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Sodium in PDB 5p8w: Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine

Enzymatic activity of Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine

All present enzymatic activity of Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine:
2.1.1.6;

Protein crystallography data

The structure of Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine, PDB code: 5p8w was solved by A.Ehler, C.Lerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.64 / 2.03
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 94.931, 176.379, 119.600, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine (pdb code 5p8w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine, PDB code: 5p8w:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5p8w

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Sodium binding site 1 out of 5 in the Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:47.4
occ:1.00
 OD1 A:ASN170 2.3 36.8 1.0
OD1 A:ASP141 2.4 42.9 1.0
OD1 A:ASN41 2.4 59.8 1.0
O A:HOH489 2.5 51.6 1.0
OD2 A:ASP169 2.6 43.8 1.0
OD2 A:ASP141 2.7 44.4 1.0
O A:HOH472 2.7 43.1 1.0
CG A:ASP141 2.9 43.6 1.0
CG A:ASN170 3.3 36.1 1.0
CG A:ASN41 3.4 60.4 1.0
CG A:ASP169 3.6 42.0 1.0
ND2 A:ASN170 3.7 34.8 1.0
ND2 A:ASN41 3.8 60.9 1.0
NZ A:LYS144 4.0 37.2 1.0
O A:ASN41 4.0 53.7 1.0
CB A:ASP169 4.3 25.6 1.0
OH A:TYR68 4.3 49.3 1.0
OD1 A:ASP169 4.4 36.2 1.0
CB A:ASP141 4.4 34.1 1.0
C A:ASN41 4.5 55.0 1.0
CB A:ASN41 4.6 47.8 1.0
CB A:ASN170 4.6 29.0 1.0
CG2 A:VAL42 4.7 42.4 1.0
CA A:ASN41 4.7 54.8 1.0
CZ A:TYR68 4.8 47.8 1.0
O C:HOH462 4.8 63.0 1.0
O A:ASP141 4.9 34.3 1.0
CE A:LYS144 5.0 38.1 1.0

Sodium binding site 2 out of 5 in 5p8w

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Sodium binding site 2 out of 5 in the Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:35.5
occ:1.00
 O A:SER186 2.3 39.0 1.0
O A:PHE189 2.4 38.7 1.0
O A:HOH531 2.4 34.7 1.0
O A:VAL183 2.5 35.1 1.0
O A:ARG184 2.6 31.6 1.0
C A:ARG184 3.2 34.0 1.0
C A:SER186 3.4 43.3 1.0
CA A:ARG184 3.5 30.6 1.0
C A:PHE189 3.5 37.8 1.0
C A:VAL183 3.6 36.5 1.0
N A:SER186 3.6 36.5 1.0
O A:HOH520 3.9 49.2 1.0
CA A:SER186 4.1 36.0 1.0
N A:ARG184 4.1 27.8 1.0
N A:GLY185 4.1 32.8 1.0
C A:GLY185 4.1 38.2 1.0
CA A:PHE189 4.2 35.8 1.0
N A:PHE189 4.3 36.9 1.0
CB A:PHE189 4.3 34.9 1.0
SG A:CYS191 4.3 36.7 1.0
N A:SER187 4.4 38.4 1.0
CA A:GLY185 4.6 33.7 1.0
N A:GLU190 4.6 34.1 1.0
O A:GLY185 4.7 36.9 1.0
CA A:SER187 4.7 41.0 1.0
CB A:SER186 4.7 39.7 1.0
CA A:GLU190 4.8 33.0 1.0
CB A:ARG184 4.9 30.2 1.0
CA A:VAL183 4.9 37.0 1.0

Sodium binding site 3 out of 5 in 5p8w

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Sodium binding site 3 out of 5 in the Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:42.4
occ:1.00
 O B:PHE189 2.3 40.4 1.0
O B:SER186 2.3 45.9 1.0
O B:VAL183 2.4 37.2 1.0
O B:HOH496 2.4 47.0 1.0
O B:ARG184 2.5 41.0 1.0
O B:HOH489 2.5 42.1 1.0
C B:ARG184 3.1 40.6 1.0
C B:SER186 3.5 48.3 1.0
CA B:ARG184 3.5 40.8 1.0
C B:PHE189 3.5 43.5 1.0
C B:VAL183 3.5 37.4 1.0
N B:SER186 3.8 44.4 1.0
N B:ARG184 4.0 37.4 1.0
N B:GLY185 4.1 38.8 1.0
CA B:SER186 4.2 48.5 1.0
C B:GLY185 4.2 42.5 1.0
CA B:PHE189 4.2 42.8 1.0
N B:PHE189 4.2 39.9 1.0
CB B:PHE189 4.3 39.7 1.0
SG B:CYS191 4.3 41.5 1.0
N B:SER187 4.5 42.9 1.0
N B:GLU190 4.5 36.9 1.0
CA B:GLY185 4.6 43.5 1.0
CA B:SER187 4.7 42.8 1.0
CA B:GLU190 4.8 37.2 1.0
CA B:VAL183 4.8 30.8 1.0
O B:GLY185 4.8 45.5 1.0
CB B:SER186 4.8 43.2 1.0
CB B:ARG184 4.8 40.9 1.0

Sodium binding site 4 out of 5 in 5p8w

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Sodium binding site 4 out of 5 in the Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:68.9
occ:1.00
 OD1 B:ASN41 2.5 85.9 1.0
O B:LYS36 2.5 89.0 1.0
O B:CYS33 2.6 72.9 1.0
O B:ALA39 2.8 95.9 1.0
CG B:ASN41 3.5 87.2 1.0
C B:LYS36 3.5 96.7 1.0
C B:ALA39 3.7 93.4 1.0
C B:CYS33 3.8 65.4 1.0
O B:THR34 3.9 90.5 1.0
CB B:ALA39 3.9 95.8 1.0
ND2 B:ASN41 3.9 90.1 1.0
N B:ALA39 4.0 0.8 1.0
CA B:GLU37 4.1 0.8 1.0
CA B:ALA39 4.1 98.5 1.0
C B:THR34 4.2 83.4 1.0
CA B:THR34 4.2 76.8 1.0
N B:GLU37 4.2 0.8 1.0
C B:GLU37 4.3 0.2 1.0
O B:GLU37 4.4 0.5 1.0
N B:LYS36 4.5 89.1 1.0
N B:THR34 4.5 68.0 1.0
CA B:LYS36 4.6 90.7 1.0
N B:ASN41 4.7 86.2 1.0
CB B:ASN41 4.7 83.7 1.0
N B:MET40 4.9 89.4 1.0
CA B:CYS33 4.9 56.6 1.0
CA B:ASN41 4.9 82.1 1.0
C B:MET40 4.9 86.6 1.0
C B:GLN35 5.0 88.7 1.0
N B:TRP38 5.0 0.1 1.0

Sodium binding site 5 out of 5 in 5p8w

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Sodium binding site 5 out of 5 in the Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Comt in Complex with [5-(2,4-Dimethyl-1,3- Thiazol-5-Yl)-1H-Pyrazol-3-Yl]Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:39.0
occ:1.00
 O C:PHE189 2.4 45.4 1.0
O C:SER186 2.4 45.4 1.0
O C:VAL183 2.4 44.5 1.0
O C:ARG184 2.6 42.1 1.0
C C:ARG184 3.1 47.9 1.0
CA C:ARG184 3.4 42.2 1.0
C C:SER186 3.5 49.9 1.0
C C:VAL183 3.5 47.8 1.0
C C:PHE189 3.5 46.2 1.0
N C:SER186 3.8 48.8 1.0
N C:ARG184 3.9 44.4 1.0
N C:GLY185 4.1 40.5 1.0
CA C:SER186 4.2 52.0 1.0
CA C:PHE189 4.2 43.5 1.0
CB C:PHE189 4.2 44.4 1.0
C C:GLY185 4.2 47.6 1.0
N C:PHE189 4.3 42.2 1.0
SG C:CYS191 4.3 44.3 1.0
N C:SER187 4.5 47.5 1.0
N C:GLU190 4.6 44.2 1.0
CA C:GLY185 4.6 49.8 1.0
CB C:ARG184 4.7 39.4 1.0
CA C:SER187 4.8 47.1 1.0
CB C:SER186 4.8 56.0 1.0
CA C:VAL183 4.8 42.5 1.0
CA C:GLU190 4.8 44.8 1.0
O C:GLY185 4.9 46.8 1.0

Reference:

C.Lerner, M.G.Rudolph. Crystal Structure of Comt Complex To Be Published.
Page generated: Mon Oct 7 23:16:08 2024

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