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Zinc in PDB 5sec: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline, PDB code: 5sec 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) 43.80 / 2.03
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.753, 135.753, 235.97, 90, 90, 120
R / Rfree (%) 18.1 / 22.5

Other elements in 5sec:

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

Zinc binding site 1 out of 4 in 5sec

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


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- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:35.1
occ:1.00
 O A:HOH954 2.1 28.2 1.0
OD2 A:ASP564 2.1 32.8 1.0
NE2 A:HIS529 2.1 36.1 1.0
NE2 A:HIS563 2.2 26.3 1.0
O A:HOH965 2.2 35.2 1.0
OD1 A:ASP674 2.3 33.9 1.0
CD2 A:HIS563 3.1 27.1 1.0
CE1 A:HIS529 3.1 30.4 1.0
CD2 A:HIS529 3.1 31.6 1.0
CG A:ASP674 3.1 35.3 1.0
CG A:ASP564 3.2 31.2 1.0
CE1 A:HIS563 3.2 30.3 1.0
OD2 A:ASP674 3.4 34.7 1.0
OD1 A:ASP564 3.6 29.4 1.0
MG A:MG802 3.8 29.7 1.0
O A:HOH984 4.0 29.2 1.0
CD2 A:HIS525 4.1 33.4 1.0
O A:HOH927 4.2 36.5 1.0
ND1 A:HIS529 4.2 31.9 1.0
CG A:HIS563 4.2 29.3 1.0
CG A:HIS529 4.3 31.5 1.0
ND1 A:HIS563 4.3 29.6 1.0
CB A:ASP564 4.4 29.2 1.0
NE2 A:HIS525 4.5 32.2 1.0
CB A:ASP674 4.5 34.1 1.0
O A:HOH912 4.6 25.1 1.0
CG2 A:VAL533 4.8 24.7 1.0
O A:ASP674 4.8 32.5 1.0
CA A:ASP674 4.9 29.3 1.0

Zinc binding site 2 out of 4 in 5sec

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


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- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:32.6
occ:1.00
 OD1 B:ASP674 2.1 27.0 1.0
O B:HOH938 2.1 23.0 1.0
OD2 B:ASP564 2.2 28.1 1.0
NE2 B:HIS563 2.2 23.9 1.0
NE2 B:HIS529 2.2 22.6 1.0
O B:HOH958 2.3 37.0 1.0
CG B:ASP674 3.0 30.4 1.0
CD2 B:HIS563 3.1 26.5 1.0
CD2 B:HIS529 3.1 28.0 1.0
CG B:ASP564 3.2 30.5 1.0
OD2 B:ASP674 3.2 31.9 1.0
CE1 B:HIS563 3.3 27.1 1.0
CE1 B:HIS529 3.3 29.1 1.0
OD1 B:ASP564 3.6 29.1 1.0
MG B:MG802 3.7 27.5 1.0
O B:HOH986 4.0 26.3 1.0
CD2 B:HIS525 4.1 29.8 1.0
O B:HOH960 4.1 34.8 1.0
O B:HOH998 4.2 52.9 1.0
CG B:HIS563 4.2 26.5 1.0
CG B:HIS529 4.3 26.4 1.0
ND1 B:HIS563 4.3 24.8 1.0
NE2 B:HIS525 4.3 34.1 1.0
CB B:ASP564 4.4 27.6 1.0
ND1 B:HIS529 4.4 23.3 1.0
CB B:ASP674 4.4 30.7 1.0
O B:HOH940 4.6 27.2 1.0
CG2 B:VAL533 4.8 22.9 1.0
CA B:ASP674 4.8 26.8 1.0
O B:ASP674 4.9 28.8 1.0

Zinc binding site 3 out of 4 in 5sec

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


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- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:34.4
occ:1.00
 O C:HOH935 2.1 27.2 1.0
NE2 C:HIS529 2.2 30.3 1.0
OD2 C:ASP564 2.2 30.2 1.0
NE2 C:HIS563 2.2 28.1 1.0
OD1 C:ASP674 2.3 27.5 1.0
O C:HOH978 2.3 38.4 1.0
CD2 C:HIS563 3.0 26.2 1.0
CD2 C:HIS529 3.1 31.5 1.0
CG C:ASP674 3.1 28.1 1.0
CG C:ASP564 3.2 30.3 1.0
CE1 C:HIS529 3.2 35.1 1.0
OD2 C:ASP674 3.2 36.1 1.0
CE1 C:HIS563 3.3 24.6 1.0
OD1 C:ASP564 3.6 28.1 1.0
MG C:MG802 3.8 29.1 1.0
O C:HOH991 4.0 32.0 1.0
CD2 C:HIS525 4.1 29.0 1.0
CG C:HIS563 4.2 24.9 1.0
CG C:HIS529 4.3 29.3 1.0
ND1 C:HIS529 4.3 28.6 1.0
O C:HOH983 4.3 35.9 1.0
ND1 C:HIS563 4.3 29.5 1.0
CB C:ASP564 4.4 27.4 1.0
O C:HOH1011 4.4 42.7 1.0
NE2 C:HIS525 4.4 34.5 1.0
CB C:ASP674 4.5 31.9 1.0
O C:HOH925 4.5 29.3 1.0
CG2 C:VAL533 4.8 27.5 1.0
CA C:ASP674 4.9 33.4 1.0
O C:ASP674 5.0 30.3 1.0

Zinc binding site 4 out of 4 in 5sec

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


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- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:42.2
occ:1.00
 O D:HOH929 2.0 30.3 1.0
NE2 D:HIS563 2.2 29.8 1.0
NE2 D:HIS529 2.2 38.5 1.0
OD2 D:ASP564 2.2 43.5 1.0
OD1 D:ASP674 2.3 35.5 1.0
O D:HOH926 2.4 43.1 1.0
CD2 D:HIS563 3.0 32.0 1.0
CG D:ASP674 3.1 36.3 1.0
CD2 D:HIS529 3.1 38.8 1.0
CG D:ASP564 3.2 37.5 1.0
CE1 D:HIS529 3.2 39.9 1.0
OD2 D:ASP674 3.3 45.3 1.0
CE1 D:HIS563 3.3 36.1 1.0
OD1 D:ASP564 3.7 35.7 1.0
MG D:MG802 3.7 38.4 1.0
O D:HOH944 4.1 38.4 1.0
CD2 D:HIS525 4.1 38.4 1.0
O D:HOH925 4.1 45.9 1.0
CG D:HIS563 4.2 32.1 1.0
CG D:HIS529 4.3 34.5 1.0
ND1 D:HIS529 4.3 37.6 1.0
ND1 D:HIS563 4.4 34.4 1.0
CB D:ASP564 4.4 37.1 1.0
NE2 D:HIS525 4.4 46.6 1.0
CB D:ASP674 4.5 35.9 1.0
O D:HOH902 4.6 37.5 1.0
CG2 D:VAL533 4.7 40.3 1.0
O D:ASP674 4.8 42.1 1.0
CA D:ASP674 4.9 34.2 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 21:37:53 2023

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