Atomistry » Magnesium » PDB 6fjm-6ftm » 6fta
Atomistry »
  Magnesium »
    PDB 6fjm-6ftm »
      6fta »

Magnesium in PDB 6fta: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098, PDB code: 6fta 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) 80.67 / 2.34
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.990, 110.760, 161.340, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 24

Other elements in 6fta:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098 also contains other interesting chemical elements:

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-3098 (pdb code 6fta). 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-3098, PDB code: 6fta:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6fta

Go back to Magnesium Binding Sites List in 6fta
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098


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-3098 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:29.2
occ:1.00
 O A:HOH629 1.8 37.0 1.0
O A:HOH659 1.8 43.4 1.0
O A:HOH624 1.9 27.7 1.0
OD1 A:ASP201 2.0 37.4 1.0
O A:HOH605 2.1 30.0 1.0
O A:HOH627 2.1 34.1 1.0
CG A:ASP201 3.0 39.8 1.0
OD2 A:ASP201 3.3 42.3 1.0
ZN A:ZN501 3.7 43.8 1.0
O A:HOH654 3.9 41.6 1.0
OG1 A:THR271 4.0 35.6 1.0
O A:HIS200 4.0 33.7 1.0
O A:HOH631 4.1 44.6 1.0
CD2 A:HIS200 4.1 39.7 1.0
OE2 A:GLU230 4.2 42.5 1.0
NE2 A:HIS233 4.3 34.6 1.0
C27 A:E6N510 4.4 63.3 1.0
CB A:ASP201 4.4 36.2 1.0
OD2 A:ASP318 4.5 46.1 1.0
CD2 A:HIS233 4.5 35.9 1.0
NE2 A:HIS200 4.5 41.5 1.0
CD2 A:HIS204 4.6 38.0 1.0
O A:THR271 4.6 45.8 1.0
CD2 A:HIS160 4.6 44.5 1.0
CB A:THR271 4.6 38.8 1.0
NE2 A:HIS160 4.7 41.8 1.0
CA A:ASP201 4.8 36.5 1.0
O A:HOH621 4.8 50.8 1.0
C26 A:E6N510 4.8 71.2 1.0
NE2 A:HIS204 4.8 41.0 1.0
CG A:GLU230 4.9 40.2 1.0
C A:HIS200 4.9 36.6 1.0

Magnesium binding site 2 out of 4 in 6fta

Go back to Magnesium Binding Sites List in 6fta
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098


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-3098 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:28.4
occ:1.00
 O B:HOH652 1.9 31.6 1.0
O B:HOH664 1.9 32.0 1.0
OD1 B:ASP201 1.9 37.6 1.0
O B:HOH615 2.0 30.4 1.0
O B:HOH627 2.1 33.7 1.0
O B:HOH650 2.2 33.6 1.0
CG B:ASP201 2.9 40.5 1.0
OD2 B:ASP201 3.2 46.1 1.0
ZN B:ZN501 3.8 44.1 1.0
OE2 B:GLU230 3.9 41.2 1.0
O B:HOH680 3.9 39.4 1.0
O B:HIS200 4.0 33.6 1.0
O B:HOH660 4.1 36.5 1.0
CD2 B:HIS200 4.1 34.0 1.0
OG1 B:THR271 4.1 39.2 1.0
C27 B:E6N508 4.3 56.2 1.0
CB B:ASP201 4.3 38.2 1.0
NE2 B:HIS233 4.4 31.4 1.0
O B:THR271 4.5 40.1 1.0
CD2 B:HIS233 4.5 33.5 1.0
NE2 B:HIS200 4.6 32.8 1.0
C26 B:E6N508 4.6 60.6 1.0
OD2 B:ASP318 4.6 37.6 1.0
CD2 B:HIS204 4.6 35.8 1.0
O B:HOH623 4.7 58.4 1.0
CB B:THR271 4.7 43.2 1.0
CA B:ASP201 4.8 34.5 1.0
CD2 B:HIS160 4.8 43.9 1.0
CD B:GLU230 4.8 43.2 1.0
NE2 B:HIS204 4.8 37.4 1.0
NE2 B:HIS160 4.9 39.4 1.0
CG B:GLU230 4.9 42.1 1.0
C B:HIS200 5.0 32.8 1.0

Magnesium binding site 3 out of 4 in 6fta

Go back to Magnesium Binding Sites List in 6fta
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098


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-3098 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:23.9
occ:1.00
 O C:HOH621 1.9 27.2 1.0
OD1 C:ASP201 1.9 32.7 1.0
O C:HOH609 1.9 31.0 1.0
O C:HOH641 2.0 26.6 1.0
O C:HOH648 2.0 25.3 1.0
O C:HOH635 2.1 34.6 1.0
CG C:ASP201 3.0 36.9 1.0
OD2 C:ASP201 3.3 43.1 1.0
ZN C:ZN501 3.8 42.8 1.0
O C:HIS200 3.8 35.5 1.0
OG1 C:THR271 3.9 40.2 1.0
OE2 C:GLU230 4.0 43.1 1.0
O C:HOH661 4.0 35.8 1.0
CD2 C:HIS200 4.1 34.4 1.0
NE2 C:HIS233 4.2 32.1 1.0
CD2 C:HIS233 4.3 31.7 1.0
CB C:ASP201 4.3 35.5 1.0
OD2 C:ASP318 4.4 39.1 1.0
O C:HOH674 4.5 35.0 1.0
C27 C:E6N506 4.5 58.2 1.0
CB C:THR271 4.5 36.3 1.0
O C:THR271 4.5 39.6 1.0
NE2 C:HIS200 4.6 34.2 1.0
CA C:ASP201 4.7 33.9 1.0
CD2 C:HIS204 4.7 30.3 1.0
C C:HIS200 4.7 37.7 1.0
O C:HOH617 4.8 43.4 1.0
CG C:GLU230 4.8 41.4 1.0
CD C:GLU230 4.9 45.5 1.0
CD2 C:HIS160 4.9 45.9 1.0
C26 C:E6N506 4.9 57.6 1.0
NE2 C:HIS160 5.0 38.5 1.0

Magnesium binding site 4 out of 4 in 6fta

Go back to Magnesium Binding Sites List in 6fta
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098


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-3098 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:22.0
occ:1.00
 O D:HOH606 2.0 24.7 1.0
O D:HOH628 2.0 31.6 1.0
O D:HOH699 2.0 30.6 1.0
OD1 D:ASP201 2.0 32.4 1.0
O D:HOH621 2.1 26.4 1.0
O D:HOH648 2.1 29.9 1.0
CG D:ASP201 3.1 34.8 1.0
OD2 D:ASP201 3.4 35.0 1.0
ZN D:ZN502 3.7 38.6 1.0
O D:HOH669 4.0 35.0 1.0
OG1 D:THR271 4.0 27.2 1.0
OE2 D:GLU230 4.0 35.4 1.0
CD2 D:HIS200 4.1 29.9 1.0
O D:HIS200 4.1 32.6 1.0
C27 D:E6N514 4.3 60.5 1.0
NE2 D:HIS233 4.3 27.5 1.0
O D:HOH689 4.4 37.4 1.0
CB D:ASP201 4.4 35.0 1.0
O D:THR271 4.5 40.1 1.0
CD2 D:HIS233 4.5 31.8 1.0
NE2 D:HIS200 4.5 31.8 1.0
OD2 D:ASP318 4.5 40.6 1.0
CD2 D:HIS204 4.6 36.6 1.0
CB D:THR271 4.7 35.5 1.0
C26 D:E6N514 4.7 64.7 1.0
NE2 D:HIS204 4.8 36.1 1.0
O D:HOH653 4.8 48.9 1.0
CG D:GLU230 4.8 37.1 1.0
CA D:ASP201 4.8 34.9 1.0
CD2 D:HIS160 4.9 44.1 1.0
NE2 D:HIS160 4.9 40.0 1.0
CD D:GLU230 4.9 41.5 1.0
C D:HIS200 5.0 35.0 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-3098 To Be Published.
Page generated: Tue Oct 1 00:38:23 2024

Last articles

Ca in 5TFK
Ca in 5TG3
Ca in 5TGQ
Ca in 5TGF
Ca in 5TFM
Ca in 5TEA
Ca in 5TFL
Ca in 5TD4
Ca in 5TF9
Ca in 5TAK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy