Magnesium in PDB 3u2e: Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++

The structure of Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++, PDB code: 3u2e 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)	30.00 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.144, 75.154, 129.066, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.7

The binding sites of Magnesium atom in the Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++ (pdb code 3u2e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++, PDB code: 3u2e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2 b:23.1 occ:1.00 OD2 A:ASP446 2.0 20.1 1.0 OD1 A:ASN384 2.1 17.0 1.0 OE1 A:GLU416 2.1 23.4 1.0 OP2 C:G601 2.1 26.5 1.0 OE2 A:GLU323 2.2 17.9 1.0 CG A:ASP446 3.1 19.2 1.0 CG A:ASN384 3.1 19.8 1.0 CD A:GLU323 3.2 17.2 1.0 P C:G601 3.3 47.0 1.0 CD A:GLU416 3.3 22.3 1.0 OP3 C:G601 3.4 26.8 1.0 ND2 A:ASN384 3.5 15.8 1.0 OD1 A:ASP446 3.5 17.7 1.0 OE1 A:GLU323 3.6 22.1 1.0 O A:HOH150 4.0 32.0 1.0 OE2 A:GLU416 4.0 24.0 1.0 OP1 C:G601 4.2 43.6 1.0 O2' C:G602 4.3 29.5 1.0 MG A:MG3 4.3 32.3 1.0 CB A:ASP446 4.4 18.9 1.0 NZ A:LYS467 4.4 13.7 1.0 CB A:GLU416 4.4 20.5 1.0 CG A:GLU416 4.4 23.0 1.0 CB A:ASN384 4.5 20.1 1.0 CG A:GLU323 4.5 15.9 1.0 O5' C:G601 4.5 53.0 1.0 OE2 A:GLU503 4.6 28.5 1.0 MG C:MG5 4.9 42.5 1.0 C5' C:G601 5.0 45.0 1.0

Magnesium binding site 2 out of 6 in the Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3 b:32.3 occ:1.00 OD1 A:ASP447 1.9 22.8 1.0 OP3 C:G601 1.9 26.8 1.0 OD1 A:ASP446 2.2 17.7 1.0 OE1 A:GLU503 2.2 33.1 1.0 OE2 A:GLU503 2.2 28.5 1.0 CD A:GLU503 2.5 26.2 1.0 CG A:ASP447 3.2 26.9 1.0 CG A:ASP446 3.2 19.2 1.0 P C:G601 3.3 47.0 1.0 N A:ASP447 3.6 19.2 1.0 OP1 C:G601 3.7 43.6 1.0 OD2 A:ASP446 3.8 20.1 1.0 CA A:ASP447 3.9 20.9 1.0 OD2 A:ASP447 4.0 33.9 1.0 CG A:GLU503 4.0 23.4 1.0 CB A:ASP447 4.1 22.8 1.0 OP2 C:G601 4.2 26.5 1.0 O A:HOH103 4.3 36.0 1.0 O A:HOH92 4.3 33.0 1.0 O5' C:G601 4.3 53.0 1.0 MG A:MG2 4.3 23.1 1.0 CB A:ASP446 4.4 18.9 1.0 OD1 A:ASP469 4.4 28.6 1.0 C A:ASP446 4.5 18.6 1.0 C5' C:G601 4.6 45.0 1.0 CA A:ASP446 4.7 17.4 1.0 CB A:GLU503 4.8 20.9 1.0 CA A:ASP469 4.9 24.8 1.0

Magnesium binding site 3 out of 6 in the Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1 b:17.8 occ:1.00 OD2 B:ASP446 2.0 16.2 1.0 OE2 B:GLU416 2.1 18.5 1.0 OE2 B:GLU323 2.1 17.6 1.0 OP2 D:G601 2.2 22.3 1.0 OD1 B:ASN384 2.2 17.6 1.0 O B:HOH2 2.3 24.4 1.0 CD B:GLU323 3.1 17.6 1.0 CG B:ASP446 3.2 17.2 1.0 CG B:ASN384 3.2 16.0 1.0 CD B:GLU416 3.3 20.1 1.0 P D:G601 3.3 37.4 1.0 OP3 D:G601 3.4 32.8 1.0 O B:HOH65 3.6 29.9 1.0 OE1 B:GLU323 3.6 21.3 1.0 OD1 B:ASP446 3.6 18.0 1.0 ND2 B:ASN384 3.6 15.8 1.0 OE1 B:GLU416 4.1 20.8 1.0 NZ B:LYS467 4.2 16.0 1.0 O2' D:G602 4.3 22.6 1.0 MG B:MG4 4.4 27.7 1.0 OP1 D:G601 4.4 37.9 1.0 CG B:GLU323 4.4 15.4 1.0 CB B:GLU416 4.4 18.9 1.0 CB B:ASP446 4.4 16.6 1.0 CG B:GLU416 4.4 20.9 1.0 CB B:ASN384 4.5 15.5 1.0 O5' D:G601 4.6 33.2 1.0 OE2 B:GLU503 4.6 24.2 1.0 MG D:MG6 4.6 46.6 1.0 O B:HOH81 4.8 40.0 1.0 C5' D:G601 5.0 24.3 1.0

Magnesium binding site 4 out of 6 in the Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4 b:27.7 occ:1.00 OP3 D:G601 1.9 32.8 1.0 OD1 B:ASP447 2.1 21.3 1.0 OE2 B:GLU503 2.2 24.2 1.0 OE1 B:GLU503 2.2 24.2 1.0 OD1 B:ASP446 2.2 18.0 1.0 CD B:GLU503 2.5 22.1 1.0 O B:HOH80 2.6 29.0 1.0 CG B:ASP446 3.2 17.2 1.0 P D:G601 3.2 37.4 1.0 CG B:ASP447 3.3 23.9 1.0 OP1 D:G601 3.5 37.9 1.0 O B:HOH2 3.6 24.4 1.0 OD2 B:ASP446 3.7 16.2 1.0 N B:ASP447 3.7 16.2 1.0 CG B:GLU503 4.0 17.9 1.0 OD2 B:ASP447 4.1 28.1 1.0 OP2 D:G601 4.1 22.3 1.0 CA B:ASP447 4.1 18.0 1.0 OD2 B:ASP469 4.2 24.4 1.0 O B:HOH121 4.2 18.3 1.0 O B:HOH63 4.2 19.3 0.5 O5' D:G601 4.2 33.2 1.0 O B:HOH63 4.3 12.1 0.5 CB B:ASP447 4.3 20.0 1.0 MG B:MG1 4.4 17.8 1.0 CB B:ASP446 4.4 16.6 1.0 C B:ASP446 4.6 17.0 1.0 CB B:GLU503 4.7 16.5 1.0 CA B:ASP446 4.8 16.3 1.0 C5' D:G601 4.8 24.3 1.0 CA B:ASP469 4.9 17.8 1.0

Magnesium binding site 5 out of 6 in the Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg5 b:42.5 occ:1.00 O A:HOH150 1.9 32.0 1.0 O A:HOH151 2.1 31.7 1.0 O A:HOH149 2.1 27.3 1.0 O3' C:G602 2.3 38.9 1.0 OP1 C:G601 2.4 43.6 1.0 O2' C:G602 2.4 29.5 1.0 C3' C:G602 3.2 34.7 1.0 C2' C:G602 3.2 31.0 1.0 P C:G601 3.4 47.0 1.0 OP2 C:G601 3.6 26.5 1.0 C1' C:G602 4.0 32.0 1.0 OD2 A:ASP447 4.3 33.9 1.0 O5' C:G601 4.3 53.0 1.0 O A:HOH92 4.4 33.0 1.0 CG2 A:THR418 4.4 24.1 1.0 OD1 A:ASN384 4.5 17.0 1.0 C4' C:G602 4.5 35.5 1.0 OP3 C:G601 4.5 26.8 1.0 OD2 A:ASP446 4.6 20.1 1.0 CG A:ASN384 4.8 19.8 1.0 MG A:MG2 4.9 23.1 1.0 O4' C:G602 4.9 34.1 1.0 CB A:ASN384 4.9 20.1 1.0

Magnesium binding site 6 out of 6 in the Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Eal Domain of Phosphodiesterase Pdea in Complex with 5'-Pgpg and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg6 b:46.6 occ:1.00 O B:HOH65 2.1 29.9 1.0 O D:HOH64 2.1 34.9 1.0 OP1 D:G601 2.4 37.9 1.0 O3' D:G602 2.4 20.0 1.0 O2' D:G602 2.5 22.6 1.0 OP2 D:G601 3.3 22.3 1.0 P D:G601 3.3 37.4 1.0 C3' D:G602 3.4 20.7 1.0 C2' D:G602 3.5 19.0 1.0 OD2 B:ASP447 4.1 28.1 1.0 OD2 B:ASP446 4.2 16.2 1.0 O5' D:G601 4.2 33.2 1.0 O B:HOH81 4.3 40.0 1.0 C1' D:G602 4.3 20.2 1.0 OP3 D:G601 4.4 32.8 1.0 O B:HOH63 4.5 12.1 0.5 CG2 B:THR418 4.5 20.9 1.0 OD1 B:ASN384 4.6 17.6 1.0 MG B:MG1 4.6 17.8 1.0 C4' D:G602 4.7 20.2 1.0 CG B:ASP446 4.8 17.2 1.0 CG B:ASP447 4.9 23.9 1.0 OD1 B:ASP447 4.9 21.3 1.0 CG B:ASN384 5.0 16.0 1.0

E.V.Filippova, G.Minasov, L.Shuvalova, O.Kiryukhina, C.Massa, T.Schirmer, A.Joachimiak, W.F.Anderson, Midwest Center For Structural Genomics (Mcsg). Eal Domain From Caulobacter Crescentus in Complex with 5'-Pgpg and Mg++ To Be Published.