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Magnesium in PDB 2fm5: Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299

Enzymatic activity of Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299

All present enzymatic activity of Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299, PDB code: 2fm5 was solved by Q.Huai, Y.Sun, H.Wang, D.Macdonald, R.Aspiotis, H.Robinson, Z.Huang, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.357, 112.812, 161.079, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 26

Other elements in 2fm5:

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299 also contains other interesting chemical elements:

Fluorine (F) 32 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299 (pdb code 2fm5). 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 PDE4D2 in Complex with Inhibitor L- 869299, PDB code: 2fm5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2fm5

Go back to Magnesium Binding Sites List in 2fm5
Magnesium binding site 1 out of 4 in the Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299


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 PDE4D2 in Complex with Inhibitor L- 869299 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:20.1
occ:1.00
OD1 A:ASP201 2.0 16.4 1.0
O A:HOH603 2.1 24.0 1.0
O A:HOH605 2.2 19.5 1.0
O A:HOH604 2.2 18.6 1.0
O A:HOH606 2.2 19.9 1.0
O A:HOH607 2.2 20.1 1.0
CG A:ASP201 3.1 15.8 1.0
OD2 A:ASP201 3.5 18.7 1.0
ZN A:ZN501 3.9 23.1 1.0
O A:HIS200 4.1 12.8 1.0
C23 A:M99601 4.1 34.1 1.0
NE2 A:HIS233 4.1 16.1 1.0
CD2 A:HIS200 4.1 19.1 1.0
O A:HOH614 4.1 31.3 1.0
OE2 A:GLU230 4.2 19.5 1.0
OG1 A:THR271 4.2 20.4 1.0
CD2 A:HIS233 4.2 16.1 1.0
O A:HOH602 4.3 22.3 1.0
CB A:ASP201 4.4 14.9 1.0
O A:HOH609 4.5 28.8 1.0
C21 A:M99601 4.6 33.7 1.0
NE2 A:HIS200 4.6 19.5 1.0
N2 A:M99601 4.6 34.8 1.0
CD2 A:HIS204 4.7 14.8 1.0
CA A:ASP201 4.7 14.1 1.0
CB A:THR271 4.7 21.9 1.0
OD2 A:ASP318 4.8 19.9 1.0
O4 A:M99601 4.8 35.7 1.0
CG A:GLU230 4.8 16.5 1.0
O A:THR271 4.9 22.8 1.0
C A:HIS200 4.9 13.5 1.0
CD A:GLU230 4.9 17.8 1.0
CD2 A:HIS160 4.9 15.2 1.0
NE2 A:HIS160 4.9 16.2 1.0

Magnesium binding site 2 out of 4 in 2fm5

Go back to Magnesium Binding Sites List in 2fm5
Magnesium binding site 2 out of 4 in the Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299


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 PDE4D2 in Complex with Inhibitor L- 869299 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:20.9
occ:1.00
OD1 B:ASP201 2.0 19.5 1.0
O B:HOH604 2.1 21.1 1.0
O B:HOH608 2.1 24.9 1.0
O B:HOH607 2.1 22.2 1.0
O B:HOH606 2.2 20.1 1.0
O B:HOH605 2.2 20.1 1.0
CG B:ASP201 3.0 18.7 1.0
OD2 B:ASP201 3.4 22.4 1.0
ZN B:ZN503 3.8 26.8 1.0
O B:HIS200 4.0 18.1 1.0
NE2 B:HIS233 4.0 17.9 1.0
O B:HOH603 4.0 25.7 1.0
CD2 B:HIS200 4.0 22.0 1.0
C23 B:M99602 4.2 42.6 1.0
CD2 B:HIS233 4.2 18.4 1.0
OE2 B:GLU230 4.3 19.0 1.0
OG1 B:THR271 4.4 28.0 1.0
CB B:ASP201 4.4 18.5 1.0
NE2 B:HIS200 4.4 23.1 1.0
O B:HOH615 4.5 33.5 1.0
C21 B:M99602 4.5 42.2 1.0
CD2 B:HIS204 4.6 15.2 1.0
CA B:ASP201 4.7 17.3 1.0
N2 B:M99602 4.8 43.0 1.0
CD2 B:HIS160 4.8 19.5 1.0
C B:HIS200 4.9 18.2 1.0
CB B:THR271 4.9 29.6 1.0
OD2 B:ASP318 4.9 25.7 1.0
NE2 B:HIS160 4.9 19.5 1.0
NE2 B:HIS204 4.9 16.4 1.0

Magnesium binding site 3 out of 4 in 2fm5

Go back to Magnesium Binding Sites List in 2fm5
Magnesium binding site 3 out of 4 in the Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299


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 PDE4D2 in Complex with Inhibitor L- 869299 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg506

b:22.2
occ:1.00
OD1 C:ASP201 2.0 19.1 1.0
O C:HOH605 2.1 22.7 1.0
O C:HOH606 2.2 23.3 1.0
O C:HOH608 2.2 21.5 1.0
O C:HOH607 2.2 22.1 1.0
O C:HOH609 2.2 25.2 1.0
CG C:ASP201 3.1 18.1 1.0
OD2 C:ASP201 3.4 20.6 1.0
ZN C:ZN505 3.9 25.8 1.0
CD2 C:HIS200 4.0 18.9 1.0
C23 C:M99603 4.0 45.3 1.0
NE2 C:HIS233 4.0 11.2 1.0
O C:HIS200 4.1 14.9 1.0
O C:HOH613 4.1 28.9 1.0
O C:HOH604 4.2 24.6 1.0
OE2 C:GLU230 4.3 19.1 1.0
CD2 C:HIS233 4.3 11.4 1.0
CB C:ASP201 4.4 17.4 1.0
OG1 C:THR271 4.4 24.1 1.0
NE2 C:HIS200 4.4 19.3 1.0
N2 C:M99603 4.5 45.8 1.0
O C:HOH611 4.6 40.0 1.0
O4 C:M99603 4.6 46.4 1.0
CD2 C:HIS204 4.6 15.6 1.0
C21 C:M99603 4.6 45.0 1.0
OD2 C:ASP318 4.7 26.9 1.0
CA C:ASP201 4.8 15.7 1.0
CB C:THR271 4.8 23.9 1.0
CD2 C:HIS160 4.8 17.3 1.0
NE2 C:HIS160 4.9 18.2 1.0
O C:THR271 4.9 24.4 1.0
NE2 C:HIS204 4.9 16.1 1.0
C C:HIS200 4.9 15.9 1.0

Magnesium binding site 4 out of 4 in 2fm5

Go back to Magnesium Binding Sites List in 2fm5
Magnesium binding site 4 out of 4 in the Crystal Structure of PDE4D2 in Complex with Inhibitor L- 869299


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 PDE4D2 in Complex with Inhibitor L- 869299 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg508

b:19.7
occ:1.00
OD1 D:ASP201 2.0 17.1 1.0
O D:HOH606 2.1 21.6 1.0
O D:HOH608 2.1 19.4 1.0
O D:HOH609 2.2 18.0 1.0
O D:HOH610 2.2 20.6 1.0
O D:HOH607 2.2 18.9 1.0
CG D:ASP201 3.1 16.3 1.0
OD2 D:ASP201 3.5 17.6 1.0
ZN D:ZN507 3.9 21.4 1.0
O D:HIS200 4.0 14.6 1.0
NE2 D:HIS233 4.0 14.2 1.0
CD2 D:HIS200 4.0 14.3 1.0
C23 D:M99604 4.1 35.2 1.0
CD2 D:HIS233 4.1 14.2 1.0
OG1 D:THR271 4.2 19.7 1.0
OE2 D:GLU230 4.2 17.0 1.0
O D:HOH639 4.2 22.8 1.0
O D:HOH605 4.4 19.0 1.0
CB D:ASP201 4.4 15.8 1.0
NE2 D:HIS200 4.4 15.4 1.0
O D:HOH612 4.5 37.3 1.0
C21 D:M99604 4.6 35.3 1.0
CA D:ASP201 4.7 14.1 1.0
CB D:THR271 4.7 20.6 1.0
CD2 D:HIS204 4.7 14.9 1.0
N2 D:M99604 4.7 35.9 1.0
O D:THR271 4.8 22.2 1.0
OD2 D:ASP318 4.8 20.2 1.0
C D:HIS200 4.8 13.7 1.0
CG D:GLU230 4.9 16.3 1.0
CD2 D:HIS160 4.9 17.3 1.0
O4 D:M99604 5.0 35.8 1.0
CD D:GLU230 5.0 15.9 1.0

Reference:

Q.Huai, Y.Sun, H.Wang, D.Macdonald, R.Aspiotis, H.Robinson, Z.Huang, H.Ke. Enantiomer Discrimination Illustrated By the High Resolution Crystal Structures of Type 4 Phosphodiesterase J.Med.Chem. V. 49 1867 2006.
ISSN: ISSN 0022-2623
PubMed: 16539372
DOI: 10.1021/JM051273D
Page generated: Mon Dec 14 07:23:11 2020

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