Atomistry » Sodium » PDB 4q3d-4qom » 4qfd
Atomistry »
  Sodium »
    PDB 4q3d-4qom »
      4qfd »

Sodium in PDB 4qfd: Co-Crystal Structure of Compound 2 (3-(7-Hydroxy-2-Oxo-4-Phenyl-2H- Chromen-6-Yl)Propanoic Acid) and Fad Bound to Human Daao at 2.85A

Enzymatic activity of Co-Crystal Structure of Compound 2 (3-(7-Hydroxy-2-Oxo-4-Phenyl-2H- Chromen-6-Yl)Propanoic Acid) and Fad Bound to Human Daao at 2.85A

All present enzymatic activity of Co-Crystal Structure of Compound 2 (3-(7-Hydroxy-2-Oxo-4-Phenyl-2H- Chromen-6-Yl)Propanoic Acid) and Fad Bound to Human Daao at 2.85A:
1.4.3.3;

Protein crystallography data

The structure of Co-Crystal Structure of Compound 2 (3-(7-Hydroxy-2-Oxo-4-Phenyl-2H- Chromen-6-Yl)Propanoic Acid) and Fad Bound to Human Daao at 2.85A, PDB code: 4qfd was solved by T.E.Edwards, L.Chun, T.L.Arakaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 2.85
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 86.490, 86.490, 187.970, 90.00, 90.00, 120.00
R / Rfree (%) 24.8 / 28.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Co-Crystal Structure of Compound 2 (3-(7-Hydroxy-2-Oxo-4-Phenyl-2H- Chromen-6-Yl)Propanoic Acid) and Fad Bound to Human Daao at 2.85A (pdb code 4qfd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Co-Crystal Structure of Compound 2 (3-(7-Hydroxy-2-Oxo-4-Phenyl-2H- Chromen-6-Yl)Propanoic Acid) and Fad Bound to Human Daao at 2.85A, PDB code: 4qfd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4qfd

Go back to Sodium Binding Sites List in 4qfd
Sodium binding site 1 out of 2 in the Co-Crystal Structure of Compound 2 (3-(7-Hydroxy-2-Oxo-4-Phenyl-2H- Chromen-6-Yl)Propanoic Acid) and Fad Bound to Human Daao at 2.85A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Co-Crystal Structure of Compound 2 (3-(7-Hydroxy-2-Oxo-4-Phenyl-2H- Chromen-6-Yl)Propanoic Acid) and Fad Bound to Human Daao at 2.85A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:60.9
occ:1.00
 O A:LEU122 2.5 75.6 1.0
O A:TYR128 2.6 83.2 1.0
O A:PHE125 2.9 77.1 1.0
C A:LEU122 3.5 75.1 1.0
O A:PRO126 3.6 88.6 1.0
C A:TYR128 3.8 84.2 1.0
C A:PHE125 3.9 76.8 1.0
C A:PRO126 4.0 85.4 1.0
CA A:PRO126 4.1 83.1 1.0
N A:ASP123 4.3 75.9 1.0
CB A:LEU122 4.3 76.2 1.0
CA A:ASP123 4.3 77.8 1.0
N A:PRO126 4.4 79.7 1.0
CA A:LEU122 4.4 74.2 1.0
N A:TYR128 4.4 84.4 1.0
CA A:GLY129 4.6 89.4 1.0
N A:GLY129 4.6 86.5 1.0
CA A:TYR128 4.7 83.6 1.0
C A:ASP123 4.8 76.0 1.0
N A:ASP127 4.9 85.2 1.0
N A:PHE125 4.9 73.8 1.0
OD1 A:ASP123 4.9 86.0 1.0
CA A:PHE125 4.9 74.3 1.0
O A:ASP123 5.0 77.9 1.0

Sodium binding site 2 out of 2 in 4qfd

Go back to Sodium Binding Sites List in 4qfd
Sodium binding site 2 out of 2 in the Co-Crystal Structure of Compound 2 (3-(7-Hydroxy-2-Oxo-4-Phenyl-2H- Chromen-6-Yl)Propanoic Acid) and Fad Bound to Human Daao at 2.85A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Co-Crystal Structure of Compound 2 (3-(7-Hydroxy-2-Oxo-4-Phenyl-2H- Chromen-6-Yl)Propanoic Acid) and Fad Bound to Human Daao at 2.85A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:73.8
occ:1.00
 O B:LEU122 2.7 0.6 1.0
O B:TYR128 2.7 0.6 1.0
O B:PHE125 2.9 97.3 1.0
O B:PRO126 3.4 0.5 1.0
C B:LEU122 3.7 0.1 1.0
C B:PRO126 3.8 0.8 1.0
C B:PHE125 3.8 98.5 1.0
C B:TYR128 3.9 0.2 1.0
CA B:PRO126 3.9 0.2 1.0
N B:PRO126 4.3 0.4 1.0
CA B:ASP123 4.3 0.5 1.0
N B:ASP123 4.4 99.9 1.0
N B:TYR128 4.4 0.7 1.0
CB B:LEU122 4.5 0.6 1.0
CA B:LEU122 4.6 99.9 1.0
CA B:GLY129 4.7 0.6 1.0
N B:GLY129 4.7 0.2 1.0
CA B:TYR128 4.8 0.3 1.0
N B:ASP127 4.8 0.1 1.0
C B:ASP123 4.8 97.4 1.0
O B:ASP123 5.0 96.9 1.0
OD1 B:ASP123 5.0 0.8 1.0
CA B:PHE125 5.0 94.7 1.0
N B:PHE125 5.0 93.4 1.0

Reference:

R.T.Terry-Lorenzo, L.E.Chun, S.P.Brown, M.L.Heffernan, Q.K.Fang, M.A.Orsini, L.Pollegioni, L.W.Hardy, K.L.Spear, T.H.Large. Novel Human D-Amino Acid Oxidase Inhibitors Stabilize An Active Site Lid Open Conformation. Biosci.Rep. 2014.
ISSN: ISSN 0144-8463
PubMed: 25001371
DOI: 10.1042/BSR20140071
Page generated: Mon Oct 7 17:58:48 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy