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Zinc in PDB 5sek: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline, PDB code: 5sek 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) 43.63 / 2.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.629, 135.629, 236.677, 90, 90, 120
R / Rfree (%) 16.4 / 19.7

Other elements in 5sek:

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

Zinc binding site 1 out of 4 in 5sek

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline


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- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:33.8
occ:1.00
 OD2 A:ASP564 2.1 29.1 1.0
NE2 A:HIS563 2.1 27.3 1.0
O A:HOH1010 2.1 34.8 1.0
NE2 A:HIS529 2.1 28.4 1.0
OD1 A:ASP674 2.2 35.4 1.0
O A:HOH942 2.2 29.8 1.0
CE1 A:HIS563 3.0 27.1 1.0
CE1 A:HIS529 3.0 28.7 1.0
CD2 A:HIS563 3.1 26.8 1.0
CG A:ASP674 3.1 33.3 1.0
CG A:ASP564 3.1 28.7 1.0
CD2 A:HIS529 3.1 28.9 1.0
OD2 A:ASP674 3.4 34.1 1.0
OD1 A:ASP564 3.7 27.5 1.0
MG A:MG802 3.8 27.1 1.0
O A:HOH999 4.0 26.6 1.0
ND1 A:HIS563 4.1 27.4 1.0
CG A:HIS563 4.2 27.1 1.0
ND1 A:HIS529 4.2 26.9 1.0
CG A:HIS529 4.2 29.0 1.0
CD2 A:HIS525 4.3 29.0 1.0
CB A:ASP564 4.3 27.5 1.0
O A:HOH998 4.3 32.8 1.0
CB A:ASP674 4.4 32.8 1.0
O A:HOH929 4.5 28.9 1.0
NE2 A:HIS525 4.6 29.5 1.0
CG2 A:VAL533 4.7 27.5 1.0
O A:HOH1037 4.7 48.1 1.0
CA A:ASP674 4.8 30.8 1.0
O A:ASP674 4.8 31.3 1.0

Zinc binding site 2 out of 4 in 5sek

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline


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- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:33.2
occ:1.00
 O B:HOH938 2.1 26.2 1.0
OD1 B:ASP674 2.1 28.4 1.0
NE2 B:HIS563 2.1 25.7 1.0
OD2 B:ASP564 2.2 24.1 1.0
NE2 B:HIS529 2.2 26.8 1.0
O B:HOH1002 2.2 37.7 1.0
CG B:ASP674 3.0 28.1 1.0
CD2 B:HIS563 3.0 26.7 1.0
CG B:ASP564 3.1 24.8 1.0
CE1 B:HIS563 3.2 26.1 1.0
CD2 B:HIS529 3.2 26.3 1.0
CE1 B:HIS529 3.2 28.4 1.0
OD2 B:ASP674 3.3 27.9 1.0
OD1 B:ASP564 3.6 25.2 1.0
MG B:MG802 3.9 23.1 1.0
O B:HOH995 4.1 28.6 1.0
CD2 B:HIS525 4.1 27.9 1.0
CG B:HIS563 4.2 25.7 1.0
ND1 B:HIS563 4.2 25.6 1.0
ND1 B:HIS529 4.3 27.0 1.0
O B:HOH1041 4.3 50.1 1.0
CG B:HIS529 4.3 26.8 1.0
CB B:ASP564 4.3 26.0 1.0
O B:HOH976 4.4 31.8 1.0
CB B:ASP674 4.4 28.3 1.0
NE2 B:HIS525 4.4 28.4 1.0
O B:HOH930 4.6 27.4 1.0
CG2 B:VAL533 4.7 29.3 1.0
CA B:ASP674 4.8 27.7 1.0
O B:ASP674 4.9 28.1 1.0

Zinc binding site 3 out of 4 in 5sek

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Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline


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- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:33.5
occ:1.00
 O C:HOH926 2.0 25.1 1.0
OD2 C:ASP564 2.1 25.9 1.0
NE2 C:HIS563 2.1 26.3 1.0
OD1 C:ASP674 2.2 28.5 1.0
NE2 C:HIS529 2.2 28.5 1.0
O C:HOH1010 2.3 44.5 1.0
CD2 C:HIS563 3.0 26.3 1.0
CD2 C:HIS529 3.1 27.8 1.0
CG C:ASP674 3.1 30.5 1.0
CG C:ASP564 3.1 26.6 1.0
CE1 C:HIS563 3.1 27.2 1.0
CE1 C:HIS529 3.3 29.0 1.0
OD2 C:ASP674 3.3 31.8 1.0
OD1 C:ASP564 3.7 27.2 1.0
MG C:MG802 3.8 27.3 1.0
CG C:HIS563 4.1 27.3 1.0
CD2 C:HIS525 4.2 29.6 1.0
ND1 C:HIS563 4.2 26.8 1.0
O C:HOH994 4.2 30.3 1.0
CB C:ASP564 4.3 26.6 1.0
CG C:HIS529 4.3 28.6 1.0
ND1 C:HIS529 4.4 27.9 1.0
CB C:ASP674 4.4 31.1 1.0
O C:HOH983 4.4 42.0 1.0
NE2 C:HIS525 4.5 29.5 1.0
O C:HOH945 4.5 32.5 1.0
O C:HOH1035 4.6 41.8 1.0
CG2 C:VAL533 4.7 32.7 1.0
CA C:ASP674 4.8 31.1 1.0
O C:ASP674 4.9 31.7 1.0

Zinc binding site 4 out of 4 in 5sek

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline


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- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:39.6
occ:1.00
 NE2 D:HIS563 2.1 32.8 1.0
O D:HOH925 2.1 28.9 1.0
OD1 D:ASP674 2.2 37.0 1.0
O D:HOH973 2.2 46.2 1.0
OD2 D:ASP564 2.2 38.5 1.0
NE2 D:HIS529 2.2 43.1 1.0
CD2 D:HIS563 2.9 33.6 1.0
CG D:ASP674 3.1 37.0 1.0
CE1 D:HIS563 3.1 34.0 1.0
CG D:ASP564 3.1 38.4 1.0
CD2 D:HIS529 3.1 44.2 1.0
CE1 D:HIS529 3.3 45.2 1.0
OD2 D:ASP674 3.3 37.0 1.0
OD1 D:ASP564 3.6 39.0 1.0
MG D:MG802 3.9 34.4 1.0
CG D:HIS563 4.1 34.2 1.0
O D:HOH911 4.1 44.2 1.0
ND1 D:HIS563 4.2 35.5 1.0
CB D:ASP564 4.3 37.8 1.0
CD2 D:HIS525 4.3 37.4 1.0
CG D:HIS529 4.3 41.5 1.0
O D:HOH976 4.3 34.5 1.0
ND1 D:HIS529 4.3 43.0 1.0
CB D:ASP674 4.4 37.9 1.0
O D:HOH906 4.4 32.4 1.0
NE2 D:HIS525 4.7 40.3 1.0
CG2 D:VAL533 4.7 37.4 1.0
O D:ASP674 4.8 37.7 1.0
CA D:ASP674 4.8 38.6 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: Fri Apr 7 21:47:00 2023

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