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Magnesium in PDB 5sex: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide, PDB code: 5sex 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) 25.60 / 1.99
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.183, 135.183, 234.932, 90, 90, 120
R / Rfree (%) 18.4 / 21.8

Other elements in 5sex:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide 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 N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide (pdb code 5sex). 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 N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide, PDB code: 5sex:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sex

Go back to Magnesium Binding Sites List in 5sex
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide


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 N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:23.1
occ:1.00
 O A:HOH1011 1.9 25.2 1.0
O A:HOH938 1.9 21.3 1.0
O A:HOH942 2.0 23.0 1.0
OD1 A:ASP564 2.0 23.8 1.0
O A:HOH975 2.1 21.5 1.0
O A:HOH925 2.2 22.2 1.0
CG A:ASP564 3.0 24.5 1.0
OD2 A:ASP564 3.4 26.4 1.0
ZN A:ZN801 3.8 29.0 1.0
OE2 A:GLU592 4.0 30.6 1.0
NE2 A:HIS595 4.0 24.2 1.0
O A:HOH998 4.1 38.7 1.0
OG1 A:THR633 4.2 26.8 1.0
O A:HOH997 4.3 32.6 1.0
O A:HIS563 4.3 24.0 1.0
CD2 A:HIS595 4.3 24.2 1.0
CD2 A:HIS567 4.3 27.6 1.0
CD2 A:HIS563 4.3 23.4 1.0
CB A:ASP564 4.4 23.7 1.0
OD2 A:ASP674 4.4 30.5 1.0
NE2 A:HIS567 4.5 26.9 1.0
O A:THR633 4.6 27.8 1.0
CD2 A:HIS525 4.6 28.9 1.0
CB A:THR633 4.7 25.3 1.0
NE2 A:HIS563 4.7 24.6 1.0
CA A:ASP564 4.7 24.1 1.0
NE2 A:HIS525 4.8 29.4 1.0
CD A:GLU592 4.8 30.2 1.0
CG A:GLU592 4.8 28.9 1.0

Magnesium binding site 2 out of 4 in 5sex

Go back to Magnesium Binding Sites List in 5sex
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide


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 N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:21.1
occ:1.00
 O B:HOH915 2.0 16.8 1.0
O B:HOH959 2.0 21.8 1.0
O B:HOH1018 2.0 24.3 1.0
O B:HOH1013 2.0 19.2 1.0
OD1 B:ASP564 2.0 22.4 1.0
O B:HOH928 2.1 21.2 1.0
CG B:ASP564 3.1 22.2 1.0
OD2 B:ASP564 3.4 21.8 1.0
ZN B:ZN801 3.7 27.9 1.0
O B:HOH985 3.9 38.4 1.0
OE2 B:GLU592 4.0 29.9 1.0
NE2 B:HIS595 4.2 25.0 1.0
OG1 B:THR633 4.2 23.6 1.0
CD2 B:HIS563 4.2 21.8 1.0
O B:HOH992 4.2 30.4 1.0
OD2 B:ASP674 4.3 28.4 1.0
CD2 B:HIS567 4.3 25.4 1.0
O B:HIS563 4.3 24.2 1.0
CD2 B:HIS595 4.4 25.6 1.0
CB B:ASP564 4.4 22.1 1.0
NE2 B:HIS567 4.4 23.6 1.0
O B:THR633 4.5 26.2 1.0
NE2 B:HIS563 4.6 20.1 1.0
CD2 B:HIS525 4.6 26.5 1.0
CB B:THR633 4.7 25.4 1.0
NE2 B:HIS525 4.7 27.4 1.0
CA B:ASP564 4.7 22.5 1.0
CG B:GLU592 4.9 28.0 1.0
CD B:GLU592 4.9 28.1 1.0

Magnesium binding site 3 out of 4 in 5sex

Go back to Magnesium Binding Sites List in 5sex
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide


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 N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:22.0
occ:1.00
 O C:HOH991 2.0 21.7 1.0
OD1 C:ASP564 2.0 23.3 1.0
O C:HOH946 2.0 24.5 1.0
O C:HOH1024 2.1 21.6 1.0
O C:HOH965 2.1 27.1 1.0
O C:HOH952 2.2 22.7 1.0
CG C:ASP564 3.1 24.2 1.0
OD2 C:ASP564 3.5 24.6 1.0
ZN C:ZN801 3.8 29.0 1.0
OE2 C:GLU592 4.0 30.8 1.0
NE2 C:HIS595 4.1 26.5 1.0
O C:HOH1011 4.1 36.1 1.0
CD2 C:HIS567 4.1 30.2 1.0
O C:HOH980 4.2 33.2 1.0
CD2 C:HIS563 4.3 22.4 1.0
O C:HIS563 4.3 24.8 1.0
OG1 C:THR633 4.3 27.2 1.0
OD2 C:ASP674 4.4 30.9 1.0
NE2 C:HIS567 4.4 29.8 1.0
CD2 C:HIS595 4.4 24.9 1.0
CB C:ASP564 4.4 23.9 1.0
O C:THR633 4.6 27.4 1.0
CD2 C:HIS525 4.6 31.2 1.0
CA C:ASP564 4.8 24.8 1.0
NE2 C:HIS525 4.8 31.6 1.0
NE2 C:HIS563 4.8 23.5 1.0
CB C:THR633 4.8 25.9 1.0
CG C:GLU592 4.9 28.4 1.0
CD C:GLU592 4.9 30.4 1.0

Magnesium binding site 4 out of 4 in 5sex

Go back to Magnesium Binding Sites List in 5sex
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide


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 N- Methyl-6-[(6-Methylpyridine-2-Carbonyl)Amino]-2-Phenyl-3H- Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:33.6
occ:1.00
 O D:HOH977 2.0 31.2 1.0
O D:HOH967 2.1 24.8 1.0
O D:HOH928 2.1 33.8 1.0
OD1 D:ASP564 2.1 33.0 1.0
O D:HOH918 2.1 25.6 1.0
O D:HOH934 2.2 30.9 1.0
CG D:ASP564 3.1 31.8 1.0
OD2 D:ASP564 3.4 34.7 1.0
O D:HOH979 3.8 43.1 1.0
ZN D:ZN801 3.8 36.0 1.0
OE2 D:GLU592 4.0 39.3 1.0
O D:HOH975 4.1 38.2 1.0
NE2 D:HIS595 4.1 33.1 1.0
CD2 D:HIS567 4.2 38.6 1.0
OG1 D:THR633 4.2 32.8 1.0
CD2 D:HIS595 4.3 34.0 1.0
CD2 D:HIS563 4.4 29.6 1.0
NE2 D:HIS567 4.4 38.4 1.0
OD2 D:ASP674 4.4 37.2 1.0
O D:HIS563 4.4 32.1 1.0
CB D:ASP564 4.4 31.7 1.0
CD2 D:HIS525 4.6 38.7 1.0
O D:THR633 4.6 34.4 1.0
NE2 D:HIS525 4.7 38.2 1.0
NE2 D:HIS563 4.7 28.4 1.0
CB D:THR633 4.8 34.0 1.0
CA D:ASP564 4.8 31.0 1.0
CD D:GLU592 4.9 38.2 1.0
CG D:GLU592 4.9 37.4 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 03:27:16 2024

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