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Zinc in PDB 5sh6: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One, PDB code: 5sh6 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) 43.44 / 1.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.064, 135.064, 233.963, 90, 90, 120
R / Rfree (%) 17.5 / 21.7

Other elements in 5sh6:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-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 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One (pdb code 5sh6). 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-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One, PDB code: 5sh6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sh6

Go back to Zinc Binding Sites List in 5sh6
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-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 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:31.2
occ:1.00
 O A:HOH962 2.1 23.4 1.0
OD2 A:ASP564 2.1 27.9 1.0
NE2 A:HIS529 2.1 28.8 1.0
OD1 A:ASP674 2.2 31.6 1.0
NE2 A:HIS563 2.2 27.1 1.0
O A:HOH1013 2.2 33.0 1.0
CD2 A:HIS563 3.0 23.9 1.0
CG A:ASP564 3.1 27.2 1.0
CG A:ASP674 3.1 29.7 1.0
CD2 A:HIS529 3.1 28.1 1.0
CE1 A:HIS529 3.1 28.2 1.0
CE1 A:HIS563 3.2 31.0 1.0
OD2 A:ASP674 3.3 33.1 1.0
OD1 A:ASP564 3.6 26.1 1.0
MG A:MG802 3.7 26.2 1.0
O A:HOH1028 4.1 24.7 1.0
CD2 A:HIS525 4.1 29.4 1.0
O A:HOH951 4.2 33.0 1.0
CG A:HIS563 4.2 26.6 1.0
CG A:HIS529 4.2 26.9 1.0
ND1 A:HIS529 4.2 25.5 1.0
ND1 A:HIS563 4.3 27.2 1.0
CB A:ASP564 4.3 26.9 1.0
CB A:ASP674 4.5 26.7 1.0
NE2 A:HIS525 4.5 31.2 1.0
O A:HOH936 4.5 22.5 1.0
CG2 A:VAL533 4.8 24.2 1.0
O A:ASP674 4.8 26.9 1.0
CA A:ASP674 4.8 26.2 1.0

Zinc binding site 2 out of 4 in 5sh6

Go back to Zinc Binding Sites List in 5sh6
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-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 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:31.0
occ:1.00
 O B:HOH958 2.1 22.1 1.0
OD1 B:ASP674 2.1 26.5 1.0
OD2 B:ASP564 2.1 27.2 1.0
NE2 B:HIS529 2.2 22.8 1.0
NE2 B:HIS563 2.2 24.5 1.0
O B:HOH973 2.4 40.4 1.0
CG B:ASP674 3.0 24.8 1.0
CD2 B:HIS563 3.1 24.2 1.0
CG B:ASP564 3.1 25.3 1.0
CD2 B:HIS529 3.1 25.0 1.0
CE1 B:HIS529 3.2 25.0 1.0
CE1 B:HIS563 3.3 25.4 1.0
OD2 B:ASP674 3.3 26.8 1.0
OD1 B:ASP564 3.6 25.4 1.0
MG B:MG802 3.7 25.1 1.0
O B:HOH1021 3.9 24.4 1.0
CD2 B:HIS525 4.1 28.9 1.0
O B:HOH1004 4.1 40.3 1.0
CG B:HIS563 4.2 24.2 1.0
CG B:HIS529 4.3 24.0 1.0
ND1 B:HIS529 4.3 23.0 1.0
CB B:ASP564 4.3 22.5 1.0
O B:HOH1038 4.3 51.1 1.0
ND1 B:HIS563 4.3 25.5 1.0
CB B:ASP674 4.4 25.4 1.0
NE2 B:HIS525 4.4 30.8 1.0
O B:HOH951 4.6 25.6 1.0
CG2 B:VAL533 4.7 24.8 1.0
CA B:ASP674 4.8 23.9 1.0
O B:ASP674 4.9 23.7 1.0

Zinc binding site 3 out of 4 in 5sh6

Go back to Zinc Binding Sites List in 5sh6
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-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 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:32.0
occ:1.00
 O C:HOH979 2.0 23.4 1.0
OD1 C:ASP674 2.1 24.6 1.0
NE2 C:HIS529 2.2 25.3 1.0
OD2 C:ASP564 2.2 25.9 1.0
NE2 C:HIS563 2.2 28.5 1.0
O C:HOH1004 2.3 36.8 1.0
CG C:ASP674 3.0 27.6 1.0
CD2 C:HIS563 3.1 26.1 1.0
CD2 C:HIS529 3.1 27.7 1.0
CG C:ASP564 3.1 26.1 1.0
CE1 C:HIS563 3.2 23.3 1.0
CE1 C:HIS529 3.3 29.8 1.0
OD2 C:ASP674 3.3 32.6 1.0
OD1 C:ASP564 3.6 23.5 1.0
MG C:MG802 3.7 27.1 1.0
O C:HOH1039 4.0 28.7 1.0
CD2 C:HIS525 4.1 29.5 1.0
O C:HOH1024 4.2 44.2 1.0
CG C:HIS563 4.2 24.0 1.0
CG C:HIS529 4.3 28.1 1.0
O C:HOH1049 4.3 46.1 1.0
ND1 C:HIS563 4.3 24.9 1.0
ND1 C:HIS529 4.3 27.3 1.0
CB C:ASP564 4.3 23.4 1.0
CB C:ASP674 4.4 29.0 1.0
NE2 C:HIS525 4.4 30.5 1.0
O C:HOH934 4.5 26.4 1.0
CA C:ASP674 4.8 28.8 1.0
CG2 C:VAL533 4.8 28.1 1.0
O C:ASP674 4.8 28.3 1.0

Zinc binding site 4 out of 4 in 5sh6

Go back to Zinc Binding Sites List in 5sh6
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-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 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.5
occ:1.00
 O D:HOH955 1.9 26.8 1.0
NE2 D:HIS529 2.2 33.2 1.0
OD2 D:ASP564 2.2 33.2 1.0
NE2 D:HIS563 2.2 26.7 1.0
OD1 D:ASP674 2.2 30.2 1.0
O D:HOH950 2.2 34.2 1.0
CD2 D:HIS563 3.0 28.1 1.0
CG D:ASP674 3.1 33.0 1.0
CD2 D:HIS529 3.1 33.8 1.0
CG D:ASP564 3.1 30.2 1.0
CE1 D:HIS529 3.3 35.0 1.0
OD2 D:ASP674 3.3 36.0 1.0
CE1 D:HIS563 3.4 29.8 1.0
OD1 D:ASP564 3.6 29.7 1.0
MG D:MG802 3.7 32.6 1.0
O D:HOH983 4.0 45.5 1.0
CD2 D:HIS525 4.1 34.4 1.0
O D:HOH960 4.1 31.9 1.0
CG D:HIS563 4.2 26.7 1.0
CG D:HIS529 4.3 30.3 1.0
CB D:ASP564 4.3 31.4 1.0
ND1 D:HIS529 4.3 30.4 1.0
ND1 D:HIS563 4.4 28.6 1.0
NE2 D:HIS525 4.4 40.1 1.0
CB D:ASP674 4.4 30.4 1.0
O D:HOH934 4.6 28.6 1.0
O D:ASP674 4.7 30.7 1.0
CG2 D:VAL533 4.8 34.2 1.0
CA D:ASP674 4.8 30.4 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 05:22:59 2024

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