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Zinc in PDB 5sgv: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One, PDB code: 5sgv was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.46 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.008, 135.008, 234.849, 90, 90, 120
R / Rfree (%) 18.9 / 22.4

Other elements in 5sgv:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One (pdb code 5sgv). 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 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One, PDB code: 5sgv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sgv

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One


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 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:28.2
occ:1.00
 OD2 A:ASP564 2.1 22.6 1.0
O A:HOH984 2.1 23.9 1.0
NE2 A:HIS529 2.1 26.0 1.0
NE2 A:HIS563 2.2 24.9 1.0
OD1 A:ASP674 2.2 26.0 1.0
O A:HOH930 2.2 20.8 1.0
CD2 A:HIS563 3.0 24.5 1.0
CD2 A:HIS529 3.1 24.2 1.0
CG A:ASP674 3.1 25.9 1.0
CG A:ASP564 3.1 22.9 1.0
CE1 A:HIS529 3.2 24.1 1.0
CE1 A:HIS563 3.2 24.7 1.0
OD2 A:ASP674 3.3 28.7 1.0
OD1 A:ASP564 3.6 20.9 1.0
MG A:MG802 3.8 22.9 1.0
O A:HOH1018 4.0 24.0 1.0
CD2 A:HIS525 4.2 25.2 1.0
CG A:HIS563 4.2 24.0 1.0
O A:HOH980 4.2 29.3 1.0
CG A:HIS529 4.2 24.1 1.0
ND1 A:HIS529 4.2 22.8 1.0
ND1 A:HIS563 4.3 24.5 1.0
CB A:ASP564 4.3 23.7 1.0
CB A:ASP674 4.5 25.4 1.0
NE2 A:HIS525 4.5 26.3 1.0
O A:HOH921 4.6 18.4 1.0
CG2 A:VAL533 4.7 24.0 1.0
O A:ASP674 4.8 24.1 1.0
CA A:ASP674 4.8 25.0 1.0

Zinc binding site 2 out of 4 in 5sgv

Go back to Zinc Binding Sites List in 5sgv
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One


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 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:26.3
occ:1.00
 O B:HOH941 2.1 20.9 1.0
OD2 B:ASP564 2.1 20.8 1.0
NE2 B:HIS529 2.1 22.4 1.0
NE2 B:HIS563 2.1 21.8 1.0
OD1 B:ASP674 2.2 20.9 1.0
O B:HOH995 2.2 24.5 1.0
CG B:ASP674 3.0 23.2 1.0
CD2 B:HIS529 3.1 22.9 1.0
CD2 B:HIS563 3.1 22.7 1.0
CG B:ASP564 3.1 21.4 1.0
CE1 B:HIS563 3.2 22.4 1.0
CE1 B:HIS529 3.2 23.8 1.0
OD2 B:ASP674 3.3 25.4 1.0
OD1 B:ASP564 3.7 23.4 1.0
MG B:MG802 3.8 21.2 1.0
O B:HOH1001 3.9 21.2 1.0
O B:HOH954 4.0 26.3 1.0
CD2 B:HIS525 4.1 23.9 1.0
CG B:HIS563 4.2 23.2 1.0
CG B:HIS529 4.2 22.8 1.0
ND1 B:HIS563 4.2 21.6 1.0
ND1 B:HIS529 4.3 20.7 1.0
CB B:ASP564 4.3 20.8 1.0
NE2 B:HIS525 4.4 25.0 1.0
CB B:ASP674 4.4 23.7 1.0
O B:HOH1048 4.5 52.1 1.0
CG2 B:VAL533 4.7 23.1 1.0
O B:HOH945 4.7 21.9 1.0
O B:ASP674 4.8 21.8 1.0
CA B:ASP674 4.8 22.9 1.0

Zinc binding site 3 out of 4 in 5sgv

Go back to Zinc Binding Sites List in 5sgv
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One


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 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:28.5
occ:1.00
 OD2 C:ASP564 2.1 22.8 1.0
O C:HOH913 2.1 21.0 1.0
NE2 C:HIS529 2.1 24.4 1.0
OD1 C:ASP674 2.2 22.8 1.0
NE2 C:HIS563 2.2 23.6 1.0
O C:HOH1003 2.3 26.7 1.0
CG C:ASP674 3.0 25.2 1.0
CD2 C:HIS563 3.1 23.2 1.0
CG C:ASP564 3.1 24.1 1.0
CE1 C:HIS529 3.1 25.1 1.0
CD2 C:HIS529 3.1 25.1 1.0
OD2 C:ASP674 3.2 28.9 1.0
CE1 C:HIS563 3.3 22.1 1.0
OD1 C:ASP564 3.6 25.2 1.0
MG C:MG802 3.8 23.5 1.0
CD2 C:HIS525 4.1 27.7 1.0
O C:HOH979 4.1 30.9 1.0
O C:HOH1031 4.1 24.5 1.0
ND1 C:HIS529 4.2 24.6 1.0
CG C:HIS529 4.3 24.5 1.0
CG C:HIS563 4.3 23.3 1.0
CB C:ASP564 4.3 23.9 1.0
ND1 C:HIS563 4.3 23.2 1.0
NE2 C:HIS525 4.4 27.0 1.0
CB C:ASP674 4.4 25.1 1.0
O C:HOH942 4.6 23.0 1.0
CG2 C:VAL533 4.8 22.0 1.0
O C:ASP674 4.8 25.4 1.0
CA C:ASP674 4.8 26.1 1.0

Zinc binding site 4 out of 4 in 5sgv

Go back to Zinc Binding Sites List in 5sgv
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One


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 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:32.7
occ:1.00
 O D:HOH922 2.1 23.8 1.0
NE2 D:HIS563 2.1 25.3 1.0
NE2 D:HIS529 2.1 32.5 1.0
OD2 D:ASP564 2.2 28.3 1.0
OD1 D:ASP674 2.2 25.7 1.0
O D:HOH982 2.2 29.4 1.0
CD2 D:HIS563 3.0 27.5 1.0
CG D:ASP564 3.1 26.1 1.0
CD2 D:HIS529 3.1 33.0 1.0
CG D:ASP674 3.1 27.8 1.0
CE1 D:HIS529 3.2 30.9 1.0
CE1 D:HIS563 3.2 27.0 1.0
OD2 D:ASP674 3.3 30.9 1.0
OD1 D:ASP564 3.5 27.8 1.0
MG D:MG802 3.8 30.3 1.0
O D:HOH990 4.1 30.8 1.0
O D:HOH952 4.1 34.1 1.0
CD2 D:HIS525 4.2 31.0 1.0
CG D:HIS563 4.2 25.6 1.0
CG D:HIS529 4.2 31.3 1.0
ND1 D:HIS529 4.2 31.4 1.0
ND1 D:HIS563 4.2 25.9 1.0
CB D:ASP564 4.3 26.6 1.0
CB D:ASP674 4.5 28.3 1.0
NE2 D:HIS525 4.5 35.2 1.0
O D:HOH919 4.7 27.2 1.0
CG2 D:VAL533 4.7 29.7 1.0
O D:ASP674 4.7 27.0 1.0
CA D:ASP674 4.8 28.2 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 05:19:15 2024

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