Atomistry » Sodium » PDB 4oci-4owc » 4oqv
Atomistry »
  Sodium »
    PDB 4oci-4owc »
      4oqv »

Sodium in PDB 4oqv: High Resolution Crystal Structure of Human Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4-(Trifluoromethyl) Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2,4]Triazolo[1,5-A]Pyrimidin- 7-Amine)

Enzymatic activity of High Resolution Crystal Structure of Human Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4-(Trifluoromethyl) Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2,4]Triazolo[1,5-A]Pyrimidin- 7-Amine)

All present enzymatic activity of High Resolution Crystal Structure of Human Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4-(Trifluoromethyl) Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2,4]Triazolo[1,5-A]Pyrimidin- 7-Amine):
1.3.5.2;

Protein crystallography data

The structure of High Resolution Crystal Structure of Human Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4-(Trifluoromethyl) Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2,4]Triazolo[1,5-A]Pyrimidin- 7-Amine), PDB code: 4oqv was solved by X.Deng, M.A.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.23
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.936, 90.936, 121.938, 90.00, 90.00, 120.00
R / Rfree (%) 14.1 / 15.7

Other elements in 4oqv:

The structure of High Resolution Crystal Structure of Human Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4-(Trifluoromethyl) Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2,4]Triazolo[1,5-A]Pyrimidin- 7-Amine) also contains other interesting chemical elements:

Fluorine (F) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution Crystal Structure of Human Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4-(Trifluoromethyl) Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2,4]Triazolo[1,5-A]Pyrimidin- 7-Amine) (pdb code 4oqv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the High Resolution Crystal Structure of Human Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4-(Trifluoromethyl) Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2,4]Triazolo[1,5-A]Pyrimidin- 7-Amine), PDB code: 4oqv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4oqv

Go back to Sodium Binding Sites List in 4oqv
Sodium binding site 1 out of 2 in the High Resolution Crystal Structure of Human Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4-(Trifluoromethyl) Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2,4]Triazolo[1,5-A]Pyrimidin- 7-Amine)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution Crystal Structure of Human Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4-(Trifluoromethyl) Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2,4]Triazolo[1,5-A]Pyrimidin- 7-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:36.5
occ:1.00
 NA A:NA509 2.5 44.1 1.0
O A:HOH650 2.9 17.7 1.0
NE2 A:GLN166 3.2 23.1 1.0
CE1 A:HIS248 3.6 11.2 1.0
OE1 A:GLN166 3.9 27.4 1.0
CD A:GLN166 4.0 22.0 1.0
NE2 A:GLN165 4.0 12.8 1.0
CG A:GLN165 4.2 10.9 1.0
NE2 A:HIS248 4.2 12.4 1.0
CD A:GLN165 4.3 11.4 1.0
CG1 A:VAL247 4.3 13.3 0.5
O A:HOH933 4.3 88.4 1.0
O A:HOH660 4.5 19.2 1.0
O A:HOH642 4.5 14.6 1.0
ND1 A:HIS248 4.5 11.1 1.0
CB A:ALA169 4.7 14.3 1.0

Sodium binding site 2 out of 2 in 4oqv

Go back to Sodium Binding Sites List in 4oqv
Sodium binding site 2 out of 2 in the High Resolution Crystal Structure of Human Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4-(Trifluoromethyl) Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2,4]Triazolo[1,5-A]Pyrimidin- 7-Amine)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Resolution Crystal Structure of Human Dihydroorotate Dehydrogenase Bound with DSM338 (N-[3,5-Difluoro-4-(Trifluoromethyl) Phenyl]-5-Methyl-2-(Trifluoromethyl)[1,2,4]Triazolo[1,5-A]Pyrimidin- 7-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na509

b:44.1
occ:1.00
 NA A:NA507 2.5 36.5 1.0
CE1 A:HIS248 3.3 11.2 1.0
O A:HOH933 3.3 88.4 1.0
NE2 A:HIS248 3.3 12.4 1.0
NE2 A:GLN166 3.4 23.1 1.0
O A:HOH911 3.6 42.1 1.0
O1 A:SO4508 3.6 30.3 1.0
NE2 A:GLN165 4.3 12.8 1.0
O A:HOH674 4.4 19.2 1.0
CD A:GLN166 4.5 22.0 1.0
ND1 A:HIS248 4.6 11.1 1.0
CD A:GLN165 4.6 11.4 1.0
CD2 A:HIS248 4.7 11.5 1.0
O A:HOH650 4.7 17.7 1.0
CG1 A:VAL247 4.8 13.3 0.5
OE1 A:GLN166 4.8 27.4 1.0
OE1 A:GLN165 4.9 12.8 1.0
O A:HOH891 4.9 53.8 1.0
O4 A:SO4508 5.0 41.1 1.0

Reference:

X.Deng, S.Kokkonda, F.El Mazouni, J.White, J.N.Burrows, W.Kaminsky, S.A.Charman, D.Matthews, P.K.Rathod, M.A.Phillips. Fluorine Modulates Species Selectivity in the Triazolopyrimidine Class of Plasmodium Falciparum Dihydroorotate Dehydrogenase Inhibitors. J.Med.Chem. V. 57 5381 2014.
ISSN: ISSN 0022-2623
PubMed: 24801997
DOI: 10.1021/JM500481T
Page generated: Tue Dec 15 06:57:10 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy