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Magnesium in PDB 3k3h: Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691

Enzymatic activity of Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691

All present enzymatic activity of Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691, PDB code: 3k3h was solved by H.Wang, X.Luo, M.Ye, J.Hou, H.Robinson, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.272, 103.272, 271.098, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 24.5

Other elements in 3k3h:

The structure of Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691 also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Zinc (Zn) 2 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691 (pdb code 3k3h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691, PDB code: 3k3h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3k3h

Go back to Magnesium Binding Sites List in 3k3h
Magnesium binding site 1 out of 2 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691


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 PDE9A Catalytic Domain in Complex with (S)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:36.8
occ:1.00
OD1 A:ASP293 2.1 33.7 1.0
O A:HOH705 2.3 35.3 1.0
O A:HOH702 2.3 32.6 1.0
O A:HOH706 2.4 32.3 1.0
O A:HOH703 2.4 30.2 1.0
O A:HOH704 2.5 28.8 1.0
CG A:ASP293 3.1 29.7 1.0
OD2 A:ASP293 3.5 31.7 1.0
NE2 A:HIS325 3.8 35.3 1.0
OE2 A:GLU322 3.8 35.5 1.0
ZN A:ZN601 4.0 51.2 1.0
O A:HIS292 4.0 31.4 1.0
CD2 A:HIS325 4.1 33.9 1.0
CD2 A:HIS292 4.1 33.3 1.0
OG1 A:THR363 4.2 30.9 1.0
O A:HOH707 4.2 43.2 1.0
CD2 A:HIS296 4.2 41.9 1.0
CB A:ASP293 4.4 29.7 1.0
CD2 A:HIS252 4.5 38.0 1.0
NE2 A:HIS252 4.5 41.1 1.0
NE2 A:HIS296 4.5 40.6 1.0
NE2 A:HIS292 4.5 39.7 1.0
CA A:ASP293 4.7 31.8 1.0
CD A:GLU322 4.8 35.4 1.0
O A:HOH701 4.8 41.8 1.0
CE1 A:HIS325 4.8 33.6 1.0
OD2 A:ASP402 4.9 37.7 1.0
CB A:THR363 4.9 32.2 1.0
C A:HIS292 4.9 32.6 1.0
CG A:GLU322 4.9 35.2 1.0

Magnesium binding site 2 out of 2 in 3k3h

Go back to Magnesium Binding Sites List in 3k3h
Magnesium binding site 2 out of 2 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (S)- BAY73-6691


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 PDE9A Catalytic Domain in Complex with (S)- BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:38.3
occ:1.00
OD1 B:ASP293 2.1 43.8 1.0
O B:HOH715 2.3 28.8 1.0
O B:HOH716 2.3 33.6 1.0
O B:HOH712 2.4 40.5 1.0
O B:HOH713 2.5 40.5 1.0
O B:HOH714 2.6 38.9 1.0
CG B:ASP293 3.0 41.4 1.0
OD2 B:ASP293 3.2 46.5 1.0
ZN B:ZN601 3.7 55.8 1.0
NE2 B:HIS325 3.9 35.4 1.0
OE2 B:GLU322 4.0 32.0 1.0
CD2 B:HIS292 4.0 39.4 1.0
O B:HOH711 4.1 37.8 1.0
OG1 B:THR363 4.2 31.9 1.0
CD2 B:HIS325 4.2 35.3 1.0
O B:HIS292 4.3 36.8 1.0
CB B:ASP293 4.4 39.2 1.0
CD2 B:HIS296 4.4 42.4 1.0
NE2 B:HIS292 4.5 44.4 1.0
CD2 B:HIS252 4.5 38.6 1.0
OD2 B:ASP402 4.6 35.0 1.0
NE2 B:HIS252 4.7 37.9 1.0
CA B:ASP293 4.7 37.0 1.0
NE2 B:HIS296 4.8 42.3 1.0
CB B:THR363 4.9 34.5 1.0
CD B:GLU322 4.9 34.3 1.0
CE1 B:HIS325 5.0 33.0 1.0
C B:HIS292 5.0 37.1 1.0

Reference:

H.Wang, X.Luo, M.Ye, J.Hou, H.Robinson, H.Ke. Insight Into Binding of Phosphodiesterase-9A Selective Inhibitors By Crystal Structures and Mutagenesis J.Med.Chem. V. 53 1726 2010.
ISSN: ISSN 0022-2623
PubMed: 20121115
DOI: 10.1021/JM901519F
Page generated: Mon Dec 14 08:21:22 2020

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