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Manganese 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:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3dys

Go back to Manganese Binding Sites List in 3dys
Manganese binding site 1 out of 4 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 Manganese with other atoms in the Mn 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:Mn901

b:36.3
occ:1.00
 OD2 A:ASP293 2.0 37.4 1.0
NE2 A:HIS256 2.1 38.0 1.0
NE2 A:HIS292 2.1 36.3 1.0
OD1 A:ASP402 2.2 41.2 1.0
O2P A:5GP900 2.3 40.0 1.0
O3P A:5GP900 2.4 40.4 1.0
P A:5GP900 2.8 44.6 1.0
CD2 A:HIS292 3.0 35.8 1.0
CD2 A:HIS256 3.0 39.5 1.0
CG A:ASP293 3.1 37.5 1.0
CE1 A:HIS256 3.1 37.0 1.0
CG A:ASP402 3.2 40.1 1.0
CE1 A:HIS292 3.2 38.0 1.0
OD2 A:ASP402 3.5 41.2 1.0
OD1 A:ASP293 3.6 36.5 1.0
O A:HOH914 3.8 31.9 1.0
O1P A:5GP900 4.0 39.8 1.0
MG A:MG902 4.1 33.5 1.0
O5' A:5GP900 4.1 42.9 1.0
CB A:ASP293 4.2 37.7 1.0
CG A:HIS292 4.2 35.6 1.0
CG A:HIS256 4.2 38.3 1.0
ND1 A:HIS256 4.2 35.8 1.0
ND1 A:HIS292 4.3 35.7 1.0
CD2 A:HIS252 4.3 39.0 1.0
CB A:ASP402 4.6 40.3 1.0
CG2 A:VAL260 4.6 37.1 1.0
C5' A:5GP900 4.7 42.7 1.0
NE2 A:HIS252 4.7 39.0 1.0
O A:HOH1132 4.8 24.4 1.0
O A:ASP402 4.8 39.9 1.0
CA A:ASP402 5.0 40.2 1.0

Manganese binding site 2 out of 4 in 3dys

Go back to Manganese Binding Sites List in 3dys
Manganese binding site 2 out of 4 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 Manganese with other atoms in the Mn 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
A:Mn65

b:0.8
occ:1.00
 O A:HOH990 2.5 55.0 1.0
O A:TYR246 2.5 42.0 1.0
O A:HOH1046 2.6 39.2 1.0
O A:HOH1110 2.7 45.6 1.0
O A:ASP244 2.8 41.1 1.0
C A:ASP244 3.6 41.6 1.0
C A:TYR246 3.6 41.6 1.0
O A:HOH1096 4.1 63.5 1.0
O A:HIS243 4.1 42.3 1.0
CA A:ASP244 4.2 42.0 1.0
CA A:ARG247 4.3 42.8 1.0
N A:TYR246 4.3 40.9 1.0
O A:HOH1055 4.3 58.9 1.0
N A:ARG247 4.4 42.3 1.0
N A:ASN245 4.4 41.7 1.0
O A:HOH936 4.5 40.8 1.0
OD1 A:ASP244 4.6 45.3 1.0
CA A:TYR246 4.6 41.3 1.0
C A:ASN245 4.7 40.9 1.0
O A:HOH998 4.7 45.7 1.0
CA A:ASN245 4.7 41.2 1.0
OD1 A:ASN248 4.8 51.7 1.0
C A:ARG247 5.0 42.7 1.0

Manganese binding site 3 out of 4 in 3dys

Go back to Manganese Binding Sites List in 3dys
Manganese binding site 3 out of 4 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 Manganese with other atoms in the Mn binding site number 3 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:Mn901

b:37.4
occ:1.00
 OD2 B:ASP293 2.1 40.3 1.0
NE2 B:HIS292 2.1 38.0 1.0
OD1 B:ASP402 2.1 39.5 1.0
O1 B:FMT1 2.1 46.6 1.0
NE2 B:HIS256 2.1 36.4 1.0
O B:HOH1185 2.4 29.5 1.0
CD2 B:HIS292 2.9 38.2 1.0
CG B:ASP402 3.0 40.8 1.0
CD2 B:HIS256 3.1 38.0 1.0
CG B:ASP293 3.1 39.2 1.0
CE1 B:HIS256 3.2 36.5 1.0
CE1 B:HIS292 3.2 39.4 1.0
C B:FMT1 3.2 48.3 1.0
OD2 B:ASP402 3.3 42.9 1.0
O2 B:FMT1 3.6 46.7 1.0
OD1 B:ASP293 3.7 38.9 1.0
MG B:MG902 4.0 32.1 1.0
O B:HOH1186 4.1 29.4 1.0
CG B:HIS292 4.1 37.8 1.0
CB B:ASP293 4.2 38.1 1.0
CG B:HIS256 4.2 38.6 1.0
ND1 B:HIS292 4.2 38.4 1.0
ND1 B:HIS256 4.2 35.9 1.0
CD2 B:HIS252 4.3 40.1 1.0
CB B:ASP402 4.4 40.2 1.0
O B:HOH1058 4.5 46.5 1.0
O B:ASP402 4.6 38.9 1.0
CG2 B:VAL260 4.6 37.3 1.0
NE2 B:HIS252 4.8 39.6 1.0
O B:HOH1189 4.8 23.3 1.0
CA B:ASP402 4.9 40.4 1.0

Manganese binding site 4 out of 4 in 3dys

Go back to Manganese Binding Sites List in 3dys
Manganese binding site 4 out of 4 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 Manganese with other atoms in the Mn binding site number 4 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:Mn89

b:0.6
occ:1.00
 O B:HOH1184 2.5 56.4 1.0
O B:HOH1129 2.5 45.3 1.0
O B:HOH1147 2.5 53.2 1.0
O B:ASP244 2.8 41.4 1.0
O B:HOH1037 2.8 42.4 1.0
O B:TYR246 2.8 41.5 1.0
C B:ASP244 3.7 41.5 1.0
O B:HOH1180 3.7 55.9 1.0
C B:TYR246 3.9 41.4 1.0
CA B:ASP244 4.2 41.9 1.0
O B:HIS243 4.3 42.5 1.0
CA B:ARG247 4.4 42.8 1.0
OD1 B:ASP244 4.5 45.4 1.0
N B:TYR246 4.6 41.0 1.0
N B:ARG247 4.6 42.0 1.0
O B:HOH1021 4.6 46.1 1.0
N B:ASN245 4.7 41.1 1.0
OD1 B:ASN248 4.8 51.8 1.0
O B:HOH1025 4.9 42.1 1.0
CA B:TYR246 4.9 41.2 1.0
CG B:ASP244 5.0 44.1 1.0
CA B:ASN245 5.0 41.2 1.0
C B:ASN245 5.0 41.0 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: Tue Dec 15 04:08:55 2020

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