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Zinc in PDB 5se6: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine, PDB code: 5se6 was solved by C.Joseph, K.Groebke-Zbinden, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.50 / 1.95
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.828, 134.828, 234.402, 90, 90, 120
R / Rfree (%) 17.7 / 21.9

Other elements in 5se6:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine 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 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine (pdb code 5se6). 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 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine, PDB code: 5se6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5se6

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine


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 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:30.1
occ:1.00
 O A:HOH972 2.1 22.8 1.0
OD2 A:ASP564 2.1 28.1 1.0
NE2 A:HIS529 2.1 25.5 1.0
NE2 A:HIS563 2.1 26.2 1.0
OD1 A:ASP674 2.2 27.2 1.0
O A:HOH1013 2.3 36.3 1.0
CD2 A:HIS563 3.0 23.9 1.0
CG A:ASP674 3.1 28.4 1.0
CD2 A:HIS529 3.1 26.8 1.0
CG A:ASP564 3.1 23.6 1.0
CE1 A:HIS529 3.1 25.3 1.0
CE1 A:HIS563 3.2 28.2 1.0
OD2 A:ASP674 3.4 30.9 1.0
OD1 A:ASP564 3.6 25.0 1.0
MG A:MG802 3.7 25.1 1.0
O A:HOH1025 4.0 24.4 1.0
CD2 A:HIS525 4.1 30.5 1.0
CG A:HIS563 4.2 23.8 1.0
O A:HOH965 4.2 42.9 1.0
ND1 A:HIS563 4.2 24.6 1.0
ND1 A:HIS529 4.2 25.1 1.0
CG A:HIS529 4.2 27.2 1.0
CB A:ASP564 4.3 23.6 1.0
CB A:ASP674 4.4 26.8 1.0
NE2 A:HIS525 4.5 30.7 1.0
O A:HOH922 4.5 24.2 1.0
CG2 A:VAL533 4.7 22.2 1.0
CA A:ASP674 4.8 24.3 1.0
O A:ASP674 4.9 29.0 1.0

Zinc binding site 2 out of 4 in 5se6

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine


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 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:29.6
occ:1.00
 O B:HOH974 2.1 19.8 1.0
O B:HOH987 2.1 35.7 1.0
OD2 B:ASP564 2.1 23.1 1.0
OD1 B:ASP674 2.1 26.6 1.0
NE2 B:HIS563 2.2 22.1 1.0
NE2 B:HIS529 2.2 21.7 1.0
CD2 B:HIS563 3.0 23.1 1.0
CG B:ASP674 3.0 25.4 1.0
CG B:ASP564 3.1 22.9 1.0
CD2 B:HIS529 3.1 24.7 1.0
CE1 B:HIS529 3.2 26.8 1.0
OD2 B:ASP674 3.3 27.9 1.0
CE1 B:HIS563 3.3 23.8 1.0
OD1 B:ASP564 3.5 24.1 1.0
MG B:MG802 3.8 22.1 1.0
O B:HOH1015 3.9 25.4 1.0
CD2 B:HIS525 4.0 26.5 1.0
O B:HOH970 4.1 37.0 1.0
CG B:HIS563 4.2 22.4 1.0
CG B:HIS529 4.3 22.6 1.0
ND1 B:HIS529 4.3 21.8 1.0
CB B:ASP564 4.3 23.7 1.0
ND1 B:HIS563 4.3 23.5 1.0
NE2 B:HIS525 4.3 28.8 1.0
CB B:ASP674 4.4 23.4 1.0
O B:HOH947 4.5 21.6 1.0
CG2 B:VAL533 4.8 20.4 1.0
CA B:ASP674 4.8 22.9 1.0
O B:ASP674 4.9 23.3 1.0

Zinc binding site 3 out of 4 in 5se6

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Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine


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 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.4
occ:1.00
 O C:HOH981 2.0 24.2 1.0
NE2 C:HIS529 2.2 23.8 1.0
OD1 C:ASP674 2.2 24.0 1.0
NE2 C:HIS563 2.2 25.5 1.0
OD2 C:ASP564 2.2 24.1 1.0
O C:HOH969 2.4 39.0 1.0
CG C:ASP674 3.0 28.2 1.0
CD2 C:HIS563 3.0 24.1 1.0
CD2 C:HIS529 3.1 27.7 1.0
CG C:ASP564 3.2 23.4 1.0
CE1 C:HIS529 3.3 27.9 1.0
OD2 C:ASP674 3.3 35.8 1.0
CE1 C:HIS563 3.3 25.5 1.0
OD1 C:ASP564 3.6 23.7 1.0
MG C:MG802 3.8 26.0 1.0
O C:HOH1037 4.1 25.5 1.0
CD2 C:HIS525 4.1 32.0 1.0
CG C:HIS563 4.2 24.1 1.0
CG C:HIS529 4.2 26.3 1.0
ND1 C:HIS529 4.3 26.2 1.0
O C:HOH1018 4.3 45.7 1.0
ND1 C:HIS563 4.3 24.4 1.0
CB C:ASP564 4.3 23.2 1.0
NE2 C:HIS525 4.4 31.0 1.0
CB C:ASP674 4.4 29.9 1.0
O C:HOH1052 4.4 51.4 1.0
O C:HOH961 4.5 26.8 1.0
CG2 C:VAL533 4.8 24.5 1.0
CA C:ASP674 4.8 27.4 1.0
O C:ASP674 4.9 26.7 1.0

Zinc binding site 4 out of 4 in 5se6

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine


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 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.0
occ:1.00
 O D:HOH947 2.1 25.9 1.0
NE2 D:HIS563 2.1 25.9 1.0
NE2 D:HIS529 2.2 32.5 1.0
OD1 D:ASP674 2.2 30.1 1.0
OD2 D:ASP564 2.2 33.0 1.0
O D:HOH966 2.3 34.8 1.0
CD2 D:HIS563 3.0 29.1 1.0
CD2 D:HIS529 3.1 33.8 1.0
CG D:ASP564 3.1 26.9 1.0
CG D:ASP674 3.1 32.8 1.0
CE1 D:HIS529 3.2 31.3 1.0
CE1 D:HIS563 3.3 27.9 1.0
OD2 D:ASP674 3.3 36.3 1.0
OD1 D:ASP564 3.6 27.7 1.0
MG D:MG802 3.7 30.5 1.0
O D:HOH998 4.0 32.1 1.0
CD2 D:HIS525 4.0 37.2 1.0
CG D:HIS563 4.2 24.5 1.0
CG D:HIS529 4.2 32.7 1.0
CB D:ASP564 4.3 29.3 1.0
O D:HOH967 4.3 46.1 1.0
ND1 D:HIS563 4.3 26.4 1.0
ND1 D:HIS529 4.3 29.4 1.0
NE2 D:HIS525 4.4 37.0 1.0
CB D:ASP674 4.5 29.9 1.0
O D:HOH919 4.6 30.6 1.0
O D:ASP674 4.7 30.9 1.0
CG2 D:VAL533 4.7 33.0 1.0
CA D:ASP674 4.8 29.9 1.0

Reference:

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X
Page generated: Mon Oct 28 04:34:57 2024

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