Magnesium 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:

Manganese (Mn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Trequinsin, PDB code: 7l28:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7l28

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1103

b:36.8
occ:1.00
 O A:HOH1213 1.9 40.7 1.0
O A:HOH1226 2.0 42.9 1.0
O A:HOH1202 2.1 44.2 1.0
O A:HOH1222 2.1 40.9 1.0
O A:HOH1208 2.2 42.5 1.0
OD1 A:ASP837 2.3 44.3 1.0
CG A:ASP837 3.1 43.9 1.0
OD2 A:ASP837 3.3 43.8 1.0
MN A:MN1102 3.8 47.3 1.0
NE2 A:HIS869 4.1 42.5 1.0
OG1 A:THR908 4.2 40.0 1.0
OE2 A:GLU866 4.2 57.7 1.0
O A:HIS836 4.3 48.2 1.0
CD2 A:HIS836 4.3 46.7 1.0
CD2 A:HIS869 4.3 42.7 1.0
CD2 A:HIS840 4.3 40.2 1.0
O A:HOH1229 4.4 51.0 1.0
OD2 A:ASP950 4.4 49.7 1.0
NE2 A:HIS840 4.5 42.3 1.0
CB A:ASP837 4.5 42.1 1.0
CG A:GLU866 4.6 46.8 1.0
NE2 A:HIS836 4.6 48.3 1.0
CD2 A:HIS752 4.7 48.1 1.0
CB A:THR908 4.8 41.1 1.0
CD A:GLU866 4.8 51.0 1.0
CA A:ASP837 4.8 43.7 1.0
O A:THR908 4.9 48.1 1.0
NE2 A:HIS752 4.9 47.9 1.0

Magnesium binding site 2 out of 4 in 7l28

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1103

b:35.5
occ:1.00
 O B:HOH1213 2.0 41.0 1.0
O B:HOH1209 2.1 40.1 1.0
O B:HOH1218 2.1 43.1 1.0
O B:HOH1224 2.3 40.0 1.0
O B:HOH1220 2.3 40.2 1.0
OD1 B:ASP837 2.3 46.1 1.0
CG B:ASP837 3.1 47.9 1.0
OD2 B:ASP837 3.3 48.7 1.0
MN B:MN1102 3.9 40.3 1.0
O B:HOH1221 3.9 43.8 1.0
NE2 B:HIS869 4.1 40.8 1.0
OE2 B:GLU866 4.2 42.3 1.0
OG1 B:THR908 4.3 40.4 1.0
CD2 B:HIS840 4.3 47.3 1.0
CD2 B:HIS836 4.3 33.6 1.0
CD2 B:HIS869 4.4 40.6 1.0
O B:HIS836 4.4 37.5 1.0
OD2 B:ASP950 4.5 40.4 1.0
NE2 B:HIS840 4.5 48.3 1.0
CB B:ASP837 4.5 44.2 1.0
CD2 B:HIS752 4.6 42.3 1.0
NE2 B:HIS836 4.7 33.1 1.0
CG B:GLU866 4.7 41.0 1.0
NE2 B:HIS752 4.7 39.6 1.0
CB B:THR908 4.9 39.4 1.0
CD B:GLU866 4.9 42.6 1.0
CA B:ASP837 4.9 43.9 1.0
O B:THR908 4.9 40.1 1.0

Magnesium binding site 3 out of 4 in 7l28

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1103

b:39.9
occ:1.00
 O C:HOH1210 2.1 44.1 1.0
O C:HOH1217 2.1 42.6 1.0
O C:HOH1218 2.1 40.8 1.0
O C:HOH1216 2.2 43.0 1.0
OD1 C:ASP837 2.2 44.8 1.0
O C:HOH1225 2.3 44.4 1.0
CG C:ASP837 3.2 48.0 1.0
OD2 C:ASP837 3.4 50.1 1.0
MN C:MN1102 3.9 46.5 1.0
O C:HOH1224 3.9 52.9 1.0
O C:HIS836 4.2 42.8 1.0
OG1 C:THR908 4.2 45.9 1.0
CD2 C:HIS869 4.3 40.8 1.0
CD2 C:HIS836 4.3 36.4 1.0
OE2 C:GLU866 4.3 52.3 1.0
CD2 C:HIS840 4.4 45.3 1.0
NE2 C:HIS869 4.4 41.2 1.0
OD2 C:ASP950 4.5 52.6 1.0
NE2 C:HIS840 4.5 46.7 1.0
CB C:ASP837 4.6 45.1 1.0
ND1 C:HIS752 4.6 53.7 1.0
CE1 C:HIS752 4.6 52.6 1.0
CG C:GLU866 4.7 47.2 1.0
NE2 C:HIS836 4.7 40.4 1.0
CB C:THR908 4.8 43.8 1.0
CA C:ASP837 4.9 43.6 1.0
O C:THR908 4.9 47.2 1.0
CD C:GLU866 5.0 50.4 1.0

Magnesium binding site 4 out of 4 in 7l28

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1103

b:42.4
occ:1.00
 O D:HOH1209 2.0 50.2 1.0
O D:HOH1224 2.0 51.1 1.0
O D:HOH1218 2.1 39.7 1.0
O D:HOH1214 2.1 45.9 1.0
O D:HOH1210 2.2 42.3 1.0
OD1 D:ASP837 2.3 48.0 1.0
CG D:ASP837 3.1 47.8 1.0
OD2 D:ASP837 3.3 45.5 1.0
MN D:MN1102 3.8 46.8 1.0
O D:HOH1222 3.9 30.0 1.0
NE2 D:HIS869 4.1 45.9 1.0
OE2 D:GLU866 4.2 51.2 1.0
CD2 D:HIS836 4.3 41.6 1.0
O D:HIS836 4.3 42.6 1.0
OG1 D:THR908 4.3 47.6 1.0
CD2 D:HIS869 4.3 44.4 1.0
CD2 D:HIS840 4.4 43.3 1.0
OD2 D:ASP950 4.4 49.3 1.0
CB D:ASP837 4.5 45.0 1.0
NE2 D:HIS840 4.5 43.0 1.0
CD2 D:HIS752 4.6 43.7 1.0
NE2 D:HIS836 4.6 39.6 1.0
CG D:GLU866 4.7 45.3 1.0
NE2 D:HIS752 4.8 43.6 1.0
CA D:ASP837 4.8 44.0 1.0
CB D:THR908 4.9 43.5 1.0
CD D:GLU866 4.9 47.0 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 Jul 11 17:43:29 2021

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