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Magnesium in PDB 3dys: Human Phosphodiestrase-5'Gmp Complex (Ep), Produced By Soaking with 20MM Cgmp+20 Mm MNCL2+20 Mm MGCL2 For 2 Hours, and Flash-Cooled to Liquid Nitrogen Temperature When Substrate Was Still Abudant.

Enzymatic activity of Human Phosphodiestrase-5'Gmp Complex (Ep), Produced By Soaking with 20MM Cgmp+20 Mm MNCL2+20 Mm MGCL2 For 2 Hours, and Flash-Cooled to Liquid Nitrogen Temperature When Substrate Was Still Abudant.

All present enzymatic activity of Human Phosphodiestrase-5'Gmp Complex (Ep), Produced By Soaking with 20MM Cgmp+20 Mm MNCL2+20 Mm MGCL2 For 2 Hours, and Flash-Cooled to Liquid Nitrogen Temperature When Substrate Was Still Abudant.:
3.1.4.35;

Protein crystallography data

The structure of Human Phosphodiestrase-5'Gmp Complex (Ep), Produced By Soaking with 20MM Cgmp+20 Mm MNCL2+20 Mm MGCL2 For 2 Hours, and Flash-Cooled to Liquid Nitrogen Temperature When Substrate Was Still Abudant., PDB code: 3dys was solved by S.Liu, M.N.Mansour, K.Dillman, J.Perez, D.Danley, F.Menniti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.992, 103.992, 269.762, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.2

Other elements in 3dys:

The structure of Human Phosphodiestrase-5'Gmp Complex (Ep), Produced By Soaking with 20MM Cgmp+20 Mm MNCL2+20 Mm MGCL2 For 2 Hours, and Flash-Cooled to Liquid Nitrogen Temperature When Substrate Was Still Abudant. also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Phosphodiestrase-5'Gmp Complex (Ep), Produced By Soaking with 20MM Cgmp+20 Mm MNCL2+20 Mm MGCL2 For 2 Hours, and Flash-Cooled to Liquid Nitrogen Temperature When Substrate Was Still Abudant. (pdb code 3dys). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Phosphodiestrase-5'Gmp Complex (Ep), Produced By Soaking with 20MM Cgmp+20 Mm MNCL2+20 Mm MGCL2 For 2 Hours, and Flash-Cooled to Liquid Nitrogen Temperature When Substrate Was Still Abudant., PDB code: 3dys:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3dys

Go back to Magnesium Binding Sites List in 3dys
Magnesium binding site 1 out of 2 in the Human Phosphodiestrase-5'Gmp Complex (Ep), Produced By Soaking with 20MM Cgmp+20 Mm MNCL2+20 Mm MGCL2 For 2 Hours, and Flash-Cooled to Liquid Nitrogen Temperature When Substrate Was Still Abudant.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Phosphodiestrase-5'Gmp Complex (Ep), Produced By Soaking with 20MM Cgmp+20 Mm MNCL2+20 Mm MGCL2 For 2 Hours, and Flash-Cooled to Liquid Nitrogen Temperature When Substrate Was Still Abudant. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:33.5
occ:1.00
 O A:HOH1132 2.0 24.4 1.0
OD1 A:ASP293 2.1 36.5 1.0
O A:HOH1133 2.2 25.7 1.0
O A:HOH1131 2.2 27.2 1.0
O2P A:5GP900 2.3 40.0 1.0
O1P A:5GP900 2.3 39.8 1.0
P A:5GP900 2.7 44.6 1.0
CG A:ASP293 3.2 37.5 1.0
OD2 A:ASP293 3.6 37.4 1.0
O5' A:5GP900 3.6 42.9 1.0
OE2 A:GLU322 3.8 41.5 1.0
O A:HOH917 3.9 27.5 1.0
NE2 A:HIS325 3.9 37.5 1.0
O3P A:5GP900 4.0 40.4 1.0
MN A:MN901 4.1 36.3 1.0
O A:HIS292 4.2 38.0 1.0
CD2 A:HIS325 4.2 36.4 1.0
CD2 A:HIS292 4.3 35.8 1.0
OG1 A:THR363 4.3 39.6 1.0
CD2 A:HIS296 4.3 36.5 1.0
CB A:ASP293 4.5 37.7 1.0
OD2 A:ASP402 4.6 41.2 1.0
NE2 A:HIS296 4.6 36.4 1.0
O A:HOH956 4.6 31.1 1.0
CD A:GLU322 4.7 39.5 1.0
CG A:GLU322 4.8 37.4 1.0
CA A:ASP293 4.8 37.5 1.0
O A:THR363 4.8 38.9 1.0
NE2 A:HIS292 4.8 36.3 1.0
CB A:THR363 4.8 39.1 1.0
CD2 A:HIS252 4.9 39.0 1.0
NE2 A:HIS252 5.0 39.0 1.0

