA A:ASP447 4.8 30.0 1.0 CA A:ASP446 4.9 23.8 1.0 OD2 A:ASP447 5.0 46.4 1.0 CA A:ASP469 5.0 23.1 1.0

Calcium binding site 3 out of 3 in the Eal Domain of Phosphodiesterase Pdea in Complex with 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 Eal Domain of Phosphodiesterase Pdea in Complex with C-Di-Gmp and Ca++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:48.3 occ:0.50 CA A:CA602 0.0 48.3 0.5 CA A:CA602 1.7 23.4 0.5 OD1 A:ASP447 2.4 50.4 1.0 OD2 A:ASP469 2.6 31.3 1.0 O21 A:C2E603 3.1 20.6 1.0 OE1 A:GLU503 3.2 37.4 1.0 OD1 A:ASP446 3.2 40.3 1.0 CG A:ASP447 3.5 44.3 1.0 O A:HOH829 3.6 36.5 1.0 CG A:ASP469 3.7 27.6 1.0 O A:HOH735 3.7 31.7 1.0 N A:ASP447 3.8 28.7 1.0 CA A:ASP447 3.8 30.0 1.0 O A:HOH851 4.0 44.0 1.0 CD A:GLU503 4.0 31.0 1.0 CB A:ASP469 4.1 25.8 1.0 CG A:ASP446 4.1 30.8 1.0 CA A:ASP469 4.2 23.1 1.0 OE2 A:GLU503 4.2 35.6 1.0 CB A:ASP447 4.2 27.9 1.0 P11 A:C2E603 4.4 20.3 1.0 OD2 A:ASP447 4.4 46.4 1.0 O A:HOH825 4.7 31.8 1.0 OD2 A:ASP446 4.7 33.0 1.0 OD1 A:ASP469 4.8 25.5 1.0 N A:ASP469 4.9 21.7 1.0 C A:ASP446 4.9 24.8 1.0 O A:HOH817 4.9 23.0 1.0

E.V.Filippova, G.Minasov, L.Shuvalova, O.Kiryukhina, C.Massa, T.Schirmer, A.Joachimiak, W.F.Anderson. Crystal Structure of Eal Domain From Caulobacter Crescentus in Complex with C-Di-Gmp and Ca To Be Published.