Manganese 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:

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 Dnmdp (pdb code 7kwe). 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 Dnmdp, PDB code: 7kwe:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7kwe

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Manganese 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 Manganese with other atoms in the Mn 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:Mn1102

b:37.5
occ:1.00
 OD2 A:ASP837 2.1 30.7 1.0
OD1 A:ASP950 2.1 35.8 1.0
NE2 A:HIS836 2.2 30.2 1.0
NE2 A:HIS756 2.3 30.3 1.0
O A:HOH1225 2.3 35.7 1.0
O A:HOH1272 2.6 48.2 1.0
CD2 A:HIS836 2.9 30.3 1.0
CG A:ASP950 3.1 37.4 1.0
CD2 A:HIS756 3.1 33.2 1.0
CG A:ASP837 3.1 32.1 1.0
CE1 A:HIS836 3.3 33.2 1.0
OD2 A:ASP950 3.4 41.4 1.0
CE1 A:HIS756 3.4 35.0 1.0
OD1 A:ASP837 3.7 32.5 1.0
MG A:MG1103 3.8 27.2 1.0
O A:HOH1262 4.1 41.2 1.0
CG A:HIS836 4.1 31.1 1.0
CD2 A:HIS752 4.2 36.1 1.0
ND1 A:HIS836 4.3 29.5 1.0
CB A:ASP837 4.3 30.5 1.0
O A:HOH1243 4.3 51.4 1.0
CG A:HIS756 4.3 34.3 1.0
O A:HOH1260 4.4 52.9 1.0
ND1 A:HIS756 4.4 34.4 1.0
CB A:ASP950 4.4 32.7 1.0
O A:HOH1235 4.6 29.5 1.0
CG2 A:VAL760 4.7 30.6 1.0
NE2 A:HIS752 4.7 37.7 1.0
O A:ASP950 4.8 36.0 1.0
CA A:ASP950 4.9 32.7 1.0

Manganese binding site 2 out of 4 in 7kwe

Go back to Manganese Binding Sites List in 7kwe
Manganese 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 Manganese with other atoms in the Mn 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:Mn1102

b:32.4
occ:1.00
 O D:HOH1218 2.0 35.2 1.0
OD1 D:ASP950 2.2 28.3 1.0
OD2 D:ASP837 2.2 28.6 1.0
NE2 D:HIS836 2.2 31.1 1.0
NE2 D:HIS756 2.4 26.1 1.0
O D:HOH1296 2.5 41.0 1.0
CD2 D:HIS836 2.9 26.3 1.0
CG D:ASP950 3.1 33.7 1.0
CG D:ASP837 3.1 28.7 1.0
CD2 D:HIS756 3.2 26.6 1.0
CE1 D:HIS836 3.3 27.4 1.0
CE1 D:HIS756 3.4 27.2 1.0
OD2 D:ASP950 3.4 34.1 1.0
OD1 D:ASP837 3.6 31.9 1.0
MG D:MG1103 3.7 25.6 1.0
O D:HOH1292 3.9 31.9 1.0
CG D:HIS836 4.1 29.1 1.0
O D:HOH1222 4.2 40.8 1.0
CD2 D:HIS752 4.2 29.1 1.0
ND1 D:HIS836 4.2 31.9 1.0
O D:HOH1295 4.3 48.3 1.0
CB D:ASP837 4.3 28.5 1.0
CG D:HIS756 4.4 26.9 1.0
CB D:ASP950 4.5 28.5 1.0
ND1 D:HIS756 4.5 27.0 1.0
O D:HOH1240 4.6 26.8 1.0
NE2 D:HIS752 4.7 30.0 1.0
CG2 D:VAL760 4.8 27.3 1.0
O D:ASP950 4.8 32.9 1.0
CA D:ASP950 4.9 25.6 1.0

Manganese binding site 3 out of 4 in 7kwe

Go back to Manganese Binding Sites List in 7kwe
Manganese 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 Manganese with other atoms in the Mn 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:Mn1102

b:36.7
occ:1.00
 OD2 C:ASP837 2.0 33.7 1.0
OD1 C:ASP950 2.1 32.4 1.0
NE2 C:HIS836 2.2 29.9 1.0
NE2 C:HIS756 2.3 33.8 1.0
O C:HOH1229 2.4 35.0 1.0
O C:HOH1283 2.5 47.8 1.0
CD2 C:HIS836 3.0 29.4 1.0
CG C:ASP950 3.0 33.8 1.0
CD2 C:HIS756 3.1 32.9 1.0
CG C:ASP837 3.1 31.6 1.0
CE1 C:HIS836 3.3 30.6 1.0
OD2 C:ASP950 3.3 38.3 1.0
CE1 C:HIS756 3.3 33.3 1.0
OD1 C:ASP837 3.7 30.7 1.0
MG C:MG1103 3.8 27.2 1.0
O C:HOH1282 4.1 36.1 1.0
O C:HOH1295 4.1 46.7 1.0
CG C:HIS836 4.2 28.2 1.0
CD2 C:HIS752 4.2 32.2 1.0
O C:HOH1293 4.2 47.5 1.0
CB C:ASP837 4.2 30.5 1.0
ND1 C:HIS836 4.3 28.4 1.0
CG C:HIS756 4.3 33.0 1.0
ND1 C:HIS756 4.4 33.9 1.0
CB C:ASP950 4.4 31.3 1.0
O C:HOH1240 4.6 31.1 1.0
NE2 C:HIS752 4.7 33.5 1.0
CG2 C:VAL760 4.7 28.5 1.0
O C:ASP950 4.8 34.9 1.0
CA C:ASP950 4.9 32.3 1.0
O C:HOH1278 5.0 33.0 1.0

Manganese binding site 4 out of 4 in 7kwe

Go back to Manganese Binding Sites List in 7kwe
Manganese 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 Manganese with other atoms in the Mn 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:Mn1102

b:37.6
occ:1.00
 OD2 B:ASP837 2.0 33.6 1.0
OD1 B:ASP950 2.1 34.7 1.0
NE2 B:HIS836 2.2 33.6 1.0
NE2 B:HIS756 2.3 31.2 1.0
O B:HOH1222 2.5 39.5 1.0
O B:HOH1264 2.6 46.8 1.0
CD2 B:HIS836 2.9 31.7 1.0
CG B:ASP950 3.0 35.3 1.0
CG B:ASP837 3.1 32.9 1.0
CD2 B:HIS756 3.1 33.7 1.0
CE1 B:HIS836 3.2 35.2 1.0
OD2 B:ASP950 3.3 38.3 1.0
CE1 B:HIS756 3.3 34.1 1.0
OD1 B:ASP837 3.7 31.2 1.0
MG B:MG1103 3.8 29.6 1.0
O B:HOH1258 4.0 34.6 1.0
CG B:HIS836 4.1 32.1 1.0
ND1 B:HIS836 4.2 33.3 1.0
CB B:ASP837 4.2 31.2 1.0
CD2 B:HIS752 4.3 32.3 1.0
CG B:HIS756 4.3 32.2 1.0
CB B:ASP950 4.4 33.8 1.0
ND1 B:HIS756 4.4 33.8 1.0
O B:HOH1239 4.6 30.8 1.0
CG2 B:VAL760 4.7 31.8 1.0
O B:ASP950 4.7 34.7 1.0
NE2 B:HIS752 4.8 32.0 1.0
CA B:ASP950 4.8 31.8 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: Mon Jul 12 15:24:05 2021

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