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Magnesium in PDB 5sfc: Crystal Structure of Human Phosphodiesterase 10 in Complex with

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with, PDB code: 5sfc was solved by C.Joseph, J.U.Peters, 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) 43.51 / 2.18
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.257, 135.257, 235.691, 90, 90, 120
R / Rfree (%) 18.3 / 23.1

Other elements in 5sfc:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with (pdb code 5sfc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with, PDB code: 5sfc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sfc

Go back to Magnesium Binding Sites List in 5sfc
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Phosphodiesterase 10 in Complex with within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:31.5
occ:1.00
 O A:HOH991 2.0 29.8 1.0
O A:HOH926 2.0 25.6 1.0
OD1 A:ASP564 2.1 28.5 1.0
O A:HOH945 2.1 28.9 1.0
O A:HOH931 2.1 34.2 1.0
O A:HOH943 2.2 28.0 1.0
CG A:ASP564 3.1 30.2 1.0
OD2 A:ASP564 3.5 33.4 1.0
ZN A:ZN801 3.9 34.3 1.0
OE2 A:GLU592 3.9 39.4 1.0
NE2 A:HIS595 4.0 32.5 1.0
O A:HOH968 4.1 40.4 1.0
CD2 A:HIS567 4.2 34.8 1.0
O A:HOH975 4.2 48.7 1.0
OG1 A:THR633 4.3 36.5 1.0
CD2 A:HIS595 4.4 31.2 1.0
NE2 A:HIS567 4.4 31.5 1.0
O A:HIS563 4.4 33.1 1.0
CB A:ASP564 4.5 28.7 1.0
CD2 A:HIS563 4.5 27.7 1.0
O A:THR633 4.5 36.0 1.0
OD2 A:ASP674 4.5 42.2 1.0
CD2 A:HIS525 4.7 35.2 1.0
CG A:GLU592 4.7 35.0 1.0
NE2 A:HIS525 4.8 34.3 1.0
CD A:GLU592 4.8 37.8 1.0
CB A:THR633 4.8 32.5 1.0
NE2 A:HIS563 4.8 26.2 1.0
CA A:ASP564 4.8 32.1 1.0

Magnesium binding site 2 out of 4 in 5sfc

Go back to Magnesium Binding Sites List in 5sfc
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Phosphodiesterase 10 in Complex with within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:28.6
occ:1.00
 O B:HOH943 1.9 22.5 1.0
O B:HOH920 1.9 29.7 1.0
O B:HOH983 2.0 27.6 1.0
OD1 B:ASP564 2.1 29.3 1.0
O B:HOH909 2.1 23.9 1.0
O B:HOH946 2.1 22.8 1.0
CG B:ASP564 3.1 28.4 1.0
OD2 B:ASP564 3.5 29.6 1.0
ZN B:ZN801 3.8 34.1 1.0
O B:HOH975 4.0 38.1 1.0
OE2 B:GLU592 4.0 36.6 1.0
NE2 B:HIS595 4.1 29.9 1.0
CD2 B:HIS563 4.2 28.9 1.0
O B:HIS563 4.2 31.5 1.0
CD2 B:HIS567 4.3 29.1 1.0
OG1 B:THR633 4.3 31.1 1.0
OD2 B:ASP674 4.3 36.7 1.0
CD2 B:HIS595 4.3 31.2 1.0
O B:HOH970 4.3 41.5 1.0
CB B:ASP564 4.4 27.6 1.0
NE2 B:HIS567 4.4 29.9 1.0
O B:THR633 4.5 32.5 1.0
NE2 B:HIS563 4.6 27.3 1.0
CD2 B:HIS525 4.6 34.0 1.0
CB B:THR633 4.7 32.8 1.0
NE2 B:HIS525 4.8 33.5 1.0
CA B:ASP564 4.8 28.6 1.0
CD B:GLU592 4.8 34.8 1.0
CG B:GLU592 4.8 35.9 1.0

Magnesium binding site 3 out of 4 in 5sfc

Go back to Magnesium Binding Sites List in 5sfc
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Phosphodiesterase 10 in Complex with within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:31.3
occ:1.00
 O C:HOH951 1.9 27.1 1.0
O C:HOH936 2.0 37.5 1.0
O C:HOH995 2.0 29.2 1.0
O C:HOH947 2.1 27.0 1.0
OD1 C:ASP564 2.1 30.2 1.0
O C:HOH932 2.1 30.8 1.0
CG C:ASP564 3.2 33.1 1.0
OD2 C:ASP564 3.6 35.0 1.0
ZN C:ZN801 3.8 38.5 1.0
NE2 C:HIS595 4.0 35.7 1.0
O C:HOH975 4.0 40.0 1.0
OE2 C:GLU592 4.1 37.9 1.0
CD2 C:HIS563 4.2 29.4 1.0
CD2 C:HIS567 4.2 33.6 1.0
OG1 C:THR633 4.3 37.7 1.0
CD2 C:HIS595 4.3 33.4 1.0
OD2 C:ASP674 4.4 34.2 1.0
NE2 C:HIS567 4.4 34.9 1.0
O C:HOH978 4.4 41.6 1.0
O C:HIS563 4.4 33.8 1.0
O C:THR633 4.4 33.8 1.0
CB C:ASP564 4.5 28.7 1.0
NE2 C:HIS563 4.5 30.6 1.0
CB C:THR633 4.7 36.8 1.0
CD2 C:HIS525 4.8 41.5 1.0
CA C:ASP564 4.8 30.3 1.0
CG C:GLU592 4.8 33.5 1.0
NE2 C:HIS525 4.9 41.9 1.0
CD C:GLU592 4.9 35.6 1.0

Magnesium binding site 4 out of 4 in 5sfc

Go back to Magnesium Binding Sites List in 5sfc
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Phosphodiesterase 10 in Complex with within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:43.0
occ:1.00
 O D:HOH939 2.1 38.5 1.0
O D:HOH911 2.1 30.2 1.0
O D:HOH929 2.1 38.6 1.0
O D:HOH928 2.1 41.0 1.0
O D:HOH941 2.1 32.3 1.0
OD1 D:ASP564 2.2 46.8 1.0
CG D:ASP564 3.2 40.1 1.0
OD2 D:ASP564 3.5 50.2 1.0
O D:HOH947 3.8 42.7 1.0
O D:HOH942 3.8 46.6 1.0
ZN D:ZN801 3.9 47.8 1.0
OE2 D:GLU592 4.0 44.6 1.0
NE2 D:HIS595 4.1 45.2 1.0
CD2 D:HIS567 4.2 45.6 1.0
NE2 D:HIS567 4.3 42.6 1.0
OG1 D:THR633 4.4 44.5 1.0
CD2 D:HIS595 4.4 45.9 1.0
OD2 D:ASP674 4.5 44.9 1.0
CD2 D:HIS563 4.5 36.3 1.0
CB D:ASP564 4.5 40.0 1.0
O D:HIS563 4.6 37.7 1.0
CD2 D:HIS525 4.6 48.1 1.0
O D:THR633 4.7 48.6 1.0
NE2 D:HIS525 4.7 45.4 1.0
NE2 D:HIS563 4.8 37.8 1.0
CB D:THR633 4.8 43.9 1.0
CD D:GLU592 4.8 46.3 1.0
CG D:GLU592 4.9 48.2 1.0
CA D:ASP564 4.9 37.9 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 Sep 30 03:33:04 2024

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