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Magnesium in PDB 1so2: Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor

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

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor, PDB code: 1so2 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 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.482, 121.772, 126.671, 90.00, 100.74, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1so2:

The structure of Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor also contains other interesting chemical elements:

Iodine (I) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor (pdb code 1so2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor, PDB code: 1so2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 1so2

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Magnesium binding site 1 out of 9 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


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 A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg471

b:34.7
occ:1.00
 OD2 A:ASP822 2.0 39.6 1.0
OD1 A:ASP937 2.0 32.5 1.0
O A:HOH11 2.4 30.2 1.0
NE2 A:HIS741 2.4 35.8 1.0
NE2 A:HIS821 2.6 35.9 1.0
CG A:ASP937 3.0 34.6 1.0
CD2 A:HIS741 3.1 34.0 1.0
CG A:ASP822 3.1 36.3 1.0
CD2 A:HIS821 3.3 31.3 1.0
OD2 A:ASP937 3.4 37.0 1.0
O A:HOH16 3.5 57.0 1.0
CE1 A:HIS741 3.6 34.4 1.0
OD1 A:ASP822 3.6 36.9 1.0
CE1 A:HIS821 3.6 32.1 1.0
MG A:MG472 3.9 32.7 1.0
O A:HOH15 3.9 26.8 1.0
CD2 A:HIS737 4.0 24.1 1.0
CG A:HIS741 4.4 35.5 1.0
CB A:ASP822 4.4 34.1 1.0
CB A:ASP937 4.4 34.4 1.0
O A:ASP937 4.5 31.7 1.0
O A:HOH269 4.5 37.8 1.0
CG A:HIS821 4.5 31.9 1.0
ND1 A:HIS741 4.6 36.4 1.0
NE2 A:HIS737 4.6 22.4 1.0
ND1 A:HIS821 4.7 31.2 1.0
CG2 A:VAL745 4.8 36.8 1.0
CA A:ASP937 4.9 32.7 1.0
O A:HOH14 4.9 31.2 1.0

Magnesium binding site 2 out of 9 in 1so2

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Magnesium binding site 2 out of 9 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


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 A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg472

b:32.7
occ:1.00
 OD1 A:ASP822 1.9 36.9 1.0
O A:HOH13 2.2 23.7 1.0
O A:HOH15 2.3 26.8 1.0
O A:HOH12 2.3 26.5 1.0
O A:HOH14 2.3 31.2 1.0
O A:HOH11 2.3 30.2 1.0
CG A:ASP822 3.0 36.3 1.0
OD2 A:ASP822 3.4 39.6 1.0
O A:HOH344 3.7 27.9 1.0
NE2 A:HIS854 3.8 23.1 1.0
MG A:MG471 3.9 34.7 1.0
CD2 A:HIS825 4.0 25.6 1.0
O A:HIS821 4.1 32.3 1.0
CD2 A:HIS854 4.2 21.7 1.0
O A:HOH343 4.3 36.4 1.0
OE2 A:GLU851 4.3 26.4 1.0
CB A:ASP822 4.3 34.1 1.0
NE2 A:HIS825 4.4 25.0 1.0
CD2 A:HIS821 4.4 31.3 1.0
OG1 A:THR893 4.5 24.4 1.0
O A:HOH280 4.5 61.0 1.0
CA A:ASP822 4.6 32.3 1.0
CD2 A:HIS737 4.6 24.1 1.0
O A:HOH16 4.7 57.0 1.0
CE1 A:HIS854 4.8 23.0 1.0
NE2 A:HIS737 4.9 22.4 1.0
NE2 A:HIS821 4.9 35.9 1.0
OD2 A:ASP937 4.9 37.0 1.0
C A:HIS821 5.0 31.3 1.0

Magnesium binding site 3 out of 9 in 1so2

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Magnesium binding site 3 out of 9 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


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 A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg479

b:39.1
occ:1.00
 O A:HOH51 2.0 26.1 1.0
OD1 A:ASN968 2.1 45.9 1.0
O A:HOH53 2.2 33.8 1.0
O A:HOH52 2.2 46.7 1.0
O A:HOH54 2.3 35.8 1.0
CG A:ASN968 3.1 44.8 1.0
O A:HOH425 3.3 47.5 1.0
ND2 A:ASN968 3.5 42.7 1.0
O A:ASP964 4.2 36.6 1.0
CB A:ASN968 4.4 42.9 1.0
N A:ASN968 4.7 41.0 1.0
CA A:ASN968 4.7 42.4 1.0

Magnesium binding site 4 out of 9 in 1so2

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Magnesium binding site 4 out of 9 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


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 A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg473

b:23.6
occ:1.00
 OD2 B:ASP822 1.9 37.0 1.0
OD1 B:ASP937 2.2 34.8 1.0
NE2 B:HIS821 2.4 30.4 1.0
NE2 B:HIS741 2.5 35.0 1.0
O B:HOH21 2.5 26.4 1.0
CG B:ASP822 3.0 31.0 1.0
CG B:ASP937 3.1 32.5 1.0
CD2 B:HIS741 3.2 32.6 1.0
CD2 B:HIS821 3.3 27.3 1.0
OD2 B:ASP937 3.3 31.0 1.0
O B:HOH25 3.3 43.8 1.0
CE1 B:HIS821 3.4 28.8 1.0
OD1 B:ASP822 3.5 31.1 1.0
CE1 B:HIS741 3.6 33.0 1.0
MG B:MG474 3.7 33.4 1.0
O B:HOH26 4.0 22.4 1.0
CD2 B:HIS737 4.1 23.2 1.0
CB B:ASP822 4.3 31.4 1.0
O B:HOH237 4.4 42.5 1.0
CG B:HIS821 4.4 26.9 1.0
ND1 B:HIS821 4.5 30.2 1.0
CG B:HIS741 4.5 34.0 1.0
O B:ASP937 4.5 30.5 1.0
CB B:ASP937 4.5 31.9 1.0
ND1 B:HIS741 4.6 33.8 1.0
NE2 B:HIS737 4.7 25.0 1.0
CG2 B:VAL745 4.8 34.2 1.0
O B:HOH24 4.8 32.1 1.0
CA B:ASP937 5.0 31.0 1.0
O B:HOH345 5.0 41.7 1.0

Magnesium binding site 5 out of 9 in 1so2

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Magnesium binding site 5 out of 9 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


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 A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg474

b:33.4
occ:1.00
 OD1 B:ASP822 1.8 31.1 1.0
O B:HOH21 2.0 26.4 1.0
O B:HOH23 2.0 19.9 1.0
O B:HOH26 2.1 22.4 1.0
O B:HOH24 2.2 32.1 1.0
O B:HOH22 2.5 23.1 1.0
CG B:ASP822 2.8 31.0 1.0
OD2 B:ASP822 3.2 37.0 1.0
MG B:MG473 3.7 23.6 1.0
O B:HOH177 3.8 25.3 1.0
NE2 B:HIS854 3.9 26.1 1.0
CD2 B:HIS825 4.1 26.4 1.0
O B:HOH345 4.1 41.7 1.0
CB B:ASP822 4.2 31.4 1.0
OE2 B:GLU851 4.2 31.8 1.0
CD2 B:HIS854 4.2 26.5 1.0
O B:HIS821 4.2 29.9 1.0
CD2 B:HIS821 4.3 27.3 1.0
NE2 B:HIS825 4.3 27.7 1.0
OG1 B:THR893 4.4 26.6 1.0
CD2 B:HIS737 4.5 23.2 1.0
O B:HOH25 4.5 43.8 1.0
CA B:ASP822 4.5 31.5 1.0
NE2 B:HIS821 4.6 30.4 1.0
OD2 B:ASP937 4.6 31.0 1.0
NE2 B:HIS737 4.8 25.0 1.0
CB B:THR893 5.0 26.0 1.0
C B:HIS821 5.0 31.8 1.0

Magnesium binding site 6 out of 9 in 1so2

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Magnesium binding site 6 out of 9 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


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 A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg475

b:28.2
occ:1.00
 O C:HOH31 1.9 38.8 1.0
OD1 C:ASP937 2.1 33.8 1.0
OD2 C:ASP822 2.1 36.5 1.0
OD2 C:ASP937 2.7 34.4 1.0
CG C:ASP937 2.7 33.9 1.0
NE2 C:HIS741 2.7 37.2 1.0
NE2 C:HIS821 2.8 44.2 1.0
CD2 C:HIS821 3.1 42.2 1.0
CG C:ASP822 3.2 36.8 1.0
CD2 C:HIS741 3.3 38.5 1.0
O C:HOH35 3.4 51.8 1.0
OD1 C:ASP822 3.6 37.2 1.0
MG C:MG476 3.7 37.2 1.0
CE1 C:HIS741 3.9 36.4 1.0
CE1 C:HIS821 4.0 44.4 1.0
CD2 C:HIS737 4.1 41.8 1.0
CB C:ASP937 4.2 35.5 1.0
CG C:HIS821 4.4 44.1 1.0
CB C:ASP822 4.5 37.3 1.0
NE2 C:HIS737 4.6 43.6 1.0
O C:ASP937 4.6 34.8 1.0
CG C:HIS741 4.6 37.4 1.0
O C:HOH36 4.7 35.7 1.0
O C:HOH32 4.8 29.5 1.0
ND1 C:HIS821 4.8 42.9 1.0
O C:HOH353 4.8 48.4 1.0
CG2 C:VAL745 4.8 41.2 1.0
O C:HOH34 4.8 38.9 1.0
CA C:ASP937 4.9 36.9 1.0
ND1 C:HIS741 4.9 38.1 1.0

Magnesium binding site 7 out of 9 in 1so2

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Magnesium binding site 7 out of 9 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


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 A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg476

b:37.2
occ:1.00
 OD1 C:ASP822 1.9 37.2 1.0
O C:HOH31 2.0 38.8 1.0
O C:HOH32 2.0 29.5 1.0
O C:HOH33 2.1 26.8 1.0
O C:HOH34 2.6 38.9 1.0
O C:HOH36 2.7 35.7 1.0
CG C:ASP822 3.0 36.8 1.0
OD2 C:ASP822 3.4 36.5 1.0
MG C:MG475 3.7 28.2 1.0
O C:HOH365 3.9 51.8 1.0
OE2 C:GLU851 4.1 44.7 1.0
CD2 C:HIS825 4.1 47.1 1.0
NE2 C:HIS854 4.1 39.4 1.0
O C:HIS821 4.1 40.8 1.0
CB C:ASP822 4.3 37.3 1.0
NE2 C:HIS825 4.3 47.5 1.0
CD2 C:HIS854 4.4 38.4 1.0
OG1 C:THR893 4.4 39.8 1.0
CD2 C:HIS737 4.4 41.8 1.0
OD2 C:ASP937 4.4 34.4 1.0
NE2 C:HIS737 4.6 43.6 1.0
O C:HOH35 4.7 51.8 1.0
CA C:ASP822 4.7 39.8 1.0
CD2 C:HIS821 4.8 42.2 1.0
O C:THR893 4.9 44.8 1.0
CB C:THR893 5.0 41.4 1.0

Magnesium binding site 8 out of 9 in 1so2

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Magnesium binding site 8 out of 9 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


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 A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg477

b:34.6
occ:1.00
 OD1 D:ASP937 1.9 43.6 1.0
OD2 D:ASP822 2.1 32.0 1.0
O D:HOH41 2.2 31.4 1.0
CG D:ASP937 2.6 45.0 1.0
NE2 D:HIS741 2.6 39.9 1.0
OD2 D:ASP937 2.7 43.2 1.0
NE2 D:HIS821 2.7 52.3 1.0
CG D:ASP822 3.2 34.6 1.0
O D:HOH45 3.2 60.3 1.0
CD2 D:HIS821 3.3 49.7 1.0
CD2 D:HIS741 3.4 37.2 1.0
CE1 D:HIS821 3.5 51.8 1.0
MG D:MG478 3.6 31.1 1.0
OD1 D:ASP822 3.7 33.3 1.0
CE1 D:HIS741 3.7 39.4 1.0
CD2 D:HIS737 4.0 38.2 1.0
CB D:ASP937 4.0 45.3 1.0
CG D:HIS821 4.3 50.8 1.0
ND1 D:HIS821 4.3 51.7 1.0
NE2 D:HIS737 4.4 37.7 1.0
CB D:ASP822 4.5 36.7 1.0
O D:ASP937 4.5 45.3 1.0
CG D:HIS741 4.6 37.8 1.0
CA D:ASP937 4.7 45.7 1.0
O D:HOH44 4.7 30.3 1.0
ND1 D:HIS741 4.7 39.4 1.0
O D:HOH42 4.8 24.3 1.0
CG2 D:VAL745 4.9 45.4 1.0

Magnesium binding site 9 out of 9 in 1so2

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Magnesium binding site 9 out of 9 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


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 A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg478

b:31.1
occ:1.00
 O D:HOH43 1.8 30.6 1.0
OD1 D:ASP822 1.8 33.3 1.0
O D:HOH41 1.9 31.4 1.0
O D:HOH42 2.0 24.3 1.0
O D:HOH44 2.6 30.3 1.0
CG D:ASP822 2.8 34.6 1.0
O D:HOH46 2.9 43.7 1.0
OD2 D:ASP822 3.2 32.0 1.0
MG D:MG477 3.6 34.6 1.0
O D:HIS821 3.7 43.4 1.0
O D:HOH346 3.7 36.0 1.0
NE2 D:HIS854 4.0 43.0 1.0
OE2 D:GLU851 4.1 49.1 1.0
CB D:ASP822 4.2 36.7 1.0
CD2 D:HIS854 4.2 43.1 1.0
CD2 D:HIS825 4.2 45.1 1.0
OD2 D:ASP937 4.3 43.2 1.0
OG1 D:THR893 4.3 44.3 1.0
O D:HOH45 4.3 60.3 1.0
O D:HOH389 4.5 65.8 1.0
CA D:ASP822 4.5 40.6 1.0
NE2 D:HIS825 4.5 46.5 1.0
CD2 D:HIS737 4.6 38.2 1.0
C D:HIS821 4.6 43.9 1.0
NE2 D:HIS737 4.7 37.7 1.0
CD2 D:HIS821 4.8 49.7 1.0
CB D:THR893 4.9 46.5 1.0
N D:ASP822 5.0 41.4 1.0

Reference:

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
Page generated: Tue Aug 13 13:47:04 2024

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