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Magnesium in PDB 3g58: Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq, PDB code: 3g58 was solved by B.L.Staker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.21 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.385, 113.570, 161.129, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.3

Other elements in 3g58:

The structure of Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq 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 4D with D155988/Pmnpq (pdb code 3g58). 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 4D with D155988/Pmnpq, PDB code: 3g58:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3g58

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq


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 4D with D155988/Pmnpq within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg625

b:22.5
occ:1.00
 O A:HOH1105 2.1 35.9 1.0
OD1 A:ASP367 2.3 18.4 1.0
O A:HOH792 2.3 25.4 1.0
O A:HOH672 2.3 25.1 1.0
O A:HOH776 2.4 19.2 1.0
O A:HOH756 2.4 20.3 1.0
CG A:ASP367 3.3 16.9 1.0
OD2 A:ASP367 3.6 18.2 1.0
ZN A:ZN624 3.9 33.7 1.0
O A:HIS366 4.2 15.8 1.0
NE2 A:HIS399 4.2 15.8 1.0
O A:HOH729 4.3 29.3 1.0
OE2 A:GLU396 4.3 23.5 1.0
O A:HOH156 4.3 23.5 1.0
CD2 A:HIS366 4.4 16.4 1.0
CD2 A:HIS399 4.4 14.9 1.0
OG1 A:THR437 4.4 21.0 1.0
OD2 A:ASP484 4.6 23.0 1.0
CD2 A:HIS370 4.6 17.2 1.0
CB A:ASP367 4.6 16.2 1.0
CD2 A:HIS326 4.7 18.3 1.0
NE2 A:HIS326 4.7 17.5 1.0
O A:THR437 4.8 23.5 1.0
NE2 A:HIS370 4.9 16.1 1.0
NE2 A:HIS366 4.9 17.4 1.0
CB A:THR437 4.9 22.1 1.0
CA A:ASP367 4.9 15.6 1.0
CG A:GLU396 4.9 17.5 1.0

Magnesium binding site 2 out of 4 in 3g58

Go back to Magnesium Binding Sites List in 3g58
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq


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 4D with D155988/Pmnpq within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg625

b:22.7
occ:1.00
 O B:HOH760 2.1 29.5 1.0
O B:HOH639 2.2 18.2 1.0
O B:HOH728 2.3 23.1 1.0
OD1 B:ASP367 2.3 21.3 1.0
O B:HOH758 2.3 19.6 1.0
O B:HOH876 2.4 27.9 1.0
CG B:ASP367 3.3 20.2 1.0
OD2 B:ASP367 3.7 18.4 1.0
ZN B:ZN624 4.0 34.2 1.0
O B:HOH663 4.1 24.8 1.0
NE2 B:HIS399 4.1 14.2 1.0
O B:HIS366 4.2 19.5 1.0
OE2 B:GLU396 4.2 22.1 1.0
CD2 B:HIS366 4.4 19.5 1.0
O B:HOH659 4.4 40.0 1.0
OG1 B:THR437 4.4 22.8 1.0
CD2 B:HIS399 4.4 16.4 1.0
OD2 B:ASP484 4.5 21.3 1.0
O B:THR437 4.6 23.4 1.0
CD2 B:HIS370 4.6 16.3 1.0
CB B:ASP367 4.7 19.0 1.0
CD2 B:HIS326 4.8 21.2 1.0
CG B:GLU396 4.9 19.3 1.0
NE2 B:HIS366 4.9 20.8 1.0
NE2 B:HIS370 4.9 19.0 1.0
NE2 B:HIS326 4.9 21.4 1.0
CB B:THR437 4.9 23.1 1.0
O B:HOH828 5.0 38.1 1.0
CD B:GLU396 5.0 21.5 1.0
CA B:ASP367 5.0 19.5 1.0

Magnesium binding site 3 out of 4 in 3g58

Go back to Magnesium Binding Sites List in 3g58
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq


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 4D with D155988/Pmnpq within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg625

b:24.5
occ:1.00
 O C:HOH725 2.1 29.7 1.0
O C:HOH682 2.3 25.0 1.0
O C:HOH635 2.3 17.3 1.0
OD1 C:ASP367 2.4 18.4 1.0
O C:HOH733 2.4 17.5 1.0
O C:HOH1089 2.4 26.9 1.0
CG C:ASP367 3.3 17.4 1.0
OD2 C:ASP367 3.6 16.9 1.0
ZN C:ZN624 4.0 32.9 1.0
O C:HOH230 4.2 35.0 1.0
O C:HOH32 4.2 22.9 1.0
O C:HIS366 4.3 15.9 1.0
OE2 C:GLU396 4.3 24.3 1.0
NE2 C:HIS399 4.3 15.8 1.0
CD2 C:HIS366 4.4 16.5 1.0
OG1 C:THR437 4.5 20.8 1.0
OD2 C:ASP484 4.5 21.6 1.0
CD2 C:HIS399 4.5 14.9 1.0
O C:THR437 4.6 22.6 1.0
CD2 C:HIS370 4.7 16.1 1.0
CB C:ASP367 4.7 16.2 1.0
CD2 C:HIS326 4.7 18.3 1.0
NE2 C:HIS326 4.8 16.6 1.0
NE2 C:HIS366 4.9 18.4 1.0
O C:HOH779 4.9 53.4 1.0
NE2 C:HIS370 4.9 17.5 1.0
CB C:THR437 5.0 23.7 1.0
CG C:GLU396 5.0 17.7 1.0

Magnesium binding site 4 out of 4 in 3g58

Go back to Magnesium Binding Sites List in 3g58
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq


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 4D with D155988/Pmnpq within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg625

b:22.1
occ:1.00
 O D:HOH1023 2.0 21.5 1.0
OD1 D:ASP367 2.3 18.4 1.0
O D:HOH722 2.3 21.1 1.0
O D:HOH724 2.4 26.5 1.0
O D:HOH630 2.4 21.9 1.0
O D:HOH852 2.5 21.0 1.0
CG D:ASP367 3.3 17.6 1.0
OD2 D:ASP367 3.6 16.5 1.0
ZN D:ZN624 4.0 32.2 1.0
O D:HIS366 4.2 15.1 1.0
NE2 D:HIS399 4.2 12.7 1.0
OE2 D:GLU396 4.3 19.6 1.0
CD2 D:HIS366 4.3 15.9 1.0
O D:HOH122 4.3 26.1 1.0
O D:HOH733 4.4 35.4 1.0
OG1 D:THR437 4.5 20.6 1.0
CD2 D:HIS399 4.5 15.2 1.0
CD2 D:HIS370 4.6 18.9 1.0
OD2 D:ASP484 4.6 21.9 1.0
CB D:ASP367 4.6 15.3 1.0
CD2 D:HIS326 4.7 18.0 1.0
O D:THR437 4.7 23.8 1.0
NE2 D:HIS366 4.8 17.9 1.0
NE2 D:HIS326 4.8 17.2 1.0
NE2 D:HIS370 4.8 19.2 1.0
CA D:ASP367 4.9 15.4 1.0
CG D:GLU396 5.0 17.4 1.0
CB D:THR437 5.0 21.9 1.0

Reference:

A.B.Burgin, O.T.Magnusson, J.Singh, P.Witte, B.L.Staker, J.M.Bjornsson, M.Thorsteinsdottir, S.Hrafnsdottir, T.Hagen, A.S.Kiselyov, L.J.Stewart, M.E.Gurney. Design of Phosphodiesterase 4D (PDE4D) Allosteric Modulators For Enhancing Cognition with Improved Safety. Nat.Biotechnol. V. 28 63 2010.
ISSN: ISSN 1087-0156
PubMed: 20037581
DOI: 10.1038/NBT.1598
Page generated: Wed Aug 14 14:05:18 2024

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