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Magnesium in PDB 5sjj: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine, PDB code: 5sjj was solved by C.Joseph, J.Benz, A.Flohr, J.Cai, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.85 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.49, 136.49, 236.14, 90, 90, 120
R / Rfree (%) 17.4 / 24

Other elements in 5sjj:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Fluorine (F) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine (pdb code 5sjj). 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 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine, PDB code: 5sjj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjj

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine


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 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:24.6
occ:1.00
 OD1 A:ASP564 1.9 24.2 1.0
O A:HOH1034 2.0 26.9 1.0
O A:HOH969 2.0 25.6 1.0
O A:HOH963 2.0 25.2 1.0
O A:HOH957 2.2 33.2 1.0
O A:HOH934 2.2 26.1 1.0
CG A:ASP564 3.0 26.4 1.0
OD2 A:ASP564 3.4 28.4 1.0
ZN A:ZN801 3.8 30.5 1.0
O A:HOH984 3.9 34.7 1.0
O A:HOH980 4.0 34.7 1.0
NE2 A:HIS595 4.1 25.9 1.0
OE2 A:GLU592 4.2 25.9 1.0
O A:HIS563 4.3 27.0 1.0
CB A:ASP564 4.3 28.1 1.0
CD2 A:HIS563 4.3 19.3 1.0
OG1 A:THR633 4.3 26.7 1.0
CD2 A:HIS567 4.3 29.2 1.0
CD2 A:HIS595 4.4 25.0 1.0
NE2 A:HIS567 4.5 30.9 1.0
OD2 A:ASP674 4.5 33.6 1.0
O A:THR633 4.6 28.1 1.0
CD2 A:HIS525 4.7 35.1 1.0
NE2 A:HIS563 4.7 21.1 1.0
CB A:THR633 4.7 27.0 1.0
NE2 A:HIS525 4.7 31.4 1.0
CA A:ASP564 4.8 28.9 1.0
CG A:GLU592 4.8 26.6 1.0
CD A:GLU592 5.0 27.4 1.0

Magnesium binding site 2 out of 4 in 5sjj

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine


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 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:19.6
occ:1.00
 O B:HOH967 1.8 21.5 1.0
O B:HOH1007 1.8 25.0 1.0
O B:HOH1032 2.1 21.5 1.0
O B:HOH971 2.1 23.4 1.0
O B:HOH926 2.1 20.4 1.0
OD1 B:ASP564 2.2 22.4 1.0
CG B:ASP564 3.2 23.9 1.0
OD2 B:ASP564 3.5 27.0 1.0
ZN B:ZN801 3.7 30.1 1.0
OE2 B:GLU592 4.0 28.7 1.0
NE2 B:HIS595 4.1 25.3 1.0
O B:HOH978 4.1 32.4 1.0
CD2 B:HIS567 4.3 26.8 1.0
OG1 B:THR633 4.3 26.4 1.0
CD2 B:HIS563 4.3 21.9 1.0
NE2 B:HIS567 4.3 27.3 1.0
CD2 B:HIS595 4.4 22.7 1.0
O B:HIS563 4.4 22.3 1.0
OD2 B:ASP674 4.5 26.5 1.0
CB B:ASP564 4.6 22.4 1.0
CD2 B:HIS525 4.6 28.1 1.0
NE2 B:HIS563 4.7 21.3 1.0
O B:THR633 4.7 22.0 1.0
CB B:THR633 4.7 24.2 1.0
NE2 B:HIS525 4.7 28.1 1.0
CG B:GLU592 4.7 28.9 1.0
CD B:GLU592 4.8 28.6 1.0
CA B:ASP564 4.9 22.6 1.0

Magnesium binding site 3 out of 4 in 5sjj

Go back to Magnesium Binding Sites List in 5sjj
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine


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 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:23.6
occ:1.00
 O C:HOH929 2.0 24.9 1.0
O C:HOH1032 2.0 27.0 1.0
OD1 C:ASP564 2.1 20.6 1.0
O C:HOH989 2.1 24.1 1.0
O C:HOH1011 2.1 24.5 1.0
O C:HOH927 2.2 20.6 1.0
CG C:ASP564 3.1 23.9 1.0
OD2 C:ASP564 3.5 27.0 1.0
ZN C:ZN801 3.8 32.6 1.0
OE2 C:GLU592 4.0 32.8 1.0
OG1 C:THR633 4.0 20.4 1.0
NE2 C:HIS595 4.2 29.0 1.0
O C:HOH980 4.2 46.2 1.0
CD2 C:HIS567 4.3 26.0 1.0
O C:THR633 4.3 26.4 1.0
CD2 C:HIS563 4.3 19.5 1.0
O C:HOH938 4.4 32.1 1.0
O C:HIS563 4.4 25.1 1.0
CD2 C:HIS595 4.4 30.3 1.0
OD2 C:ASP674 4.4 27.2 1.0
CB C:ASP564 4.5 22.7 1.0
NE2 C:HIS567 4.6 30.2 1.0
CB C:THR633 4.6 23.7 1.0
NE2 C:HIS525 4.7 25.6 1.0
CD2 C:HIS525 4.7 28.0 1.0
CA C:ASP564 4.8 24.2 1.0
CD C:GLU592 4.9 32.6 1.0
CG C:GLU592 4.9 30.3 1.0
NE2 C:HIS563 4.9 21.0 1.0
O C:HOH1053 4.9 54.7 1.0
O C:HOH1026 5.0 36.4 1.0

Magnesium binding site 4 out of 4 in 5sjj

Go back to Magnesium Binding Sites List in 5sjj
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine


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 10 in Complex with 4-N- Ethyl-5-[3-(Trifluoromethyl)Phenyl]-7H-Pyrrolo[2,3-D]Pyrimidine-2,4- Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:27.7
occ:1.00
 O D:HOH987 1.9 26.2 1.0
O D:HOH959 2.0 28.8 1.0
O D:HOH974 2.0 27.6 1.0
O D:HOH922 2.2 26.0 1.0
OD1 D:ASP564 2.2 27.8 1.0
O D:HOH992 2.2 26.7 1.0
CG D:ASP564 3.2 31.6 1.0
OD2 D:ASP564 3.6 32.3 1.0
O D:HOH907 3.9 46.5 1.0
ZN D:ZN801 3.9 37.2 1.0
NE2 D:HIS595 4.0 29.7 1.0
OE2 D:GLU592 4.0 34.9 1.0
OG1 D:THR633 4.1 29.4 1.0
O D:HOH971 4.1 35.9 1.0
CD2 D:HIS567 4.2 33.2 1.0
O D:HIS563 4.3 30.2 1.0
CD2 D:HIS595 4.3 31.0 1.0
CD2 D:HIS563 4.4 28.7 1.0
NE2 D:HIS567 4.4 32.4 1.0
O D:THR633 4.5 31.1 1.0
OD2 D:ASP674 4.6 36.2 1.0
CB D:ASP564 4.6 29.5 1.0
NE2 D:HIS525 4.6 39.0 1.0
CB D:THR633 4.6 33.7 1.0
CD2 D:HIS525 4.7 35.2 1.0
NE2 D:HIS563 4.8 30.8 1.0
CD D:GLU592 4.9 34.0 1.0
CA D:ASP564 4.9 27.6 1.0

Reference:

A.Flohr, D.Schlatter, B.Kuhn, M.G.Rudolph. Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Mon Sep 30 04:24:13 2024

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