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Zinc 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:

Magnesium (Mg) 4 atoms
Fluorine (F) 12 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5sjj

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:30.5
occ:1.00
 O A:HOH969 2.1 25.6 1.0
NE2 A:HIS563 2.1 21.1 1.0
NE2 A:HIS529 2.1 29.3 1.0
OD2 A:ASP564 2.1 28.4 1.0
OD1 A:ASP674 2.2 27.4 1.0
O A:HOH984 2.4 34.7 1.0
CD2 A:HIS563 2.9 19.3 1.0
CD2 A:HIS529 3.0 27.5 1.0
CG A:ASP674 3.1 24.8 1.0
CG A:ASP564 3.1 26.4 1.0
CE1 A:HIS529 3.2 25.8 1.0
CE1 A:HIS563 3.2 25.9 1.0
OD2 A:ASP674 3.3 33.6 1.0
OD1 A:ASP564 3.6 24.2 1.0
MG A:MG802 3.8 24.6 1.0
CG A:HIS563 4.1 21.9 1.0
CD2 A:HIS525 4.1 35.1 1.0
CG A:HIS529 4.2 24.6 1.0
ND1 A:HIS563 4.2 22.3 1.0
ND1 A:HIS529 4.2 23.6 1.0
O A:HOH1034 4.2 26.9 1.0
CB A:ASP564 4.4 28.1 1.0
CB A:ASP674 4.4 24.0 1.0
NE2 A:HIS525 4.5 31.4 1.0
CG2 A:VAL533 4.6 21.6 1.0
O A:HOH963 4.7 25.2 1.0
O A:ASP674 4.8 26.3 1.0
CA A:ASP674 4.8 24.0 1.0

Zinc binding site 2 out of 4 in 5sjj

Go back to Zinc Binding Sites List in 5sjj
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:30.1
occ:1.00
 NE2 B:HIS563 2.1 21.3 1.0
O B:HOH1007 2.2 25.0 1.0
OD1 B:ASP674 2.2 26.7 1.0
OD2 B:ASP564 2.2 27.0 1.0
NE2 B:HIS529 2.2 25.1 1.0
CD2 B:HIS563 2.9 21.9 1.0
CG B:ASP674 3.1 23.6 1.0
CG B:ASP564 3.1 23.9 1.0
CE1 B:HIS529 3.2 25.8 1.0
CE1 B:HIS563 3.2 22.1 1.0
CD2 B:HIS529 3.3 26.5 1.0
OD2 B:ASP674 3.3 26.5 1.0
OD1 B:ASP564 3.6 22.4 1.0
MG B:MG802 3.7 19.6 1.0
CD2 B:HIS525 4.0 28.1 1.0
O B:HOH1032 4.1 21.5 1.0
CG B:HIS563 4.1 20.9 1.0
ND1 B:HIS563 4.2 21.4 1.0
CB B:ASP564 4.3 22.4 1.0
ND1 B:HIS529 4.3 20.9 1.0
O B:HOH967 4.4 21.5 1.0
CG B:HIS529 4.4 23.3 1.0
CB B:ASP674 4.4 24.9 1.0
NE2 B:HIS525 4.5 28.1 1.0
CG2 B:VAL533 4.9 20.4 1.0
CA B:ASP674 4.9 23.6 1.0
O B:ASP674 4.9 22.7 1.0

Zinc binding site 3 out of 4 in 5sjj

Go back to Zinc Binding Sites List in 5sjj
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:32.6
occ:1.00
 O C:HOH989 1.9 24.1 1.0
NE2 C:HIS529 2.0 23.8 1.0
OD2 C:ASP564 2.2 27.0 1.0
OD1 C:ASP674 2.2 26.9 1.0
NE2 C:HIS563 2.3 21.0 1.0
O C:HOH980 2.5 46.2 1.0
CD2 C:HIS563 3.0 19.5 1.0
CD2 C:HIS529 3.0 27.3 1.0
CE1 C:HIS529 3.1 24.2 1.0
CG C:ASP674 3.1 28.6 1.0
CG C:ASP564 3.2 23.9 1.0
OD2 C:ASP674 3.4 27.2 1.0
CE1 C:HIS563 3.5 21.6 1.0
OD1 C:ASP564 3.7 20.6 1.0
MG C:MG802 3.8 23.6 1.0
CD2 C:HIS525 4.0 28.0 1.0
CG C:HIS529 4.1 24.0 1.0
ND1 C:HIS529 4.2 25.6 1.0
CG C:HIS563 4.2 22.4 1.0
O C:HOH1032 4.2 27.0 1.0
NE2 C:HIS525 4.4 25.6 1.0
CB C:ASP564 4.4 22.7 1.0
ND1 C:HIS563 4.4 21.2 1.0
CB C:ASP674 4.5 28.7 1.0
O C:HOH929 4.5 24.9 1.0
O C:HOH1053 4.6 54.7 1.0
CG2 C:VAL533 4.8 23.4 1.0
CA C:ASP674 4.9 28.0 1.0
O C:ASP674 5.0 28.1 1.0

Zinc binding site 4 out of 4 in 5sjj

Go back to Zinc Binding Sites List in 5sjj
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:37.2
occ:1.00
 O D:HOH974 2.0 27.6 1.0
NE2 D:HIS529 2.1 32.6 1.0
NE2 D:HIS563 2.2 30.8 1.0
OD2 D:ASP564 2.3 32.3 1.0
OD1 D:ASP674 2.3 38.2 1.0
O D:HOH907 2.5 46.5 1.0
CD2 D:HIS563 3.1 28.7 1.0
CD2 D:HIS529 3.1 35.5 1.0
CE1 D:HIS529 3.1 33.5 1.0
CG D:ASP674 3.2 38.8 1.0
CG D:ASP564 3.2 31.6 1.0
CE1 D:HIS563 3.4 28.4 1.0
OD2 D:ASP674 3.4 36.2 1.0
OD1 D:ASP564 3.7 27.8 1.0
MG D:MG802 3.9 27.7 1.0
CD2 D:HIS525 3.9 35.2 1.0
NE2 D:HIS525 4.2 39.0 1.0
ND1 D:HIS529 4.2 30.6 1.0
CG D:HIS529 4.2 31.6 1.0
CG D:HIS563 4.3 27.6 1.0
O D:HOH992 4.3 26.7 1.0
CB D:ASP564 4.4 29.5 1.0
ND1 D:HIS563 4.4 27.4 1.0
CB D:ASP674 4.5 35.4 1.0
O D:HOH989 4.6 46.5 1.0
CG2 D:VAL533 4.7 28.4 1.0
O D:HOH922 4.8 26.0 1.0
O D:ASP674 4.8 33.9 1.0
CA D:ASP674 4.9 30.2 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 Oct 28 06:02:37 2024

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