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Zinc in PDB 5skb: Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One:
3.1.4.17;

Protein crystallography data

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

Resolution Low / High (Å) 35.37 / 2.35
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.431, 135.431, 234.211, 90, 90, 120
R / Rfree (%) 18.8 / 24.9

Other elements in 5skb:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-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 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One (pdb code 5skb). 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 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One, PDB code: 5skb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5skb

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-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 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:40.1
occ:1.00
 OD2 A:ASP564 2.0 34.3 1.0
NE2 A:HIS529 2.1 35.2 1.0
NE2 A:HIS563 2.1 32.3 1.0
O A:HOH923 2.2 32.6 1.0
OD1 A:ASP674 2.2 39.6 1.0
CD2 A:HIS563 3.0 34.9 1.0
CD2 A:HIS529 3.0 38.8 1.0
CE1 A:HIS529 3.1 36.4 1.0
CG A:ASP674 3.1 38.9 1.0
CG A:ASP564 3.1 31.4 1.0
CE1 A:HIS563 3.1 35.1 1.0
OD2 A:ASP674 3.3 44.2 1.0
OD1 A:ASP564 3.7 35.2 1.0
MG A:MG802 3.8 34.6 1.0
CG A:HIS563 4.1 33.1 1.0
ND1 A:HIS529 4.2 40.4 1.0
ND1 A:HIS563 4.2 30.1 1.0
O A:HOH963 4.2 29.8 1.0
CG A:HIS529 4.2 36.7 1.0
CB A:ASP564 4.2 30.2 1.0
CD2 A:HIS525 4.2 37.8 1.0
CB A:ASP674 4.4 37.0 1.0
NE2 A:HIS525 4.5 38.5 1.0
O A:HOH976 4.6 53.9 1.0
CG2 A:VAL533 4.6 31.8 1.0
O A:HOH920 4.6 29.1 1.0
CA A:ASP674 4.9 35.6 1.0
O A:ASP674 4.9 39.2 1.0
O A:HOH927 4.9 36.2 1.0

Zinc binding site 2 out of 4 in 5skb

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

b:38.3
occ:1.00
 NE2 B:HIS563 2.1 31.0 1.0
O B:HOH933 2.1 29.3 1.0
OD2 B:ASP564 2.1 30.8 1.0
NE2 B:HIS529 2.1 32.9 1.0
OD1 B:ASP674 2.3 35.7 1.0
O B:HOH957 2.5 35.4 1.0
CE1 B:HIS529 3.0 34.4 1.0
CD2 B:HIS563 3.0 31.2 1.0
CE1 B:HIS563 3.1 31.1 1.0
CG B:ASP564 3.1 29.4 1.0
CG B:ASP674 3.1 37.8 1.0
CD2 B:HIS529 3.2 34.6 1.0
OD2 B:ASP674 3.3 38.9 1.0
OD1 B:ASP564 3.6 30.4 1.0
MG B:MG802 3.9 29.6 1.0
O B:HOH968 4.0 27.8 1.0
O B:HOH969 4.1 38.7 1.0
ND1 B:HIS563 4.2 28.3 1.0
ND1 B:HIS529 4.2 32.1 1.0
CG B:HIS563 4.2 31.0 1.0
CD2 B:HIS525 4.2 36.0 1.0
CG B:HIS529 4.3 33.0 1.0
CB B:ASP564 4.3 27.7 1.0
CB B:ASP674 4.5 35.5 1.0
O B:HOH913 4.5 33.4 1.0
NE2 B:HIS525 4.6 37.0 1.0
CG2 B:VAL533 4.6 31.4 1.0
O B:ASP674 4.8 30.2 1.0
CA B:ASP674 4.9 32.4 1.0

Zinc binding site 3 out of 4 in 5skb

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

b:38.7
occ:1.00
 O C:HOH929 1.9 29.6 1.0
O C:HOH936 2.0 36.1 1.0
NE2 C:HIS563 2.0 36.8 1.0
OD2 C:ASP564 2.1 38.5 1.0
OD1 C:ASP674 2.1 38.9 1.0
NE2 C:HIS529 2.2 31.4 1.0
CG C:ASP674 3.0 36.5 1.0
CD2 C:HIS563 3.0 32.1 1.0
CE1 C:HIS563 3.1 35.3 1.0
CG C:ASP564 3.1 36.7 1.0
CD2 C:HIS529 3.1 31.6 1.0
CE1 C:HIS529 3.1 35.5 1.0
OD2 C:ASP674 3.2 35.5 1.0
OD1 C:ASP564 3.6 32.9 1.0
MG C:MG802 3.8 30.3 1.0
CD2 C:HIS525 4.1 41.1 1.0
CG C:HIS563 4.2 32.8 1.0
ND1 C:HIS563 4.2 29.5 1.0
O C:HOH983 4.2 36.2 1.0
ND1 C:HIS529 4.3 35.7 1.0
CB C:ASP564 4.3 33.7 1.0
CG C:HIS529 4.3 32.2 1.0
CB C:ASP674 4.3 35.7 1.0
NE2 C:HIS525 4.3 43.8 1.0
O C:HOH945 4.4 48.5 1.0
O C:HOH917 4.6 35.6 1.0
O C:ASP674 4.7 41.2 1.0
CG2 C:VAL533 4.8 34.3 1.0
CA C:ASP674 4.8 35.2 1.0
O C:HOH972 4.9 40.7 1.0

Zinc binding site 4 out of 4 in 5skb

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

b:48.7
occ:1.00
 O D:HOH936 2.0 39.6 1.0
OD2 D:ASP564 2.0 45.9 1.0
NE2 D:HIS563 2.1 34.7 1.0
NE2 D:HIS529 2.2 42.8 1.0
OD1 D:ASP674 2.2 51.0 1.0
O D:HOH937 2.3 39.2 1.0
CD2 D:HIS563 2.9 37.1 1.0
CG D:ASP564 3.0 40.7 1.0
CD2 D:HIS529 3.1 52.0 1.0
CE1 D:HIS563 3.1 39.6 1.0
CG D:ASP674 3.2 50.4 1.0
CE1 D:HIS529 3.3 51.2 1.0
OD2 D:ASP674 3.5 58.8 1.0
OD1 D:ASP564 3.5 39.7 1.0
MG D:MG802 3.7 40.7 1.0
CG D:HIS563 4.1 40.1 1.0
CB D:ASP564 4.1 40.6 1.0
ND1 D:HIS563 4.2 40.0 1.0
O D:HOH925 4.2 40.5 1.0
CD2 D:HIS525 4.2 53.4 1.0
CG D:HIS529 4.3 44.2 1.0
O D:HOH918 4.3 39.1 1.0
ND1 D:HIS529 4.3 48.0 1.0
NE2 D:HIS525 4.5 53.0 1.0
CB D:ASP674 4.6 51.5 1.0
CG2 D:VAL533 4.8 47.2 1.0
O D:ASP674 4.9 51.2 1.0
CA D:ASP674 4.9 49.5 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 06:13:57 2024

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