Magnesium in PDB 6boj: Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004, PDB code: 6boj was solved by D.Fox Iii, J.W.Fairman, M.E.Gurney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.50 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.780, 81.890, 116.790, 90.00, 110.41, 90.00
R / Rfree (%) 16.1 / 18.6

Other elements in 6boj:

The structure of Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms
Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 (pdb code 6boj). 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 the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004, PDB code: 6boj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6boj

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Magnesium binding site 1 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004


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 PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:10.3
occ:1.00
 O A:HOH881 2.0 10.9 1.0
OD1 A:ASP367 2.1 9.8 1.0
O A:HOH1022 2.2 13.2 1.0
O A:HOH938 2.2 11.4 1.0
O A:HOH818 2.2 12.0 1.0
O A:HOH899 2.2 14.1 1.0
CG A:ASP367 3.1 9.2 1.0
OD2 A:ASP367 3.5 9.4 1.0
ZN A:ZN701 3.9 11.6 1.0
OE2 A:GLU396 4.1 13.1 1.0
O A:HIS366 4.1 9.3 1.0
NE2 A:HIS399 4.1 8.5 1.0
CD2 A:HIS366 4.1 9.0 1.0
O A:HOH963 4.1 14.5 1.0
O A:HOH923 4.3 16.3 1.0
OG1 A:THR437 4.3 11.6 1.0
CD2 A:HIS399 4.3 8.0 1.0
CB A:ASP367 4.4 9.2 1.0
O A:THR437 4.5 12.3 1.0
OD2 A:ASP484 4.5 12.9 1.0
CD2 A:HIS370 4.6 10.9 1.0
NE2 A:HIS366 4.6 8.7 1.0
NE2 A:HIS326 4.7 11.2 1.0
CA A:ASP367 4.8 9.4 1.0
CD2 A:HIS326 4.8 11.2 1.0
CG A:GLU396 4.8 10.3 1.0
NE2 A:HIS370 4.9 11.0 1.0
CB A:THR437 4.9 10.9 1.0
CD A:GLU396 4.9 11.9 1.0
C A:HIS366 4.9 9.1 1.0

Magnesium binding site 2 out of 4 in 6boj

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Magnesium binding site 2 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004


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 PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:10.1
occ:1.00
 O B:HOH1063 2.0 14.1 1.0
OD1 B:ASP367 2.1 12.8 1.0
O B:HOH1148 2.1 16.1 1.0
O B:HOH1193 2.1 18.8 1.0
O B:HOH1031 2.1 15.0 1.0
O B:HOH1121 2.2 11.8 1.0
CG B:ASP367 3.1 11.8 1.0
OD2 B:ASP367 3.5 12.1 1.0
ZN B:ZN701 3.9 13.9 1.0
O B:HIS366 4.1 10.3 1.0
CD2 B:HIS366 4.1 11.9 1.0
NE2 B:HIS399 4.1 10.6 1.0
OE2 B:GLU396 4.1 13.2 1.0
O B:HOH1131 4.1 19.5 1.0
O B:HOH1117 4.3 16.7 1.0
OG1 B:THR437 4.3 14.0 1.0
CD2 B:HIS399 4.4 9.5 1.0
O B:THR437 4.5 14.4 1.0
CB B:ASP367 4.5 11.2 1.0
OD2 B:ASP484 4.5 15.0 1.0
NE2 B:HIS366 4.6 12.5 1.0
CD2 B:HIS370 4.7 12.1 1.0
NE2 B:HIS326 4.7 14.2 1.0
CD2 B:HIS326 4.8 13.1 1.0
CG B:GLU396 4.8 11.4 1.0
CA B:ASP367 4.8 10.2 1.0
CB B:THR437 4.9 14.5 1.0
CD B:GLU396 4.9 12.3 1.0
C B:HIS366 4.9 9.9 1.0
NE2 B:HIS370 5.0 11.4 1.0

Magnesium binding site 3 out of 4 in 6boj

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Magnesium binding site 3 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004


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 the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:10.3
occ:1.00
 OD1 C:ASP367 2.0 10.3 1.0
O C:HOH868 2.1 11.6 1.0
O C:HOH1034 2.1 15.3 1.0
O C:HOH954 2.2 10.2 1.0
O C:HOH840 2.2 13.1 1.0
O C:HOH900 2.2 16.8 1.0
CG C:ASP367 3.1 9.5 1.0
OD2 C:ASP367 3.5 9.2 1.0
ZN C:ZN701 3.9 11.9 1.0
O C:HIS366 4.1 9.6 1.0
CD2 C:HIS366 4.1 10.6 1.0
OE2 C:GLU396 4.1 14.5 1.0
NE2 C:HIS399 4.1 9.0 1.0
O C:HOH974 4.1 16.8 1.0
O C:HOH933 4.3 15.1 1.0
OG1 C:THR437 4.4 11.8 1.0
CD2 C:HIS399 4.4 8.6 1.0
CB C:ASP367 4.4 9.3 1.0
O C:THR437 4.5 12.4 1.0
OD2 C:ASP484 4.5 13.0 1.0
NE2 C:HIS366 4.6 10.9 1.0
CD2 C:HIS370 4.6 10.1 1.0
O C:HOH804 4.6 34.5 1.0
NE2 C:HIS326 4.7 11.0 1.0
CD2 C:HIS326 4.7 10.8 1.0
CA C:ASP367 4.8 9.0 1.0
CG C:GLU396 4.8 10.9 1.0
NE2 C:HIS370 4.9 10.2 1.0
C C:HIS366 4.9 9.1 1.0
CB C:THR437 4.9 11.9 1.0
CD C:GLU396 4.9 11.7 1.0

Magnesium binding site 4 out of 4 in 6boj

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Magnesium binding site 4 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004


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 the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:11.6
occ:1.00
 OD1 D:ASP367 2.0 13.0 1.0
O D:HOH864 2.1 14.3 1.0
O D:HOH829 2.1 16.3 1.0
O D:HOH944 2.1 14.0 1.0
O D:HOH967 2.2 16.5 1.0
O D:HOH889 2.2 16.1 1.0
CG D:ASP367 3.1 12.1 1.0
OD2 D:ASP367 3.5 12.2 1.0
ZN D:ZN701 3.9 14.2 1.0
NE2 D:HIS399 4.1 10.7 1.0
O D:HOH937 4.1 19.7 1.0
OE2 D:GLU396 4.1 15.9 1.0
O D:HIS366 4.1 12.8 1.0
CD2 D:HIS366 4.2 11.8 1.0
O D:HOH901 4.3 18.1 1.0
CD2 D:HIS399 4.3 10.0 1.0
OG1 D:THR437 4.4 13.2 1.0
CB D:ASP367 4.4 11.3 1.0
OD2 D:ASP484 4.5 14.0 1.0
O D:THR437 4.5 14.1 1.0
CD2 D:HIS370 4.5 12.3 1.0
NE2 D:HIS366 4.6 11.6 1.0
NE2 D:HIS326 4.8 14.5 1.0
CD2 D:HIS326 4.8 14.1 1.0
CA D:ASP367 4.8 11.9 1.0
CG D:GLU396 4.8 13.2 1.0
NE2 D:HIS370 4.8 13.1 1.0
CB D:THR437 4.9 14.3 1.0
C D:HIS366 4.9 11.4 1.0
CD D:GLU396 4.9 15.0 1.0

Reference:

C.Zhang, Y.Xu, A.Chowdhary, D.Fox 3Rd., M.E.Gurney, H.T.Zhang, B.D.Auerbach, R.J.Salvi, M.Yang, G.Li, J.M.O'donnell. Memory Enhancing Effects of BPN14770, An Allosteric Inhibitor of Phosphodiesterase-4D, in Wild-Type and Humanized Mice. Neuropsychopharmacology V. 43 2299 2018.
ISSN: ISSN 1740-634X
PubMed: 30131563
DOI: 10.1038/S41386-018-0178-6
Page generated: Mon Dec 14 22:24:33 2020

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