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Zinc in PDB 5sgl: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide, PDB code: 5sgl was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.72 / 2.28
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.574, 135.574, 235.517, 90, 90, 120
R / Rfree (%) 18.1 / 23

Other elements in 5sgl:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Bromine (Br) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide (pdb code 5sgl). 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 N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide, PDB code: 5sgl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sgl

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide


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 N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:39.5
occ:1.00
 OD2 A:ASP564 2.0 37.0 1.0
NE2 A:HIS563 2.1 32.0 1.0
NE2 A:HIS529 2.1 34.6 1.0
OD1 A:ASP674 2.1 42.0 1.0
O A:HOH943 2.2 26.3 1.0
O A:HOH970 2.3 42.1 1.0
CD2 A:HIS563 3.0 33.3 1.0
CG A:ASP674 3.0 39.1 1.0
CE1 A:HIS529 3.1 32.0 1.0
CD2 A:HIS529 3.1 32.0 1.0
CG A:ASP564 3.2 34.0 1.0
CE1 A:HIS563 3.2 35.1 1.0
OD2 A:ASP674 3.3 44.5 1.0
OD1 A:ASP564 3.8 32.6 1.0
MG A:MG802 3.9 31.1 1.0
O A:HOH990 4.1 30.8 1.0
CG A:HIS563 4.1 31.9 1.0
CD2 A:HIS525 4.1 36.5 1.0
ND1 A:HIS529 4.2 33.6 1.0
ND1 A:HIS563 4.2 33.5 1.0
CG A:HIS529 4.2 33.5 1.0
O A:HOH956 4.2 51.3 1.0
CB A:ASP564 4.3 32.7 1.0
CB A:ASP674 4.4 35.1 1.0
NE2 A:HIS525 4.5 36.1 1.0
O A:HOH921 4.6 28.6 1.0
CG2 A:VAL533 4.7 29.5 1.0
O A:ASP674 4.7 34.3 1.0
CA A:ASP674 4.9 32.9 1.0

Zinc binding site 2 out of 4 in 5sgl

Go back to Zinc Binding Sites List in 5sgl
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide


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 N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:34.8
occ:1.00
 NE2 B:HIS563 2.1 28.6 1.0
OD1 B:ASP674 2.1 31.8 1.0
O B:HOH960 2.1 25.1 1.0
OD2 B:ASP564 2.1 29.5 1.0
NE2 B:HIS529 2.2 25.1 1.0
O B:HOH970 2.5 43.8 1.0
CD2 B:HIS563 3.0 30.1 1.0
CG B:ASP674 3.1 32.9 1.0
CG B:ASP564 3.1 30.9 1.0
CD2 B:HIS529 3.1 25.4 1.0
CE1 B:HIS563 3.2 31.4 1.0
CE1 B:HIS529 3.2 26.4 1.0
OD2 B:ASP674 3.4 34.6 1.0
OD1 B:ASP564 3.5 28.1 1.0
MG B:MG802 3.8 27.3 1.0
O B:HOH976 4.0 29.7 1.0
CD2 B:HIS525 4.2 31.6 1.0
CG B:HIS563 4.2 29.6 1.0
ND1 B:HIS563 4.2 28.1 1.0
CG B:HIS529 4.3 26.2 1.0
ND1 B:HIS529 4.3 25.5 1.0
CB B:ASP564 4.3 29.9 1.0
CB B:ASP674 4.4 31.7 1.0
O B:HOH977 4.5 52.3 1.0
NE2 B:HIS525 4.5 32.6 1.0
O B:HOH944 4.6 28.8 1.0
O B:ASP674 4.8 32.6 1.0
CG2 B:VAL533 4.8 32.3 1.0
CA B:ASP674 4.9 31.3 1.0

Zinc binding site 3 out of 4 in 5sgl

Go back to Zinc Binding Sites List in 5sgl
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide


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 N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:38.1
occ:1.00
 OD2 C:ASP564 2.1 31.6 1.0
OD1 C:ASP674 2.1 38.8 1.0
O C:HOH935 2.1 24.9 1.0
NE2 C:HIS529 2.2 33.7 1.0
NE2 C:HIS563 2.2 34.7 1.0
O C:HOH970 2.4 42.7 1.0
CG C:ASP674 3.0 33.4 1.0
CD2 C:HIS563 3.0 30.8 1.0
CD2 C:HIS529 3.1 32.7 1.0
CG C:ASP564 3.1 31.2 1.0
CE1 C:HIS529 3.2 34.0 1.0
OD2 C:ASP674 3.2 38.9 1.0
CE1 C:HIS563 3.3 34.4 1.0
OD1 C:ASP564 3.7 31.9 1.0
MG C:MG802 3.8 32.3 1.0
CD2 C:HIS525 4.1 39.8 1.0
CG C:HIS563 4.2 32.5 1.0
O C:HOH984 4.2 26.6 1.0
CG C:HIS529 4.3 32.9 1.0
ND1 C:HIS529 4.3 31.7 1.0
CB C:ASP564 4.3 29.9 1.0
ND1 C:HIS563 4.3 32.1 1.0
CB C:ASP674 4.4 35.4 1.0
NE2 C:HIS525 4.5 43.9 1.0
O C:HOH992 4.5 48.0 1.0
O C:HOH941 4.5 32.2 1.0
O C:ASP674 4.7 35.8 1.0
CA C:ASP674 4.8 33.3 1.0
CG2 C:VAL533 4.9 33.8 1.0

Zinc binding site 4 out of 4 in 5sgl

Go back to Zinc Binding Sites List in 5sgl
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide


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 N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:45.7
occ:1.00
 NE2 D:HIS563 2.1 37.8 1.0
OD1 D:ASP674 2.1 41.9 1.0
O D:HOH925 2.2 29.9 1.0
OD2 D:ASP564 2.2 42.9 1.0
NE2 D:HIS529 2.3 43.4 1.0
O D:HOH928 2.4 40.2 1.0
CD2 D:HIS563 3.0 39.0 1.0
CG D:ASP674 3.0 44.3 1.0
CE1 D:HIS563 3.2 41.2 1.0
CD2 D:HIS529 3.2 43.8 1.0
CG D:ASP564 3.2 40.3 1.0
OD2 D:ASP674 3.2 50.1 1.0
CE1 D:HIS529 3.3 47.1 1.0
OD1 D:ASP564 3.7 41.5 1.0
O D:HOH935 3.9 55.5 1.0
MG D:MG802 3.9 43.4 1.0
CD2 D:HIS525 4.2 50.3 1.0
CG D:HIS563 4.2 36.3 1.0
ND1 D:HIS563 4.3 38.9 1.0
CB D:ASP564 4.3 39.2 1.0
CG D:HIS529 4.4 40.8 1.0
ND1 D:HIS529 4.4 41.1 1.0
CB D:ASP674 4.4 47.0 1.0
O D:HOH909 4.5 33.4 1.0
NE2 D:HIS525 4.5 49.1 1.0
O D:ASP674 4.6 45.8 1.0
CG2 D:VAL533 4.9 43.4 1.0
CA D:ASP674 4.9 44.6 1.0
O D:HOH930 5.0 33.7 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 05:15:30 2024

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