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Zinc in PDB 5siv: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide, PDB code: 5siv 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) 41.27 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.665, 134.665, 233.615, 90, 90, 120
R / Rfree (%) 19.6 / 25.6

Other elements in 5siv:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide 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 N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide (pdb code 5siv). 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 N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide, PDB code: 5siv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5siv

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide


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 N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:31.6
occ:1.00
 OD2 A:ASP564 2.0 26.1 1.0
NE2 A:HIS563 2.0 25.6 1.0
NE2 A:HIS529 2.1 28.8 1.0
O A:HOH932 2.1 28.0 1.0
OD1 A:ASP674 2.1 33.1 1.0
O A:HOH983 2.3 32.7 1.0
CD2 A:HIS563 3.0 23.2 1.0
CE1 A:HIS529 3.0 27.8 1.0
CE1 A:HIS563 3.0 27.7 1.0
CG A:ASP674 3.0 32.4 1.0
CG A:ASP564 3.1 24.6 1.0
CD2 A:HIS529 3.1 27.9 1.0
OD2 A:ASP674 3.3 40.0 1.0
OD1 A:ASP564 3.7 25.4 1.0
MG A:MG802 3.8 27.7 1.0
ND1 A:HIS563 4.1 26.6 1.0
CG A:HIS563 4.1 24.5 1.0
ND1 A:HIS529 4.1 27.6 1.0
O A:HOH993 4.1 22.1 1.0
CD2 A:HIS525 4.2 34.1 1.0
CB A:ASP564 4.2 23.5 1.0
CG A:HIS529 4.2 26.5 1.0
CB A:ASP674 4.4 31.3 1.0
NE2 A:HIS525 4.5 35.5 1.0
O A:HOH958 4.6 23.0 1.0
CG2 A:VAL533 4.7 23.5 1.0
CA A:ASP674 4.8 28.5 1.0
O A:ASP674 4.8 30.1 1.0

Zinc binding site 2 out of 4 in 5siv

Go back to Zinc Binding Sites List in 5siv
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide


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 N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:30.1
occ:1.00
 OD2 B:ASP564 2.0 24.7 1.0
NE2 B:HIS563 2.0 24.9 1.0
O B:HOH918 2.1 22.9 1.0
OD1 B:ASP674 2.1 26.1 1.0
NE2 B:HIS529 2.2 24.0 1.0
O B:HOH971 2.5 38.6 1.0
CG B:ASP674 3.0 26.0 1.0
CD2 B:HIS563 3.0 22.6 1.0
CG B:ASP564 3.1 21.6 1.0
CE1 B:HIS563 3.1 23.4 1.0
CE1 B:HIS529 3.1 25.7 1.0
OD2 B:ASP674 3.2 28.2 1.0
CD2 B:HIS529 3.3 26.1 1.0
OD1 B:ASP564 3.6 23.2 1.0
MG B:MG802 3.7 20.0 1.0
O B:HOH976 3.9 33.4 1.0
O B:HOH995 4.0 22.0 1.0
CG B:HIS563 4.1 22.8 1.0
ND1 B:HIS563 4.1 21.5 1.0
CD2 B:HIS525 4.2 27.6 1.0
CB B:ASP564 4.3 22.6 1.0
ND1 B:HIS529 4.3 26.0 1.0
CB B:ASP674 4.4 26.0 1.0
CG B:HIS529 4.4 24.8 1.0
O B:HOH948 4.5 23.8 1.0
NE2 B:HIS525 4.6 30.8 1.0
O B:ASP674 4.8 28.1 1.0
CG2 B:VAL533 4.8 22.2 1.0
CA B:ASP674 4.8 25.2 1.0

Zinc binding site 3 out of 4 in 5siv

Go back to Zinc Binding Sites List in 5siv
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide


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 N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.1
occ:1.00
 O C:HOH936 2.0 22.6 1.0
OD2 C:ASP564 2.1 23.6 1.0
OD1 C:ASP674 2.1 27.3 1.0
NE2 C:HIS563 2.2 25.5 1.0
NE2 C:HIS529 2.2 23.4 1.0
O C:HOH990 2.2 37.1 1.0
CG C:ASP674 3.0 28.4 1.0
CD2 C:HIS563 3.0 23.6 1.0
CG C:ASP564 3.1 23.8 1.0
CE1 C:HIS529 3.1 25.6 1.0
OD2 C:ASP674 3.2 32.5 1.0
CD2 C:HIS529 3.2 24.5 1.0
CE1 C:HIS563 3.3 23.1 1.0
OD1 C:ASP564 3.6 24.2 1.0
MG C:MG802 3.7 25.0 1.0
O C:HOH1003 4.0 28.9 1.0
CD2 C:HIS525 4.2 36.1 1.0
CG C:HIS563 4.2 24.6 1.0
ND1 C:HIS529 4.3 23.8 1.0
CB C:ASP564 4.3 23.9 1.0
ND1 C:HIS563 4.3 22.3 1.0
CG C:HIS529 4.3 24.0 1.0
CB C:ASP674 4.4 28.1 1.0
O C:HOH1020 4.4 48.8 1.0
O C:HOH925 4.5 24.0 1.0
NE2 C:HIS525 4.5 38.9 1.0
CA C:ASP674 4.7 28.0 1.0
CG2 C:VAL533 4.8 22.6 1.0
O C:ASP674 4.9 27.6 1.0

Zinc binding site 4 out of 4 in 5siv

Go back to Zinc Binding Sites List in 5siv
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide


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 N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:38.9
occ:1.00
 NE2 D:HIS563 2.1 30.9 1.0
OD2 D:ASP564 2.1 36.7 1.0
O D:HOH922 2.1 27.3 1.0
O D:HOH966 2.2 34.6 1.0
NE2 D:HIS529 2.2 36.7 1.0
OD1 D:ASP674 2.2 36.2 1.0
CD2 D:HIS563 2.8 35.5 1.0
CG D:ASP564 3.1 32.5 1.0
CG D:ASP674 3.1 36.3 1.0
CD2 D:HIS529 3.1 36.0 1.0
CE1 D:HIS529 3.2 34.4 1.0
CE1 D:HIS563 3.2 32.1 1.0
OD2 D:ASP674 3.2 38.6 1.0
OD1 D:ASP564 3.6 32.7 1.0
O D:HOH957 3.9 42.0 1.0
MG D:MG802 3.9 39.9 1.0
CG D:HIS563 4.1 30.1 1.0
O D:HOH968 4.1 38.2 1.0
CB D:ASP564 4.1 30.8 1.0
ND1 D:HIS563 4.2 30.2 1.0
CD2 D:HIS525 4.3 44.6 1.0
CG D:HIS529 4.3 34.2 1.0
ND1 D:HIS529 4.3 36.8 1.0
CB D:ASP674 4.5 37.7 1.0
O D:HOH935 4.5 33.1 1.0
CG2 D:VAL533 4.7 31.1 1.0
O D:ASP674 4.8 40.5 1.0
NE2 D:HIS525 4.8 42.3 1.0
CA D:ASP674 4.9 36.4 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 05:52:52 2024

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