Magnesium binding site 2 out of 2 in 3dys

Go back to Magnesium Binding Sites List in 3dys
Magnesium binding site 2 out of 2 in the Human Phosphodiestrase-5'Gmp Complex (Ep), Produced By Soaking with 20MM Cgmp+20 Mm MNCL2+20 Mm MGCL2 For 2 Hours, and Flash-Cooled to Liquid Nitrogen Temperature When Substrate Was Still Abudant.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Phosphodiestrase-5'Gmp Complex (Ep), Produced By Soaking with 20MM Cgmp+20 Mm MNCL2+20 Mm MGCL2 For 2 Hours, and Flash-Cooled to Liquid Nitrogen Temperature When Substrate Was Still Abudant. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:32.1
occ:1.00
 OD1 B:ASP293 2.0 38.9 1.0
O B:HOH1188 2.1 26.4 1.0
O B:HOH1187 2.1 23.1 1.0
O B:HOH1189 2.1 23.3 1.0
O B:HOH1185 2.1 29.5 1.0
O B:HOH1186 2.2 29.4 1.0
CG B:ASP293 3.1 39.2 1.0
OD2 B:ASP293 3.4 40.3 1.0
OE2 B:GLU322 3.9 39.5 1.0
NE2 B:HIS325 3.9 36.4 1.0
MN B:MN901 4.0 37.4 1.0
O1 B:FMT1 4.1 46.6 1.0
O B:HOH1058 4.1 46.5 1.0
CD2 B:HIS325 4.1 36.9 1.0
O B:HOH978 4.1 29.2 1.0
CD2 B:HIS292 4.2 38.2 1.0
O B:HIS292 4.2 39.4 1.0
OG1 B:THR363 4.3 37.7 1.0
O B:HOH1115 4.3 43.0 1.0
CD2 B:HIS296 4.4 36.7 1.0
CB B:ASP293 4.4 38.1 1.0
OD2 B:ASP402 4.5 42.9 1.0
NE2 B:HIS292 4.7 38.0 1.0
CA B:ASP293 4.7 38.8 1.0
NE2 B:HIS296 4.7 36.9 1.0
CD B:GLU322 4.8 40.4 1.0
O B:THR363 4.8 38.2 1.0
CG B:GLU322 4.8 38.8 1.0
CD2 B:HIS252 4.9 40.1 1.0
CB B:THR363 4.9 38.6 1.0
O B:HOH1022 4.9 35.8 1.0
C B:HIS292 5.0 39.0 1.0
CE1 B:HIS325 5.0 37.4 1.0

Reference:

S.Liu, M.N.Mansour, K.S.Dillman, J.R.Perez, D.E.Danley, P.A.Aeed, S.P.Simons, P.K.Lemotte, F.S.Menniti. Structural Basis For the Catalytic Mechanism of Human Phosphodiesterase 9. Proc.Natl.Acad.Sci.Usa V. 105 13309 2008.
ISSN: ISSN 0027-8424
PubMed: 18757755
DOI: 10.1073/PNAS.0708850105
Page generated: Mon Dec 14 08:05:24 2020

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