Magnesium in PDB 1soj: Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx:
3.1.4.17;

The structure of Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx, PDB code: 1soj was solved by G.Scapin, S.B.Patel, C.Chung, J.P.Varnerin, S.D.Edmondson, A.Mastracchio, E.R.Parmee, J.W.Becker, S.B.Singh, L.H.Van Derploeg, M.R.Tota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	275.046, 147.078, 253.485, 90.00, 109.84, 90.00
R / Rfree (%)	n/a / n/a

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx (pdb code 1soj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx, PDB code: 1soj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2123 b:3.0 occ:1.00 O A:HOH11 1.7 6.4 1.0 O A:HOH16 1.7 11.1 1.0 NE2 A:HIS741 1.9 28.1 1.0 OD1 A:ASP937 1.9 26.3 1.0 NE2 A:HIS821 2.0 29.1 1.0 OD2 A:ASP822 2.0 32.3 1.0 CE1 A:HIS741 2.8 28.7 1.0 CE1 A:HIS821 2.9 30.0 1.0 CD2 A:HIS741 2.9 29.6 1.0 CG A:ASP937 2.9 29.6 1.0 CD2 A:HIS821 3.0 29.3 1.0 CG A:ASP822 3.2 34.4 1.0 OD2 A:ASP937 3.4 29.3 1.0 O A:HOH1125 3.8 29.2 1.0 OD1 A:ASP822 3.9 31.9 1.0 MG A:MG2124 3.9 41.3 1.0 ND1 A:HIS741 3.9 29.0 1.0 CG A:HIS741 4.0 27.7 1.0 ND1 A:HIS821 4.0 31.4 1.0 CG2 A:VAL745 4.0 27.6 1.0 CG A:HIS821 4.1 31.9 1.0 O A:HOH15 4.2 36.7 1.0 CB A:ASP937 4.3 29.0 1.0 CB A:ASP822 4.3 34.3 1.0 O A:ASP937 4.5 35.9 1.0 ND1 A:HIS737 4.5 32.7 1.0 CA A:ASP937 4.7 32.8 1.0 O A:HOH14 4.7 19.3 1.0 CE1 A:HIS737 4.8 29.8 1.0 O A:HOH12 5.0 8.6 1.0

Magnesium binding site 2 out of 24 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2124 b:41.3 occ:1.00 O A:HOH12 1.7 8.6 1.0 O A:HOH15 1.9 36.7 1.0 OD1 A:ASP822 2.0 31.9 1.0 O A:HOH13 2.0 14.5 1.0 O A:HOH14 2.2 19.3 1.0 O A:HOH11 2.4 6.4 1.0 CG A:ASP822 2.9 34.4 1.0 OD2 A:ASP822 3.2 32.3 1.0 O A:HOH16 3.6 11.1 1.0 MG A:MG2123 3.9 3.0 1.0 CD2 A:HIS821 4.0 29.3 1.0 OD2 A:ASP937 4.1 29.3 1.0 O A:HIS821 4.2 34.7 1.0 OE2 A:GLU851 4.3 38.2 1.0 CB A:ASP822 4.3 34.3 1.0 NE2 A:HIS821 4.3 29.1 1.0 OG1 A:THR893 4.4 29.3 1.0 NE2 A:HIS854 4.5 38.7 1.0 CE1 A:HIS737 4.5 29.8 1.0 ND1 A:HIS825 4.6 34.3 1.0 O A:THR893 4.6 29.6 1.0 CE1 A:HIS825 4.6 33.2 1.0 ND1 A:HIS737 4.7 32.7 1.0 CA A:ASP822 4.7 33.6 1.0 CD2 A:HIS854 4.7 37.6 1.0 OD1 A:ASP937 4.8 26.3 1.0 CG A:ASP937 4.8 29.6 1.0 CB A:THR893 4.8 29.4 1.0 C A:HIS821 4.9 31.9 1.0

Magnesium binding site 3 out of 24 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2125 b:4.9 occ:1.00 O B:HOH25 1.7 20.4 1.0 NE2 B:HIS821 1.9 39.3 1.0 OD1 B:ASP937 1.9 34.4 1.0 OD2 B:ASP822 2.0 30.4 1.0 NE2 B:HIS741 2.0 40.2 1.0 O B:HOH21 2.1 14.2 1.0 CD2 B:HIS821 2.8 37.9 1.0 CD2 B:HIS741 2.9 37.4 1.0 CG B:ASP937 2.9 39.3 1.0 CE1 B:HIS821 2.9 42.7 1.0 CE1 B:HIS741 3.1 38.3 1.0 CG B:ASP822 3.2 34.0 1.0 OD2 B:ASP937 3.3 39.3 1.0 MG B:MG2126 3.8 56.5 1.0 OD1 B:ASP822 3.9 33.0 1.0 O B:HOH1130 3.9 79.5 1.0 CG B:HIS821 4.0 38.2 1.0 ND1 B:HIS821 4.0 40.9 1.0 CG B:HIS741 4.1 37.8 1.0 ND1 B:HIS741 4.1 37.1 1.0 O B:HOH26 4.2 56.6 1.0 CB B:ASP937 4.3 39.5 1.0 CG2 B:VAL745 4.3 38.2 1.0 CB B:ASP822 4.4 33.2 1.0 O B:ASP937 4.5 47.7 1.0 O B:HOH24 4.5 53.0 1.0 ND1 B:HIS737 4.5 47.9 1.0 CA B:ASP937 4.6 43.0 1.0 CE1 B:HIS737 4.7 46.6 1.0

Magnesium binding site 4 out of 24 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2126 b:56.5 occ:1.00 O B:HOH22 1.8 29.5 1.0 O B:HOH26 1.9 56.6 1.0 O B:HOH21 1.9 14.2 1.0 O B:HOH24 2.1 53.0 1.0 O B:HOH23 2.3 18.4 1.0 OD1 B:ASP822 2.3 33.0 1.0 CG B:ASP822 3.1 34.0 1.0 OD2 B:ASP822 3.2 30.4 1.0 O B:HOH25 3.4 20.4 1.0 MG B:MG2125 3.8 4.9 1.0 OD2 B:ASP937 3.9 39.3 1.0 CD2 B:HIS821 4.0 37.9 1.0 OG1 B:THR893 4.2 39.2 1.0 OE2 B:GLU851 4.2 45.2 1.0 O B:HIS821 4.3 36.9 1.0 NE2 B:HIS821 4.4 39.3 1.0 CE1 B:HIS825 4.5 46.1 1.0 CE1 B:HIS737 4.6 46.6 1.0 CB B:ASP822 4.6 33.2 1.0 CB B:THR893 4.6 37.6 1.0 ND1 B:HIS825 4.6 47.7 1.0 O B:THR893 4.6 44.4 1.0 NE2 B:HIS854 4.7 39.6 1.0 ND1 B:HIS737 4.7 47.9 1.0 OD1 B:ASP937 4.7 34.4 1.0 CG B:ASP937 4.7 39.3 1.0 CD2 B:HIS854 4.9 37.2 1.0 CA B:ASP822 5.0 34.2 1.0

Magnesium binding site 5 out of 24 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2127 b:5.2 occ:1.00 O C:HOH31 1.6 1.9 1.0 O C:HOH36 1.7 27.2 1.0 NE2 C:HIS741 1.8 27.5 1.0 OD2 C:ASP822 1.8 27.2 1.0 OD1 C:ASP937 2.1 22.0 1.0 NE2 C:HIS821 2.2 32.7 1.0 CD2 C:HIS741 2.8 30.4 1.0 CE1 C:HIS741 2.8 26.9 1.0 CG C:ASP822 3.1 34.5 1.0 CE1 C:HIS821 3.1 33.6 1.0 CG C:ASP937 3.1 26.3 1.0 CD2 C:HIS821 3.2 33.0 1.0 OD2 C:ASP937 3.4 26.4 1.0 O C:HOH1225 3.7 31.4 1.0 OD1 C:ASP822 3.7 34.6 1.0 ND1 C:HIS741 3.9 26.4 1.0 CG C:HIS741 3.9 28.7 1.0 MG C:MG2128 4.0 29.2 1.0 O C:HOH35 4.2 32.0 1.0 ND1 C:HIS821 4.2 34.8 1.0 CB C:ASP822 4.2 34.6 1.0 CG2 C:VAL745 4.2 28.3 1.0 ND1 C:HIS737 4.3 33.9 1.0 CG C:HIS821 4.3 35.1 1.0 CB C:ASP937 4.5 27.5 1.0 CE1 C:HIS737 4.5 30.4 1.0 O C:ASP937 4.5 35.4 1.0 O C:HOH34 4.7 28.3 1.0 CA C:ASP937 4.9 32.5 1.0 O C:HOH32 4.9 14.8 1.0

Magnesium binding site 6 out of 24 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2128 b:29.2 occ:1.00 O C:HOH32 1.8 14.8 1.0 OD1 C:ASP822 1.9 34.6 1.0 O C:HOH33 2.0 18.0 1.0 O C:HOH34 2.1 28.3 1.0 O C:HOH35 2.1 32.0 1.0 O C:HOH31 2.8 1.9 1.0 CG C:ASP822 2.9 34.5 1.0 OD2 C:ASP822 3.3 27.2 1.0 O C:HOH36 3.7 27.2 1.0 MG C:MG2127 4.0 5.2 1.0 CD2 C:HIS821 4.1 33.0 1.0 OE2 C:GLU851 4.1 41.3 1.0 O C:HIS821 4.2 37.7 1.0 NE2 C:HIS854 4.2 39.3 1.0 CB C:ASP822 4.3 34.6 1.0 OD2 C:ASP937 4.3 26.4 1.0 ND1 C:HIS825 4.4 35.7 1.0 CE1 C:HIS825 4.4 35.7 1.0 CD2 C:HIS854 4.5 37.3 1.0 NE2 C:HIS821 4.5 32.7 1.0 OG1 C:THR893 4.5 28.6 1.0 CA C:ASP822 4.6 35.0 1.0 CE1 C:HIS737 4.6 30.4 1.0 ND1 C:HIS737 4.7 33.9 1.0 O C:THR893 4.7 31.8 1.0 C C:HIS821 4.9 34.9 1.0 CB C:THR893 5.0 28.7 1.0

Magnesium binding site 7 out of 24 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2129 b:9.9 occ:1.00 O D:HOH41 1.7 5.9 1.0 O D:HOH45 1.7 19.8 1.0 OD2 D:ASP822 1.9 25.9 1.0 NE2 D:HIS821 1.9 36.2 1.0 NE2 D:HIS741 2.0 35.4 1.0 OD1 D:ASP937 2.0 27.3 1.0 CD2 D:HIS821 2.8 33.9 1.0 CD2 D:HIS741 2.9 35.1 1.0 CE1 D:HIS821 3.0 37.3 1.0 CG D:ASP937 3.0 34.6 1.0 CG D:ASP822 3.1 31.2 1.0 CE1 D:HIS741 3.1 36.1 1.0 OD2 D:ASP937 3.4 33.8 1.0 OD1 D:ASP822 3.8 29.9 1.0 MG D:MG2130 3.9 22.9 1.0 CG D:HIS821 4.0 33.9 1.0 ND1 D:HIS821 4.0 33.6 1.0 CG D:HIS741 4.1 33.6 1.0 ND1 D:HIS741 4.1 32.9 1.0 O D:HOH46 4.2 38.6 1.0 O D:HOH1230 4.2 43.0 1.0 CB D:ASP822 4.3 28.4 1.0 ND1 D:HIS737 4.4 41.9 1.0 CB D:ASP937 4.4 34.8 1.0 CG2 D:VAL745 4.4 36.5 1.0 O D:ASP937 4.6 42.2 1.0 CE1 D:HIS737 4.6 42.2 1.0 CA D:ASP937 4.8 39.0 1.0 O D:HOH44 4.8 24.9 1.0

Magnesium binding site 8 out of 24 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2130 b:22.9 occ:1.00 O D:HOH42 1.8 10.1 1.0 O D:HOH46 2.1 38.6 1.0 O D:HOH44 2.2 24.9 1.0 OD1 D:ASP822 2.2 29.9 1.0 O D:HOH43 2.2 14.8 1.0 O D:HOH41 2.4 5.9 1.0 CG D:ASP822 3.1 31.2 1.0 OD2 D:ASP822 3.3 25.9 1.0 MG D:MG2129 3.9 9.9 1.0 O D:HOH45 3.9 19.8 1.0 CD2 D:HIS821 4.0 33.9 1.0 O D:HIS821 4.1 34.5 1.0 OE2 D:GLU851 4.1 39.5 1.0 OD2 D:ASP937 4.1 33.8 1.0 OG1 D:THR893 4.1 31.3 1.0 NE2 D:HIS854 4.4 37.9 1.0 CB D:ASP822 4.5 28.4 1.0 CE1 D:HIS825 4.5 41.9 1.0 NE2 D:HIS821 4.5 36.2 1.0 ND1 D:HIS825 4.6 42.7 1.0 CB D:THR893 4.6 32.4 1.0 CD2 D:HIS854 4.6 37.4 1.0 O D:THR893 4.7 38.6 1.0 CE1 D:HIS737 4.7 42.2 1.0 ND1 D:HIS737 4.8 41.9 1.0 CA D:ASP822 4.8 32.3 1.0 OD1 D:ASP937 4.9 27.3 1.0 C D:HIS821 4.9 34.1 1.0 CG D:ASP937 4.9 34.6 1.0 CD D:GLU851 5.0 37.8 1.0

Magnesium binding site 9 out of 24 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg2131 b:1.0 occ:1.00 O E:HOH51 1.7 7.2 1.0 OD2 E:ASP822 1.8 27.2 1.0 NE2 E:HIS741 1.8 20.5 1.0 O E:HOH56 1.9 18.3 1.0 OD1 E:ASP937 2.2 16.9 1.0 NE2 E:HIS821 2.2 25.3 1.0 CD2 E:HIS741 2.7 25.9 1.0 CE1 E:HIS741 2.9 22.9 1.0 CG E:ASP822 3.0 33.5 1.0 CE1 E:HIS821 3.1 25.9 1.0 CG E:ASP937 3.2 21.8 1.0 CD2 E:HIS821 3.2 27.1 1.0 OD2 E:ASP937 3.5 21.9 1.0 OD1 E:ASP822 3.7 32.8 1.0 MG E:MG2132 3.8 29.8 1.0 O E:HOH1325 3.9 18.2 1.0 CG E:HIS741 3.9 24.7 1.0 ND1 E:HIS741 3.9 22.2 1.0 CB E:ASP822 4.1 33.3 1.0 ND1 E:HIS737 4.2 34.2 1.0 ND1 E:HIS821 4.2 27.3 1.0 CG E:HIS821 4.3 29.4 1.0 CG2 E:VAL745 4.3 26.6 1.0 O E:HOH55 4.3 37.5 1.0 CE1 E:HIS737 4.4 31.7 1.0 CB E:ASP937 4.5 24.3 1.0 O E:ASP937 4.6 33.1 1.0 O E:HOH54 4.6 17.4 1.0 CA E:ASP937 4.9 30.2 1.0

Magnesium binding site 10 out of 24 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg2132 b:29.8 occ:1.00 O E:HOH52 1.9 9.2 1.0 O E:HOH54 2.0 17.4 1.0 O E:HOH55 2.1 37.5 1.0 OD1 E:ASP822 2.2 32.8 1.0 O E:HOH51 2.3 7.2 1.0 O E:HOH53 2.4 18.9 1.0 CG E:ASP822 3.1 33.5 1.0 OD2 E:ASP822 3.3 27.2 1.0 O E:HOH56 3.5 18.3 1.0 MG E:MG2131 3.8 1.0 1.0 OD2 E:ASP937 3.8 21.9 1.0 CD2 E:HIS821 4.0 27.1 1.0 OE2 E:GLU851 4.2 39.8 1.0 NE2 E:HIS821 4.4 25.3 1.0 OG1 E:THR893 4.4 22.9 1.0 O E:THR893 4.4 28.8 1.0 O E:HIS821 4.4 33.0 1.0 CB E:ASP822 4.5 33.3 1.0 CE1 E:HIS737 4.5 31.7 1.0 NE2 E:HIS854 4.7 41.3 1.0 OD1 E:ASP937 4.7 16.9 1.0 CG E:ASP937 4.7 21.8 1.0 ND1 E:HIS825 4.7 32.6 1.0 CB E:THR893 4.7 26.8 1.0 ND1 E:HIS737 4.7 34.2 1.0 CE1 E:HIS825 4.7 34.1 1.0 CD2 E:HIS854 4.9 40.5 1.0 CA E:ASP822 4.9 34.0 1.0

G.Scapin, S.B.Patel, C.Chung, J.P.Varnerin, S.D.Edmondson, A.Mastracchio, E.R.Parmee, S.B.Singh, J.W.Becker, L.H.Van Der Ploeg, M.R.Tota. Crystal Structure of Human Phosphodiesterase 3B: Atomic Basis For Substrate and Inhibitor Specificity Biochemistry V. 43 6091 2004.
ISSN: ISSN 0006-2960
PubMed: 15147193
DOI: 10.1021/BI049868I