Atomistry » Manganese » PDB 3cev-3ea3 » 3dys
Atomistry »
  Manganese »
    PDB 3cev-3ea3 »
      3dys »

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: Sat Oct 5 16:08:07 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy