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Magnesium in PDB 7l29: Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp

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

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

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp, PDB code: 7l29 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) 47.90 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.415, 58.783, 156.996, 90, 90.74, 90
R / Rfree (%) 23.5 / 25.3

Other elements in 7l29:

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

Calcium (Ca) 1 atom
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 Amp (pdb code 7l29). 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 Amp, PDB code: 7l29:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7l29

Go back to Magnesium Binding Sites List in 7l29
Magnesium binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:27.3
occ:1.00
 O2P A:AMP1101 2.1 52.9 1.0
O A:HOH1220 2.1 36.7 1.0
OD1 A:ASP837 2.1 50.4 1.0
O A:HOH1218 2.1 31.1 1.0
O1P A:AMP1101 2.1 48.2 1.0
O A:HOH1243 2.2 34.7 1.0
P A:AMP1101 2.5 80.0 1.0
CG A:ASP837 3.1 48.4 1.0
OD2 A:ASP837 3.5 47.8 1.0
O5' A:AMP1101 3.5 81.5 1.0
O3P A:AMP1101 3.8 53.6 1.0
MN A:MN1102 3.9 34.9 1.0
O A:HOH1202 3.9 49.3 1.0
OE2 A:GLU866 4.1 54.7 1.0
NE2 A:HIS869 4.1 48.5 1.0
OG1 A:THR908 4.2 42.5 1.0
O A:HIS836 4.2 43.4 1.0
CD2 A:HIS836 4.2 42.7 1.0
CD2 A:HIS869 4.3 47.5 1.0
OD2 A:ASP950 4.5 52.1 1.0
CB A:ASP837 4.5 47.0 1.0
CD2 A:HIS840 4.6 50.3 1.0
NE2 A:HIS836 4.6 46.2 1.0
CG A:GLU866 4.6 47.8 1.0
CB A:THR908 4.7 44.1 1.0
CD2 A:HIS752 4.8 50.8 1.0
CD A:GLU866 4.8 54.0 1.0
NE2 A:HIS840 4.9 54.4 1.0
CA A:ASP837 4.9 47.1 1.0
C5' A:AMP1101 4.9 73.5 1.0
O A:THR908 4.9 55.9 1.0

Magnesium binding site 2 out of 4 in 7l29

Go back to Magnesium Binding Sites List in 7l29
Magnesium binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1103

b:27.4
occ:1.00
 O2P B:AMP1101 2.0 81.5 1.0
O B:HOH1220 2.1 35.0 1.0
OD1 B:ASP837 2.2 41.0 1.0
O B:HOH1213 2.2 32.3 1.0
O B:HOH1212 2.2 30.4 1.0
O B:HOH1201 2.5 30.0 1.0
P B:AMP1101 3.0 64.9 1.0
O3P B:AMP1101 3.2 57.1 1.0
CG B:ASP837 3.2 43.5 1.0
OD2 B:ASP837 3.6 43.1 1.0
O B:HOH1217 3.7 43.2 1.0
MN B:MN1102 3.8 33.0 1.0
O1P B:AMP1101 3.8 39.3 1.0
OE2 B:GLU866 4.1 48.6 1.0
NE2 B:HIS869 4.2 39.4 1.0
O5' B:AMP1101 4.3 63.9 1.0
OG1 B:THR908 4.3 44.6 1.0
O B:HIS836 4.4 43.9 1.0
CD2 B:HIS869 4.4 39.0 1.0
CD2 B:HIS840 4.5 45.0 1.0
OD2 B:ASP950 4.5 45.1 1.0
CB B:ASP837 4.6 42.1 1.0
O B:HOH1202 4.6 50.7 1.0
C5' B:AMP1101 4.6 61.9 1.0
CD2 B:HIS836 4.7 41.5 1.0
CD2 B:HIS752 4.7 50.9 1.0
NE2 B:HIS840 4.8 49.0 1.0
CG B:GLU866 4.8 46.5 1.0
CB B:THR908 4.8 42.9 1.0
O B:THR908 4.9 49.6 1.0
CD B:GLU866 4.9 53.5 1.0
NE2 B:HIS752 5.0 49.3 1.0
CA B:ASP837 5.0 40.2 1.0

Magnesium binding site 3 out of 4 in 7l29

Go back to Magnesium Binding Sites List in 7l29
Magnesium binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:27.8
occ:1.00
 O C:HOH1242 2.1 36.6 1.0
O2P C:AMP1101 2.1 47.1 1.0
O C:HOH1233 2.1 33.2 1.0
OD1 C:ASP837 2.2 54.0 1.0
O C:HOH1223 2.2 32.3 1.0
O1P C:AMP1101 2.2 46.1 1.0
P C:AMP1101 2.6 81.2 1.0
CG C:ASP837 3.3 47.4 1.0
OD2 C:ASP837 3.7 46.7 1.0
O3P C:AMP1101 3.7 38.3 1.0
O C:HOH1203 3.8 38.7 1.0
O5' C:AMP1101 3.9 61.1 1.0
MN C:MN1102 3.9 33.4 1.0
OE2 C:GLU866 4.1 61.1 1.0
OG1 C:THR908 4.1 50.1 1.0
NE2 C:HIS869 4.2 44.0 1.0
C5' C:AMP1101 4.3 83.4 1.0
O C:HIS836 4.3 44.2 1.0
CD2 C:HIS869 4.3 43.0 1.0
CD2 C:HIS836 4.6 42.0 1.0
CD2 C:HIS840 4.6 49.7 1.0
CB C:ASP837 4.6 46.5 1.0
CB C:THR908 4.6 48.8 1.0
O C:THR908 4.7 54.2 1.0
CG C:GLU866 4.8 50.5 1.0
CD2 C:HIS752 4.8 56.2 1.0
CD C:GLU866 4.8 55.5 1.0
NE2 C:HIS752 4.9 56.0 1.0
NE2 C:HIS840 4.9 51.6 1.0
CA C:ASP837 5.0 44.0 1.0

Magnesium binding site 4 out of 4 in 7l29

Go back to Magnesium Binding Sites List in 7l29
Magnesium binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1103

b:25.6
occ:1.00
 O D:HOH1201 1.9 30.0 1.0
O D:HOH1244 2.0 29.4 1.0
O2P D:AMP1101 2.0 72.2 1.0
OD1 D:ASP837 2.1 33.6 1.0
O D:HOH1238 2.2 27.6 1.0
O D:HOH1215 2.2 28.6 1.0
O3P D:AMP1101 2.9 42.7 1.0
P D:AMP1101 2.9 60.8 1.0
CG D:ASP837 3.1 39.1 1.0
OD2 D:ASP837 3.5 39.3 1.0
MN D:MN1102 3.9 29.7 1.0
O D:HOH1219 3.9 40.2 1.0
O1P D:AMP1101 3.9 41.1 1.0
OE2 D:GLU866 4.0 51.0 1.0
NE2 D:HIS869 4.1 36.5 1.0
OG1 D:THR908 4.3 41.6 1.0
O5' D:AMP1101 4.3 55.3 1.0
O D:HIS836 4.3 41.0 1.0
CD2 D:HIS869 4.3 37.2 1.0
CD2 D:HIS840 4.5 39.5 1.0
CB D:ASP837 4.5 37.9 1.0
OD2 D:ASP950 4.5 47.8 1.0
CD2 D:HIS836 4.6 36.4 1.0
C5' D:AMP1101 4.7 53.4 1.0
CD2 D:HIS752 4.7 40.1 1.0
CG D:GLU866 4.8 45.6 1.0
NE2 D:HIS840 4.8 38.6 1.0
CD D:GLU866 4.8 50.8 1.0
CB D:THR908 4.8 39.0 1.0
CA D:ASP837 4.9 37.5 1.0
O D:THR908 4.9 46.7 1.0
NE2 D:HIS752 5.0 39.0 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: Wed Oct 2 23:15:59 2024

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