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Zinc in PDB 5shm: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide, PDB code: 5shm 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) 43.65 / 2.26
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.246, 135.246, 235.217, 90, 90, 120
R / Rfree (%) 18.6 / 23.6

Other elements in 5shm:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide (pdb code 5shm). 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- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide, PDB code: 5shm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5shm

Go back to Zinc Binding Sites List in 5shm
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide


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- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:37.8
occ:1.00
 OD2 A:ASP564 2.1 35.1 1.0
NE2 A:HIS529 2.1 37.1 1.0
NE2 A:HIS563 2.1 31.2 1.0
O A:HOH938 2.2 31.6 1.0
OD1 A:ASP674 2.2 39.5 1.0
O A:HOH959 2.4 35.2 1.0
CD2 A:HIS563 3.0 32.0 1.0
CD2 A:HIS529 3.1 35.7 1.0
CG A:ASP674 3.1 38.0 1.0
CG A:ASP564 3.1 35.2 1.0
CE1 A:HIS529 3.2 35.2 1.0
CE1 A:HIS563 3.2 33.0 1.0
OD2 A:ASP674 3.3 43.7 1.0
OD1 A:ASP564 3.7 32.1 1.0
MG A:MG802 3.8 35.4 1.0
O A:HOH941 4.1 45.2 1.0
O A:HOH971 4.1 30.9 1.0
CG A:HIS563 4.2 33.4 1.0
CG A:HIS529 4.2 33.7 1.0
ND1 A:HIS529 4.3 34.1 1.0
CB A:ASP564 4.3 32.8 1.0
CD2 A:HIS525 4.3 36.7 1.0
ND1 A:HIS563 4.3 29.9 1.0
CB A:ASP674 4.5 36.8 1.0
O A:HOH910 4.5 27.0 1.0
NE2 A:HIS525 4.6 36.3 1.0
CG2 A:VAL533 4.7 31.5 1.0
O A:ASP674 4.8 36.0 1.0
CA A:ASP674 4.9 33.9 1.0

Zinc binding site 2 out of 4 in 5shm

Go back to Zinc Binding Sites List in 5shm
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide


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- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:37.7
occ:1.00
 OD2 B:ASP564 2.1 31.1 1.0
O B:HOH953 2.1 27.6 1.0
NE2 B:HIS563 2.1 29.9 1.0
OD1 B:ASP674 2.2 33.9 1.0
NE2 B:HIS529 2.2 32.0 1.0
O B:HOH958 2.3 35.1 1.0
CD2 B:HIS563 3.0 31.2 1.0
CG B:ASP674 3.1 34.4 1.0
CG B:ASP564 3.1 31.4 1.0
CD2 B:HIS529 3.1 32.6 1.0
CE1 B:HIS529 3.2 33.1 1.0
CE1 B:HIS563 3.2 32.7 1.0
OD2 B:ASP674 3.4 38.4 1.0
OD1 B:ASP564 3.6 30.1 1.0
MG B:MG802 3.8 29.5 1.0
O B:HOH967 4.1 29.5 1.0
CD2 B:HIS525 4.2 34.9 1.0
CG B:HIS563 4.2 30.0 1.0
O B:HOH936 4.2 42.0 1.0
ND1 B:HIS563 4.3 31.7 1.0
ND1 B:HIS529 4.3 32.9 1.0
CG B:HIS529 4.3 30.8 1.0
CB B:ASP564 4.3 32.4 1.0
NE2 B:HIS525 4.4 39.0 1.0
CB B:ASP674 4.5 36.2 1.0
O B:HOH934 4.6 31.3 1.0
CG2 B:VAL533 4.8 31.9 1.0
CA B:ASP674 4.9 36.3 1.0
O B:ASP674 4.9 36.5 1.0

Zinc binding site 3 out of 4 in 5shm

Go back to Zinc Binding Sites List in 5shm
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide


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- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:40.6
occ:1.00
 OD2 C:ASP564 2.1 31.9 1.0
NE2 C:HIS563 2.1 36.0 1.0
O C:HOH933 2.2 28.3 1.0
OD1 C:ASP674 2.2 32.6 1.0
O C:HOH956 2.2 43.0 1.0
NE2 C:HIS529 2.2 36.0 1.0
CD2 C:HIS563 3.0 37.5 1.0
CG C:ASP674 3.0 37.2 1.0
CG C:ASP564 3.1 30.1 1.0
CD2 C:HIS529 3.1 36.8 1.0
CE1 C:HIS563 3.2 34.2 1.0
CE1 C:HIS529 3.3 38.6 1.0
OD2 C:ASP674 3.3 40.3 1.0
OD1 C:ASP564 3.7 31.5 1.0
MG C:MG802 3.7 33.2 1.0
CD2 C:HIS525 4.1 43.5 1.0
O C:HOH957 4.2 47.2 1.0
CG C:HIS563 4.2 30.8 1.0
O C:HOH963 4.2 38.9 1.0
ND1 C:HIS563 4.2 30.4 1.0
CB C:ASP564 4.3 29.6 1.0
CG C:HIS529 4.3 36.6 1.0
ND1 C:HIS529 4.3 35.0 1.0
NE2 C:HIS525 4.4 42.8 1.0
CB C:ASP674 4.4 37.4 1.0
O C:HOH934 4.5 30.6 1.0
O C:HOH962 4.7 47.1 1.0
CG2 C:VAL533 4.8 34.4 1.0
CA C:ASP674 4.8 37.8 1.0
O C:ASP674 4.8 35.9 1.0

Zinc binding site 4 out of 4 in 5shm

Go back to Zinc Binding Sites List in 5shm
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide


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- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-6-Cyclopropyl-3- Methoxypyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:47.7
occ:1.00
 O D:HOH915 2.0 33.4 1.0
NE2 D:HIS563 2.0 34.4 1.0
OD2 D:ASP564 2.1 47.7 1.0
NE2 D:HIS529 2.2 40.4 1.0
OD1 D:ASP674 2.2 42.2 1.0
O D:HOH937 2.3 42.8 1.0
CD2 D:HIS563 2.9 38.8 1.0
CG D:ASP674 3.1 42.6 1.0
CG D:ASP564 3.1 42.0 1.0
CE1 D:HIS563 3.1 35.4 1.0
CD2 D:HIS529 3.1 48.8 1.0
CE1 D:HIS529 3.3 44.7 1.0
OD2 D:ASP674 3.3 46.5 1.0
OD1 D:ASP564 3.6 43.9 1.0
MG D:MG802 3.9 47.1 1.0
O D:HOH933 4.1 36.5 1.0
CG D:HIS563 4.1 37.9 1.0
ND1 D:HIS563 4.2 39.1 1.0
CB D:ASP564 4.2 41.3 1.0
CD2 D:HIS525 4.3 49.7 1.0
CG D:HIS529 4.3 45.3 1.0
ND1 D:HIS529 4.4 44.1 1.0
O D:HOH911 4.4 37.6 1.0
CB D:ASP674 4.5 45.5 1.0
NE2 D:HIS525 4.6 50.9 1.0
O D:ASP674 4.7 50.8 1.0
CG2 D:VAL533 4.8 47.5 1.0
CA D:ASP674 4.9 47.0 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 05:31:55 2024

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