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Magnesium in PDB 4htx: Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550

Enzymatic activity of Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550

All present enzymatic activity of Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550, PDB code: 4htx was solved by J.Zhu, Q.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.16 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.260, 73.820, 92.470, 109.59, 91.93, 90.88
R / Rfree (%) 17.3 / 22.7

Other elements in 4htx:

The structure of Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550 (pdb code 4htx). 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 PDE2 Catalytic Domain in Complex with BAY60-7550, PDB code: 4htx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4htx

Go back to Magnesium Binding Sites List in 4htx
Magnesium binding site 1 out of 4 in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550


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 PDE2 Catalytic Domain in Complex with BAY60-7550 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:14.2
occ:1.00
 O A:HOH1261 2.1 13.3 1.0
OD1 A:ASP697 2.1 9.7 1.0
O A:HOH1101 2.1 11.3 1.0
O A:HOH1102 2.1 13.9 1.0
O A:HOH1297 2.2 15.6 1.0
O A:HOH1103 2.3 13.8 1.0
CG A:ASP697 3.1 11.4 1.0
OD2 A:ASP697 3.5 13.0 1.0
ZN A:ZN1001 3.8 18.2 1.0
NE2 A:HIS730 4.0 9.7 1.0
OG1 A:THR768 4.1 14.1 1.0
O A:HOH1299 4.1 35.3 1.0
O A:HOH1284 4.1 36.1 1.0
CD2 A:HIS696 4.2 9.4 1.0
O A:HOH1117 4.2 15.8 1.0
OE2 A:GLU727 4.2 22.6 1.0
CD2 A:HIS730 4.2 9.4 1.0
O A:HIS696 4.2 12.0 1.0
O A:HOH1109 4.4 18.8 1.0
CB A:ASP697 4.5 9.6 1.0
CB A:THR768 4.5 12.4 1.0
NE2 A:HIS696 4.6 12.0 1.0
OD2 A:ASP808 4.6 23.1 1.0
CD2 A:HIS700 4.6 16.0 1.0
O A:HOH1210 4.7 40.9 1.0
CA A:ASP697 4.8 9.3 1.0
NE2 A:HIS656 4.8 16.3 1.0
O A:THR768 4.8 23.4 1.0
CD2 A:HIS656 4.9 14.2 1.0
NE2 A:HIS700 5.0 16.5 1.0
CG A:GLU727 5.0 12.3 1.0

Magnesium binding site 2 out of 4 in 4htx

Go back to Magnesium Binding Sites List in 4htx
Magnesium binding site 2 out of 4 in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550


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 PDE2 Catalytic Domain in Complex with BAY60-7550 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:13.5
occ:1.00
 O B:HOH1103 2.1 14.4 1.0
OD1 B:ASP697 2.1 11.4 1.0
O B:HOH1219 2.2 12.3 1.0
O B:HOH1101 2.2 12.6 1.0
O B:HOH1102 2.2 15.5 1.0
O B:HOH1104 2.2 13.5 1.0
CG B:ASP697 3.0 13.6 1.0
OD2 B:ASP697 3.3 15.0 1.0
ZN B:ZN1001 3.8 19.3 1.0
OG1 B:THR768 4.0 12.5 1.0
O B:HOH1137 4.1 39.1 1.0
O B:HOH1281 4.1 36.3 1.0
NE2 B:HIS730 4.1 11.2 1.0
CD2 B:HIS696 4.2 10.4 1.0
O B:HIS696 4.2 10.1 1.0
OE2 B:GLU727 4.2 26.5 1.0
CD2 B:HIS730 4.3 12.1 1.0
O B:HOH1133 4.4 19.6 1.0
CB B:ASP697 4.4 10.4 1.0
O B:HOH1105 4.4 18.3 1.0
CB B:THR768 4.5 16.2 1.0
NE2 B:HIS696 4.6 14.5 1.0
OD2 B:ASP808 4.6 31.9 1.0
CD2 B:HIS700 4.6 12.1 1.0
CA B:ASP697 4.7 11.6 1.0
NE2 B:HIS656 4.8 21.8 1.0
CG B:GLU727 4.9 19.6 1.0
CD2 B:HIS656 4.9 20.5 1.0
O B:THR768 4.9 24.7 1.0
NE2 B:HIS700 4.9 16.2 1.0
C B:HIS696 5.0 12.8 1.0
CD B:GLU727 5.0 24.8 1.0

