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Zinc in PDB 5se2: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline, PDB code: 5se2 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) 43.72 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.003, 135.003, 235.705, 90, 90, 120
R / Rfree (%) 19.4 / 22.1

Other elements in 5se2:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline 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-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline (pdb code 5se2). 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-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline, PDB code: 5se2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5se2

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


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

b:35.2
occ:1.00
 O A:HOH981 1.9 50.6 1.0
NE2 A:HIS563 2.1 30.4 1.0
OD2 A:ASP564 2.1 29.4 1.0
NE2 A:HIS529 2.2 38.1 1.0
OD1 A:ASP674 2.2 35.1 1.0
O A:HOH959 2.2 34.3 1.0
CD2 A:HIS563 3.0 29.6 1.0
CE1 A:HIS563 3.0 31.7 1.0
CG A:ASP674 3.1 34.9 1.0
CG A:ASP564 3.1 32.3 1.0
CE1 A:HIS529 3.1 37.6 1.0
CD2 A:HIS529 3.2 35.7 1.0
OD2 A:ASP674 3.3 34.8 1.0
OD1 A:ASP564 3.6 32.3 1.0
MG A:MG802 3.7 32.9 1.0
O A:HOH993 4.1 31.5 1.0
ND1 A:HIS563 4.1 31.4 1.0
CG A:HIS563 4.1 30.5 1.0
CD2 A:HIS525 4.2 37.9 1.0
ND1 A:HIS529 4.2 37.1 1.0
CG A:HIS529 4.3 35.2 1.0
CB A:ASP564 4.3 31.6 1.0
CB A:ASP674 4.4 34.9 1.0
O A:HOH949 4.4 41.2 1.0
NE2 A:HIS525 4.5 34.9 1.0
O A:HOH933 4.5 31.3 1.0
CG2 A:VAL533 4.7 30.8 1.0
O A:HOH1020 4.8 51.6 1.0
O A:ASP674 4.8 30.4 1.0
CA A:ASP674 4.8 32.9 1.0

Zinc binding site 2 out of 4 in 5se2

Go back to Zinc Binding Sites List in 5se2
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline


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

b:37.3
occ:1.00
 NE2 B:HIS563 2.0 29.5 1.0
O B:HOH965 2.0 32.7 1.0
O B:HOH940 2.1 39.8 1.0
NE2 B:HIS529 2.1 30.8 1.0
OD1 B:ASP674 2.2 36.4 1.0
OD2 B:ASP564 2.2 26.4 1.0
CD2 B:HIS563 3.0 29.6 1.0
CE1 B:HIS563 3.0 29.5 1.0
CD2 B:HIS529 3.1 31.0 1.0
CG B:ASP674 3.1 35.4 1.0
CG B:ASP564 3.2 29.2 1.0
CE1 B:HIS529 3.2 30.7 1.0
OD2 B:ASP674 3.4 34.2 1.0
OD1 B:ASP564 3.6 30.8 1.0
MG B:MG802 3.9 32.6 1.0
CD2 B:HIS525 4.1 31.4 1.0
ND1 B:HIS563 4.1 28.9 1.0
O B:HOH991 4.1 28.6 1.0
CG B:HIS563 4.1 29.5 1.0
CG B:HIS529 4.2 30.8 1.0
ND1 B:HIS529 4.2 29.7 1.0
O B:HOH964 4.3 44.6 1.0
CB B:ASP564 4.4 28.2 1.0
NE2 B:HIS525 4.4 30.9 1.0
CB B:ASP674 4.4 33.6 1.0
O B:HOH937 4.6 27.6 1.0
CG2 B:VAL533 4.7 32.2 1.0
O B:HOH976 4.7 61.5 1.0
CA B:ASP674 4.8 32.9 1.0
O B:ASP674 4.9 33.7 1.0

Zinc binding site 3 out of 4 in 5se2

Go back to Zinc Binding Sites List in 5se2
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline


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

b:40.0
occ:1.00
 O C:HOH976 1.9 34.1 1.0
NE2 C:HIS563 2.1 33.4 1.0
NE2 C:HIS529 2.2 35.9 1.0
O C:HOH981 2.2 43.8 1.0
OD2 C:ASP564 2.2 34.1 1.0
OD1 C:ASP674 2.2 33.9 1.0
CD2 C:HIS563 3.0 31.0 1.0
CD2 C:HIS529 3.1 36.1 1.0
CE1 C:HIS563 3.1 34.5 1.0
CG C:ASP674 3.2 34.6 1.0
CE1 C:HIS529 3.2 35.5 1.0
CG C:ASP564 3.2 31.7 1.0
OD2 C:ASP674 3.5 37.3 1.0
OD1 C:ASP564 3.6 32.0 1.0
MG C:MG802 3.9 34.2 1.0
CD2 C:HIS525 4.1 35.2 1.0
O C:HOH1012 4.2 33.0 1.0
CG C:HIS563 4.2 31.6 1.0
ND1 C:HIS563 4.2 33.3 1.0
CG C:HIS529 4.3 34.2 1.0
ND1 C:HIS529 4.3 38.2 1.0
O C:HOH991 4.3 47.8 1.0
CB C:ASP564 4.4 30.9 1.0
NE2 C:HIS525 4.4 34.8 1.0
CB C:ASP674 4.5 35.8 1.0
O C:HOH933 4.7 36.1 1.0
O C:HOH1017 4.7 60.4 1.0
CG2 C:VAL533 4.7 32.8 1.0
CA C:ASP674 4.8 37.6 1.0
O C:ASP674 5.0 32.7 1.0

Zinc binding site 4 out of 4 in 5se2

Go back to Zinc Binding Sites List in 5se2
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline


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

b:48.3
occ:1.00
 O D:HOH917 2.0 37.3 1.0
NE2 D:HIS563 2.1 37.2 1.0
OD2 D:ASP564 2.2 51.8 1.0
OD1 D:ASP674 2.2 45.3 1.0
NE2 D:HIS529 2.2 49.4 1.0
O D:HOH932 2.2 44.4 1.0
CD2 D:HIS563 2.9 38.9 1.0
CG D:ASP674 3.0 46.1 1.0
CG D:ASP564 3.1 42.5 1.0
CD2 D:HIS529 3.2 53.2 1.0
CE1 D:HIS563 3.2 36.7 1.0
OD2 D:ASP674 3.2 43.4 1.0
CE1 D:HIS529 3.3 53.1 1.0
OD1 D:ASP564 3.7 40.9 1.0
MG D:MG802 3.9 42.5 1.0
CG D:HIS563 4.1 36.1 1.0
O D:HOH927 4.1 40.7 1.0
CD2 D:HIS525 4.2 47.9 1.0
ND1 D:HIS563 4.2 35.6 1.0
O D:HOH956 4.2 41.6 1.0
CB D:ASP564 4.3 42.6 1.0
CG D:HIS529 4.3 47.0 1.0
ND1 D:HIS529 4.3 49.8 1.0
CB D:ASP674 4.4 46.3 1.0
NE2 D:HIS525 4.5 50.2 1.0
O D:HOH920 4.6 44.1 1.0
CG2 D:VAL533 4.7 41.0 1.0
O D:ASP674 4.7 42.7 1.0
CA D:ASP674 4.9 44.9 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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