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Magnesium in PDB 7kwe: Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Dnmdp

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

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

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Dnmdp, PDB code: 7kwe 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) 47.70 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.21, 58.52, 157.54, 90, 90.66, 90
R / Rfree (%) 18.5 / 21.9

Other elements in 7kwe:

The structure of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Dnmdp 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 Dnmdp (pdb code 7kwe). 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 Dnmdp, PDB code: 7kwe:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7kwe

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Dnmdp


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

b:27.2
occ:1.00
 O A:HOH1225 1.9 35.7 1.0
O A:HOH1253 2.0 28.9 1.0
O A:HOH1262 2.0 41.2 1.0
O A:HOH1246 2.1 31.9 1.0
O A:HOH1235 2.1 29.5 1.0
OD1 A:ASP837 2.3 32.5 1.0
CG A:ASP837 3.2 32.1 1.0
OD2 A:ASP837 3.5 30.7 1.0
MN A:MN1102 3.8 37.5 1.0
OE2 A:GLU866 4.1 38.8 1.0
NE2 A:HIS869 4.2 30.6 1.0
O A:HOH1272 4.3 48.2 1.0
O A:HIS836 4.3 30.1 1.0
OG1 A:THR908 4.3 31.1 1.0
CD2 A:HIS869 4.4 28.5 1.0
OD2 A:ASP950 4.4 41.4 1.0
CD2 A:HIS840 4.5 35.1 1.0
CD2 A:HIS836 4.5 30.3 1.0
CB A:ASP837 4.6 30.5 1.0
CD2 A:HIS752 4.6 36.1 1.0
O A:HOH1260 4.7 52.9 1.0
NE2 A:HIS840 4.8 35.9 1.0
NE2 A:HIS752 4.8 37.7 1.0
CG A:GLU866 4.8 32.9 1.0
CB A:THR908 4.9 31.4 1.0
O A:THR908 4.9 37.4 1.0
CD A:GLU866 4.9 37.5 1.0
CA A:ASP837 4.9 29.3 1.0
NE2 A:HIS836 5.0 30.2 1.0

Magnesium binding site 2 out of 4 in 7kwe

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Magnesium binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Dnmdp


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

b:25.6
occ:1.00
 O D:HOH1292 2.0 31.9 1.0
O D:HOH1269 2.1 28.3 1.0
O D:HOH1218 2.2 35.2 1.0
O D:HOH1247 2.2 30.4 1.0
O D:HOH1240 2.2 26.8 1.0
OD1 D:ASP837 2.2 31.9 1.0
CG D:ASP837 3.1 28.7 1.0
OD2 D:ASP837 3.4 28.6 1.0
MN D:MN1102 3.7 32.4 1.0
OE2 D:GLU866 4.0 35.1 1.0
O D:HOH1298 4.2 46.6 1.0
OG1 D:THR908 4.2 30.7 1.0
NE2 D:HIS869 4.2 26.8 1.0
O D:HIS836 4.3 28.1 1.0
CD2 D:HIS869 4.3 25.3 1.0
O D:HOH1296 4.4 41.0 1.0
CD2 D:HIS836 4.4 26.3 1.0
OD2 D:ASP950 4.5 34.1 1.0
CD2 D:HIS840 4.5 24.1 1.0
CB D:ASP837 4.5 28.5 1.0
CD2 D:HIS752 4.6 29.1 1.0
O D:HOH1295 4.7 48.3 1.0
CG D:GLU866 4.7 29.2 1.0
NE2 D:HIS840 4.8 25.6 1.0
CD D:GLU866 4.8 31.6 1.0
NE2 D:HIS752 4.8 30.0 1.0
CB D:THR908 4.8 29.0 1.0
NE2 D:HIS836 4.9 31.1 1.0
CA D:ASP837 4.9 27.1 1.0
O D:THR908 4.9 27.8 1.0

Magnesium binding site 3 out of 4 in 7kwe

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Magnesium binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Dnmdp


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

b:27.2
occ:1.00
 O C:HOH1229 1.9 35.0 1.0
O C:HOH1274 2.1 29.2 1.0
O C:HOH1278 2.1 33.0 1.0
O C:HOH1282 2.1 36.1 1.0
OD1 C:ASP837 2.1 30.7 1.0
O C:HOH1240 2.2 31.1 1.0
CG C:ASP837 3.1 31.6 1.0
OD2 C:ASP837 3.3 33.7 1.0
MN C:MN1102 3.8 36.7 1.0
O C:HOH1289 4.0 48.9 1.0
OE2 C:GLU866 4.1 34.5 1.0
O C:HIS836 4.2 27.3 1.0
NE2 C:HIS869 4.2 29.7 1.0
O C:HOH1283 4.2 47.8 1.0
OG1 C:THR908 4.3 34.1 1.0
O C:HOH1303 4.3 53.0 1.0
CD2 C:HIS869 4.3 29.0 1.0
OD2 C:ASP950 4.4 38.3 1.0
CB C:ASP837 4.4 30.5 1.0
CD2 C:HIS836 4.4 29.4 1.0
CD2 C:HIS840 4.5 29.5 1.0
CD2 C:HIS752 4.5 32.2 1.0
O C:HOH1293 4.5 47.5 1.0
NE2 C:HIS752 4.7 33.5 1.0
NE2 C:HIS840 4.7 31.7 1.0
CG C:GLU866 4.7 30.4 1.0
CA C:ASP837 4.8 31.6 1.0
O C:THR908 4.9 35.8 1.0
O C:HOH1211 4.9 44.5 1.0
NE2 C:HIS836 4.9 29.9 1.0
CD C:GLU866 4.9 34.0 1.0
CB C:THR908 4.9 31.9 1.0

Magnesium binding site 4 out of 4 in 7kwe

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Magnesium binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Dnmdp


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

b:29.6
occ:1.00
 O B:HOH1222 1.8 39.5 1.0
O B:HOH1258 2.0 34.6 1.0
O B:HOH1239 2.1 30.8 1.0
OD1 B:ASP837 2.2 31.2 1.0
O B:HOH1241 2.2 31.7 1.0
O B:HOH1246 2.3 28.3 1.0
CG B:ASP837 3.1 32.9 1.0
OD2 B:ASP837 3.3 33.6 1.0
MN B:MN1102 3.8 37.6 1.0
O B:HOH1242 4.0 45.5 1.0
OE2 B:GLU866 4.1 33.5 1.0
O B:HIS836 4.2 32.1 1.0
NE2 B:HIS869 4.2 29.5 1.0
O B:HOH1264 4.3 46.8 1.0
CD2 B:HIS869 4.3 27.8 1.0
OG1 B:THR908 4.3 29.1 1.0
OD2 B:ASP950 4.4 38.3 1.0
CD2 B:HIS840 4.4 33.3 1.0
CD2 B:HIS836 4.4 31.7 1.0
CB B:ASP837 4.5 31.2 1.0
CD2 B:HIS752 4.6 32.3 1.0
NE2 B:HIS840 4.7 34.5 1.0
CG B:GLU866 4.8 34.1 1.0
NE2 B:HIS752 4.8 32.0 1.0
NE2 B:HIS836 4.8 33.6 1.0
CA B:ASP837 4.9 31.0 1.0
CD B:GLU866 4.9 38.2 1.0
CB B:THR908 4.9 30.2 1.0
O B:THR908 5.0 36.4 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 22:57:07 2024

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