Magnesium binding site 3 out of 4 in 4htx

Go back to Magnesium Binding Sites List in 4htx
Magnesium binding site 3 out of 4 in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550


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 PDE2 Catalytic Domain in Complex with BAY60-7550 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:16.0
occ:1.00
 O C:HOH1106 2.1 19.4 1.0
O C:HOH1105 2.1 21.8 1.0
OD1 C:ASP697 2.1 14.0 1.0
O C:HOH1103 2.1 11.7 1.0
O C:HOH1104 2.2 17.2 1.0
O C:HOH1122 2.2 16.5 1.0
CG C:ASP697 3.1 18.3 1.0
OD2 C:ASP697 3.4 19.3 1.0
ZN C:ZN1001 3.8 23.1 1.0
O C:HOH1154 4.0 39.3 1.0
NE2 C:HIS730 4.1 16.9 1.0
CD2 C:HIS696 4.2 14.9 1.0
OE2 C:GLU727 4.2 30.9 1.0
OG1 C:THR768 4.2 24.9 1.0
O C:HOH1120 4.2 20.8 1.0
O C:HOH1123 4.3 22.2 1.0
O C:HIS696 4.3 16.6 1.0
CD2 C:HIS730 4.4 17.2 1.0
CB C:ASP697 4.4 18.3 1.0
CD2 C:HIS700 4.5 16.6 1.0
OD2 C:ASP808 4.5 27.3 1.0
NE2 C:HIS696 4.6 15.1 1.0
CB C:THR768 4.6 23.8 1.0
NE2 C:HIS656 4.7 18.7 1.0
NE2 C:HIS700 4.7 17.2 1.0
CD2 C:HIS656 4.8 18.9 1.0
CA C:ASP697 4.8 18.6 1.0
O C:THR768 4.8 24.8 1.0
O C:HOH1165 5.0 41.1 1.0
CG C:GLU727 5.0 19.7 1.0
CD C:GLU727 5.0 27.4 1.0

Magnesium binding site 4 out of 4 in 4htx

Go back to Magnesium Binding Sites List in 4htx
Magnesium binding site 4 out of 4 in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550


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 PDE2 Catalytic Domain in Complex with BAY60-7550 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:15.3
occ:1.00
 O D:HOH1105 2.1 15.5 1.0
OD1 D:ASP697 2.1 16.6 1.0
O D:HOH1103 2.1 15.9 1.0
O D:HOH1238 2.1 18.9 1.0
O D:HOH1104 2.2 17.5 1.0
O D:HOH1237 2.2 15.4 1.0
CG D:ASP697 3.1 18.4 1.0
OD2 D:ASP697 3.4 17.4 1.0
ZN D:ZN1001 3.8 23.9 1.0
O D:HOH1149 4.0 31.9 1.0
OG1 D:THR768 4.0 24.4 1.0
OE2 D:GLU727 4.1 24.8 1.0
NE2 D:HIS730 4.1 22.9 1.0
CD2 D:HIS696 4.2 16.0 1.0
O D:HOH1117 4.2 23.2 1.0
O D:HOH1106 4.2 26.3 1.0
O D:HIS696 4.3 19.2 1.0
CD2 D:HIS730 4.4 18.3 1.0
CB D:ASP697 4.4 20.2 1.0
OD2 D:ASP808 4.4 32.9 1.0
CD2 D:HIS700 4.5 19.1 1.0
CB D:THR768 4.5 23.9 1.0
NE2 D:HIS656 4.6 23.9 1.0
O D:HOH1209 4.6 35.8 1.0
O D:THR768 4.6 17.4 1.0
NE2 D:HIS700 4.6 23.5 1.0
NE2 D:HIS696 4.7 16.6 1.0
CD2 D:HIS656 4.7 20.5 1.0
CA D:ASP697 4.8 18.6 1.0
CD D:GLU727 4.9 23.7 1.0
CG D:GLU727 5.0 16.2 1.0

Reference:

J.Zhu, Q.Yang, D.Dai, Q.Huang. X-Ray Crystal Structure of Phosphodiesterase 2 in Complex with A Highly Selective, Nanomolar Inhibitor Reveals A Binding-Induced Pocket Important For Selectivity. J.Am.Chem.Soc. V. 135 11708 2013.
ISSN: ISSN 0002-7863
PubMed: 23899287
DOI: 10.1021/JA404449G
Page generated: Fri Aug 16 16:23:46 2024

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