Atomistry » Sodium » PDB 5oqw-5pol » 5p8w
Atomistry »
  Sodium »
    PDB 5oqw-5pol »
      5p8w »

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

Go back to Sodium Binding Sites List in 5p8w
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

Go back to Sodium Binding Sites List in 5p8w
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

Go back to Sodium Binding Sites List in 5p8w
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

Go back to Sodium Binding Sites List in 5p8w
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

Go back to Sodium Binding Sites List in 5p8w
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy