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Zinc in PDB 5sjk: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One, PDB code: 5sjk was solved by C.Joseph, J.Benz, A.Flohr, E.Kyburz, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.38 / 2.24
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.878, 134.878, 234.027, 90, 90, 120
R / Rfree (%) 18.3 / 23.5

Other elements in 5sjk:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One also contains other interesting chemical elements:

Chlorine (Cl) 8 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 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One (pdb code 5sjk). 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 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One, PDB code: 5sjk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sjk

Go back to Zinc Binding Sites List in 5sjk
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-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 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:35.8
occ:1.00
 OD2 A:ASP564 2.1 30.9 1.0
NE2 A:HIS529 2.1 32.3 1.0
OD1 A:ASP674 2.1 38.4 1.0
NE2 A:HIS563 2.1 27.6 1.0
O A:HOH956 2.1 26.6 1.0
O A:HOH969 2.6 33.3 1.0
CD2 A:HIS563 3.0 26.3 1.0
CD2 A:HIS529 3.1 31.2 1.0
CG A:ASP674 3.1 34.9 1.0
CE1 A:HIS529 3.1 29.0 1.0
CG A:ASP564 3.1 29.2 1.0
CE1 A:HIS563 3.1 27.6 1.0
OD2 A:ASP674 3.4 39.4 1.0
OD1 A:ASP564 3.6 26.2 1.0
MG A:MG802 3.9 27.5 1.0
O A:HOH1005 4.2 38.6 1.0
CG A:HIS563 4.2 26.9 1.0
ND1 A:HIS529 4.2 29.9 1.0
CG A:HIS529 4.2 28.9 1.0
ND1 A:HIS563 4.2 25.4 1.0
CD2 A:HIS525 4.2 28.3 1.0
CB A:ASP564 4.2 27.9 1.0
O A:HOH1002 4.3 31.2 1.0
CB A:ASP674 4.4 29.4 1.0
NE2 A:HIS525 4.6 28.5 1.0
O A:HOH987 4.6 43.9 1.0
O A:HOH934 4.7 26.4 1.0
O A:ASP674 4.7 32.0 1.0
CG2 A:VAL533 4.8 26.9 1.0
CA A:ASP674 4.8 30.0 1.0

Zinc binding site 2 out of 4 in 5sjk

Go back to Zinc Binding Sites List in 5sjk
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-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 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:33.7
occ:1.00
 OD2 B:ASP564 2.1 27.6 1.0
NE2 B:HIS563 2.1 26.9 1.0
O B:HOH950 2.1 21.3 1.0
NE2 B:HIS529 2.2 26.4 1.0
OD1 B:ASP674 2.2 30.4 1.0
O B:HOH980 2.4 34.6 1.0
CD2 B:HIS563 3.1 25.7 1.0
CD2 B:HIS529 3.1 26.0 1.0
CG B:ASP564 3.1 28.7 1.0
CG B:ASP674 3.1 30.4 1.0
CE1 B:HIS563 3.1 26.6 1.0
CE1 B:HIS529 3.2 27.3 1.0
OD2 B:ASP674 3.3 32.9 1.0
OD1 B:ASP564 3.6 27.8 1.0
MG B:MG802 3.8 24.0 1.0
O B:HOH1009 4.0 21.3 1.0
O B:HOH1007 4.0 38.1 1.0
CD2 B:HIS525 4.2 31.6 1.0
CG B:HIS563 4.2 26.0 1.0
ND1 B:HIS563 4.2 25.1 1.0
CG B:HIS529 4.3 27.9 1.0
CB B:ASP564 4.3 28.4 1.0
ND1 B:HIS529 4.3 28.0 1.0
CB B:ASP674 4.5 30.4 1.0
O B:HOH943 4.6 25.4 1.0
NE2 B:HIS525 4.6 31.3 1.0
CG2 B:VAL533 4.8 27.9 1.0
O B:ASP674 4.8 30.2 1.0
CA B:ASP674 4.8 28.6 1.0

Zinc binding site 3 out of 4 in 5sjk

Go back to Zinc Binding Sites List in 5sjk
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-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 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:34.3
occ:1.00
 O C:HOH929 2.0 25.4 1.0
O C:HOH981 2.1 40.3 1.0
OD1 C:ASP674 2.1 29.8 1.0
OD2 C:ASP564 2.1 30.8 1.0
NE2 C:HIS529 2.2 28.4 1.0
NE2 C:HIS563 2.3 29.2 1.0
CG C:ASP674 2.9 27.1 1.0
CD2 C:HIS563 3.1 28.3 1.0
OD2 C:ASP674 3.1 25.9 1.0
CG C:ASP564 3.1 31.7 1.0
CE1 C:HIS529 3.1 31.9 1.0
CD2 C:HIS529 3.2 31.4 1.0
CE1 C:HIS563 3.3 28.8 1.0
OD1 C:ASP564 3.7 29.9 1.0
MG C:MG802 3.7 29.9 1.0
CD2 C:HIS525 4.0 37.1 1.0
O C:HOH1019 4.1 53.6 1.0
O C:HOH1003 4.1 41.4 1.0
O C:HOH1006 4.2 29.4 1.0
CB C:ASP564 4.3 28.5 1.0
ND1 C:HIS529 4.3 30.9 1.0
CG C:HIS563 4.3 27.2 1.0
CG C:HIS529 4.3 30.1 1.0
CB C:ASP674 4.3 29.3 1.0
ND1 C:HIS563 4.4 26.8 1.0
NE2 C:HIS525 4.4 38.0 1.0
O C:HOH941 4.6 29.8 1.0
CA C:ASP674 4.8 30.9 1.0
O C:ASP674 4.8 33.1 1.0
CG2 C:VAL533 4.8 28.4 1.0

Zinc binding site 4 out of 4 in 5sjk

Go back to Zinc Binding Sites List in 5sjk
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-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 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:50.5
occ:1.00
 NE2 D:HIS563 2.0 35.5 1.0
O D:HOH931 2.1 30.1 1.0
OD1 D:ASP674 2.2 47.2 1.0
OD2 D:ASP564 2.2 46.1 1.0
NE2 D:HIS529 2.3 46.3 1.0
O D:HOH941 2.5 43.8 1.0
CD2 D:HIS563 3.0 39.7 1.0
CE1 D:HIS563 3.1 39.0 1.0
CG D:ASP564 3.1 41.0 1.0
CD2 D:HIS529 3.1 47.2 1.0
CG D:ASP674 3.2 45.3 1.0
CE1 D:HIS529 3.3 45.5 1.0
OD2 D:ASP674 3.5 48.6 1.0
OD1 D:ASP564 3.7 46.6 1.0
MG D:MG802 3.8 44.4 1.0
O D:HOH940 4.0 35.5 1.0
O D:HOH917 4.0 56.0 1.0
CG D:HIS563 4.1 37.4 1.0
ND1 D:HIS563 4.2 35.5 1.0
CB D:ASP564 4.2 42.8 1.0
CD2 D:HIS525 4.3 50.6 1.0
CG D:HIS529 4.3 42.6 1.0
ND1 D:HIS529 4.4 46.8 1.0
CB D:ASP674 4.5 47.4 1.0
O D:HOH913 4.5 45.9 1.0
O D:ASP674 4.7 49.0 1.0
NE2 D:HIS525 4.8 51.9 1.0
CG2 D:VAL533 4.8 49.1 1.0
CA D:ASP674 4.9 46.5 1.0
O D:HOH930 4.9 37.6 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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