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Manganese in PDB 7l28: Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin, PDB code: 7l28 was solved by S.W.Horner, C.Garvie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.29 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.24, 59.65, 158.12, 90, 90.48, 90
R / Rfree (%) 23.3 / 26.3

Other elements in 7l28:

The structure of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin (pdb code 7l28). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin, PDB code: 7l28:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7l28

Go back to Manganese Binding Sites List in 7l28
Manganese binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1102

b:47.3
occ:1.00
 OD1 A:ASP950 2.1 50.1 1.0
NE2 A:HIS836 2.1 48.3 1.0
O A:HOH1202 2.2 44.2 1.0
NE2 A:HIS756 2.2 47.5 1.0
OD2 A:ASP837 2.3 43.8 1.0
CG A:ASP950 3.0 47.9 1.0
CD2 A:HIS836 3.0 46.7 1.0
CD2 A:HIS756 3.1 47.7 1.0
OD2 A:ASP950 3.2 49.7 1.0
CE1 A:HIS836 3.2 47.3 1.0
O A:HOH1229 3.2 51.0 1.0
CG A:ASP837 3.2 43.9 1.0
CE1 A:HIS756 3.3 48.1 1.0
MG A:MG1103 3.8 36.8 1.0
OD1 A:ASP837 3.9 44.3 1.0
O A:HOH1226 4.1 42.9 1.0
CG A:HIS836 4.2 47.2 1.0
ND1 A:HIS836 4.2 44.9 1.0
CB A:ASP837 4.3 42.1 1.0
CG A:HIS756 4.3 46.8 1.0
CD2 A:HIS752 4.3 48.1 1.0
ND1 A:HIS756 4.3 47.9 1.0
CB A:ASP950 4.4 46.4 1.0
CG2 A:VAL760 4.6 46.7 1.0
O A:HOH1208 4.6 42.5 1.0
O A:ASP950 4.7 47.2 1.0
NE2 A:HIS752 4.8 47.9 1.0
CA A:ASP950 4.8 46.0 1.0

Manganese binding site 2 out of 4 in 7l28

Go back to Manganese Binding Sites List in 7l28
Manganese binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1102

b:40.3
occ:1.00
 O B:HOH1221 2.0 43.8 1.0
NE2 B:HIS836 2.1 33.1 1.0
OD1 B:ASP950 2.1 43.0 1.0
NE2 B:HIS756 2.2 44.0 1.0
OD2 B:ASP837 2.3 48.7 1.0
O B:HOH1213 2.3 41.0 1.0
CD2 B:HIS836 3.0 33.6 1.0
CG B:ASP950 3.0 39.9 1.0
CD2 B:HIS756 3.1 42.7 1.0
CE1 B:HIS836 3.1 36.1 1.0
CE1 B:HIS756 3.2 45.0 1.0
OD2 B:ASP950 3.2 40.4 1.0
CG B:ASP837 3.3 47.9 1.0
MG B:MG1103 3.9 35.5 1.0
OD1 B:ASP837 3.9 46.1 1.0
CG B:HIS836 4.2 32.9 1.0
ND1 B:HIS836 4.2 34.0 1.0
CB B:ASP837 4.2 44.2 1.0
CG B:HIS756 4.3 44.2 1.0
ND1 B:HIS756 4.3 42.4 1.0
CD2 B:HIS752 4.3 42.3 1.0
CB B:ASP950 4.4 41.4 1.0
O B:HOH1224 4.5 40.0 1.0
CG2 B:VAL760 4.6 38.6 1.0
O B:HOH1209 4.6 40.1 1.0
O B:ASP950 4.7 43.1 1.0
NE2 B:HIS752 4.8 39.6 1.0
CA B:ASP950 4.9 40.1 1.0

Manganese binding site 3 out of 4 in 7l28

Go back to Manganese Binding Sites List in 7l28
Manganese binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1102

b:46.5
occ:1.00
 NE2 C:HIS836 2.0 40.4 1.0
NE2 C:HIS756 2.1 48.9 1.0
O C:HOH1210 2.2 44.1 1.0
OD2 C:ASP837 2.2 50.1 1.0
OD1 C:ASP950 2.2 53.7 1.0
O C:HOH1224 2.5 52.9 1.0
CD2 C:HIS836 2.9 36.4 1.0
CD2 C:HIS756 3.0 50.5 1.0
CE1 C:HIS836 3.1 40.5 1.0
CG C:ASP950 3.1 48.6 1.0
CE1 C:HIS756 3.2 52.6 1.0
CG C:ASP837 3.2 48.0 1.0
OD2 C:ASP950 3.3 52.6 1.0
OD1 C:ASP837 3.7 44.8 1.0
MG C:MG1103 3.9 39.9 1.0
CG C:HIS836 4.0 39.5 1.0
ND1 C:HIS836 4.1 43.1 1.0
O C:HOH1225 4.2 44.4 1.0
CG C:HIS756 4.2 51.8 1.0
ND1 C:HIS752 4.3 53.7 1.0
ND1 C:HIS756 4.3 51.8 1.0
CB C:ASP837 4.3 45.1 1.0
CB C:ASP950 4.5 47.9 1.0
CE1 C:HIS752 4.6 52.6 1.0
CG2 C:VAL760 4.6 37.8 1.0
O C:HOH1218 4.7 40.8 1.0
O C:ASP950 4.8 49.0 1.0
CA C:ASP950 4.9 45.5 1.0

Manganese binding site 4 out of 4 in 7l28

Go back to Manganese Binding Sites List in 7l28
Manganese binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1102

b:46.8
occ:1.00
 OD1 D:ASP950 2.1 48.6 1.0
NE2 D:HIS836 2.1 39.6 1.0
OD2 D:ASP837 2.2 45.5 1.0
O D:HOH1209 2.2 50.2 1.0
NE2 D:HIS756 2.2 46.2 1.0
CG D:ASP950 3.0 50.8 1.0
O D:HOH1222 3.0 30.0 1.0
CD2 D:HIS836 3.0 41.6 1.0
CD2 D:HIS756 3.1 45.8 1.0
CE1 D:HIS836 3.2 40.0 1.0
CG D:ASP837 3.2 47.8 1.0
OD2 D:ASP950 3.3 49.3 1.0
CE1 D:HIS756 3.3 49.5 1.0
MG D:MG1103 3.8 42.4 1.0
O D:HOH1216 3.8 49.0 1.0
OD1 D:ASP837 3.8 48.0 1.0
O D:HOH1224 4.1 51.1 1.0
CG D:HIS836 4.2 40.8 1.0
CB D:ASP837 4.2 45.0 1.0
ND1 D:HIS836 4.2 39.0 1.0
CG D:HIS756 4.3 46.6 1.0
CD2 D:HIS752 4.3 43.7 1.0
ND1 D:HIS756 4.4 44.8 1.0
CB D:ASP950 4.4 47.6 1.0
O D:HOH1214 4.6 45.9 1.0
CG2 D:VAL760 4.6 44.5 1.0
NE2 D:HIS752 4.8 43.6 1.0
CA D:ASP950 4.8 45.0 1.0
O D:ASP950 4.9 47.6 1.0

Reference:

C.W.Garvie, S.W.Horner. Structure of PDE3A-SLFN12 Complex Reveals Requirements For Activation of SLFN12 Rnase To Be Published.
Page generated: Sun Oct 6 09:48:46 2024

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