Atomistry » Magnesium » PDB 1s9d-1so5 » 1so2
Atomistry »
  Magnesium »
    PDB 1s9d-1so5 »
      1so2 »

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

Go back to Magnesium Binding Sites List in 1so2
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

Go back to Magnesium Binding Sites List in 1so2
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

Go back to Magnesium Binding Sites List in 1so2
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

Go back to Magnesium Binding Sites List in 1so2
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

Go back to Magnesium Binding Sites List in 1so2
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

Go back to Magnesium Binding Sites List in 1so2
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

Go back to Magnesium Binding Sites List in 1so2
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

Go back to Magnesium Binding Sites List in 1so2
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

Go back to Magnesium Binding Sites List in 1so2
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy