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Magnesium in PDB 6ibf: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417, PDB code: 6ibf was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.11 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.476, 110.511, 160.298, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 26.2

Other elements in 6ibf:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417 also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417 (pdb code 6ibf). 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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417, PDB code: 6ibf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6ibf

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:23.9
occ:1.00
 O A:HOH646 1.7 34.4 1.0
O A:HOH611 1.9 33.0 1.0
O A:HOH606 2.1 29.8 1.0
O A:HOH665 2.1 26.4 1.0
O A:HOH608 2.2 27.1 1.0
OD1 A:ASP201 2.2 31.1 1.0
CG A:ASP201 3.2 27.4 1.0
OD2 A:ASP201 3.5 26.8 1.0
ZN A:ZN501 3.7 37.2 1.0
O A:HOH639 3.9 39.6 1.0
O A:HOH651 3.9 37.5 1.0
OG1 A:THR271 4.0 34.2 1.0
OE2 A:GLU230 4.0 33.5 1.0
CD2 A:HIS200 4.1 31.1 1.0
O A:HIS200 4.1 25.7 1.0
OD2 A:ASP318 4.3 34.7 1.0
C31 A:4I7513 4.3 54.3 1.0
NE2 A:HIS233 4.4 33.1 1.0
O A:THR271 4.5 40.0 1.0
CD2 A:HIS233 4.5 32.3 1.0
CB A:THR271 4.6 37.5 1.0
CB A:ASP201 4.6 28.4 1.0
NE2 A:HIS200 4.6 33.3 1.0
C30 A:4I7513 4.7 57.5 1.0
CG A:GLU230 4.7 28.7 1.0
O A:HOH618 4.8 47.5 1.0
CD2 A:HIS204 4.8 32.4 1.0
CD A:GLU230 4.8 32.1 1.0
CA A:ASP201 4.9 28.0 1.0
NE2 A:HIS160 4.9 39.4 1.0
CD2 A:HIS160 4.9 39.0 1.0
C A:HIS200 5.0 27.2 1.0

Magnesium binding site 2 out of 4 in 6ibf

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:21.6
occ:1.00
 O B:HOH653 2.0 22.8 1.0
OD1 B:ASP201 2.0 30.5 1.0
O B:HOH617 2.0 27.8 1.0
O B:HOH659 2.1 21.2 1.0
O B:HOH650 2.2 30.0 1.0
O B:HOH603 2.3 21.9 1.0
CG B:ASP201 3.1 32.4 1.0
OD2 B:ASP201 3.5 35.3 1.0
ZN B:ZN501 3.9 39.5 1.0
O B:HIS200 4.0 27.1 1.0
O B:HOH673 4.0 31.6 1.0
OE2 B:GLU230 4.1 32.5 1.0
CD2 B:HIS200 4.1 28.1 1.0
NE2 B:HIS233 4.1 26.0 1.0
OG1 B:THR271 4.2 37.7 1.0
CD2 B:HIS233 4.3 26.9 1.0
C31 B:4I7513 4.4 53.5 1.0
O B:HOH665 4.4 20.1 1.0
CB B:ASP201 4.4 32.2 1.0
OD2 B:ASP318 4.5 38.5 1.0
NE2 B:HIS200 4.5 27.3 1.0
CD2 B:HIS204 4.6 26.9 1.0
CA B:ASP201 4.7 30.0 1.0
CG B:GLU230 4.7 33.4 1.0
CB B:THR271 4.7 34.5 1.0
C30 B:4I7513 4.7 54.5 1.0
O B:THR271 4.7 34.8 1.0
NE2 B:HIS204 4.8 25.5 1.0
O B:HOH640 4.8 32.5 1.0
CD B:GLU230 4.8 35.2 1.0
C B:HIS200 4.8 27.4 1.0
CD2 B:HIS160 4.8 34.1 1.0
NE2 B:HIS160 4.9 33.8 1.0

Magnesium binding site 3 out of 4 in 6ibf

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Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:19.0
occ:1.00
 O C:HOH630 1.9 23.2 1.0
OD1 C:ASP201 2.0 25.9 1.0
O C:HOH678 2.0 19.7 1.0
O C:HOH615 2.0 31.4 1.0
O C:HOH629 2.0 16.5 1.0
O C:HOH627 2.2 29.5 1.0
CG C:ASP201 3.0 27.7 1.0
OD2 C:ASP201 3.4 32.2 1.0
ZN C:ZN501 3.7 36.8 1.0
O C:HIS200 4.0 30.4 1.0
O C:HOH638 4.0 25.0 1.0
OE2 C:GLU230 4.0 25.0 1.0
NE2 C:HIS233 4.1 21.1 1.0
OG1 C:THR271 4.1 31.1 1.0
CD2 C:HIS200 4.2 28.4 1.0
O C:HOH665 4.2 28.6 1.0
CD2 C:HIS233 4.3 21.4 1.0
CB C:ASP201 4.4 27.4 1.0
CD2 C:HIS204 4.5 26.0 1.0
OD2 C:ASP318 4.5 38.1 1.0
O C:THR271 4.5 29.2 1.0
C31 C:4I7508 4.5 50.7 1.0
NE2 C:HIS200 4.6 25.6 1.0
CD2 C:HIS160 4.7 29.0 1.0
O C:HOH612 4.7 29.1 1.0
CB C:THR271 4.7 31.1 1.0
CA C:ASP201 4.7 26.2 1.0
NE2 C:HIS204 4.8 22.3 1.0
CG C:GLU230 4.8 27.5 1.0
NE2 C:HIS160 4.9 27.5 1.0
CD C:GLU230 4.9 26.6 1.0
C C:HIS200 4.9 29.6 1.0
C30 C:4I7508 4.9 48.9 1.0

Magnesium binding site 4 out of 4 in 6ibf

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-417 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:16.4
occ:1.00
 O D:HOH673 2.0 24.7 1.0
O D:HOH656 2.0 28.1 1.0
O D:HOH641 2.1 18.7 1.0
O D:HOH608 2.1 19.0 1.0
O D:HOH640 2.1 30.2 1.0
OD1 D:ASP201 2.2 22.8 1.0
CG D:ASP201 3.3 23.0 1.0
OD2 D:ASP201 3.7 23.2 1.0
ZN D:ZN501 3.8 31.0 1.0
O D:HOH669 3.9 25.9 1.0
OE2 D:GLU230 3.9 28.5 1.0
O D:HOH685 4.1 34.3 1.0
OG1 D:THR271 4.2 23.6 1.0
NE2 D:HIS233 4.3 24.2 1.0
C31 D:4I7520 4.3 47.4 1.0
CD2 D:HIS200 4.4 19.0 1.0
OD2 D:ASP318 4.4 25.8 1.0
O D:HIS200 4.4 24.3 1.0
CD2 D:HIS204 4.4 29.0 1.0
CD2 D:HIS233 4.5 24.9 1.0
O D:THR271 4.5 26.5 1.0
C30 D:4I7520 4.6 47.2 1.0
CB D:ASP201 4.6 22.7 1.0
O D:HOH679 4.7 35.4 1.0
NE2 D:HIS204 4.7 28.5 1.0
NE2 D:HIS160 4.7 32.7 1.0
NE2 D:HIS200 4.7 19.4 1.0
CG D:GLU230 4.7 28.1 1.0
CD D:GLU230 4.8 29.6 1.0
CD2 D:HIS160 4.8 30.9 1.0
CA D:ASP201 4.9 23.2 1.0
CB D:THR271 4.9 24.6 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-417 To Be Published.
Page generated: Tue Oct 1 03:17:58 2024

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