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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: Tue Dec 15 07:05:18 2020

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