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Sodium in PDB 5ty1: Identification of A New Zinc Binding Chemotype By Fragment Screening

Enzymatic activity of Identification of A New Zinc Binding Chemotype By Fragment Screening

All present enzymatic activity of Identification of A New Zinc Binding Chemotype By Fragment Screening:
4.2.1.1;

Protein crystallography data

The structure of Identification of A New Zinc Binding Chemotype By Fragment Screening, PDB code: 5ty1 was solved by T.S.Peat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.50 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.514, 41.539, 71.981, 90.00, 104.46, 90.00
R / Rfree (%) 13.7 / 18.7

Other elements in 5ty1:

The structure of Identification of A New Zinc Binding Chemotype By Fragment Screening also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Identification of A New Zinc Binding Chemotype By Fragment Screening (pdb code 5ty1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Identification of A New Zinc Binding Chemotype By Fragment Screening, PDB code: 5ty1:

Sodium binding site 1 out of 1 in 5ty1

Go back to Sodium Binding Sites List in 5ty1
Sodium binding site 1 out of 1 in the Identification of A New Zinc Binding Chemotype By Fragment Screening


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Identification of A New Zinc Binding Chemotype By Fragment Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:38.3
occ:1.00
OD2 A:ASP34 2.3 12.5 0.5
O A:HOH480 2.4 19.3 1.0
O A:HOH649 2.6 16.5 1.0
OD1 A:ASP110 3.1 12.3 1.0
OD1 A:ASP34 3.1 14.6 0.5
CG A:ASP34 3.2 13.5 0.5
CG A:ASP34 3.5 12.1 0.5
CG A:ASP110 3.6 10.5 1.0
CB A:ASP110 3.7 10.6 1.0
OD2 A:ASP34 3.7 10.7 0.5
CA A:ASP110 3.7 9.0 1.0
OD1 A:ASP34 3.8 16.0 0.5
O A:HOH512 3.8 18.9 1.0
CD2 A:HIS36 3.8 21.4 0.5
ND1 A:HIS36 4.1 20.2 0.5
CB A:ASP34 4.1 11.7 0.5
CB A:ASP34 4.2 11.0 0.5
CA A:ASP34 4.3 10.4 0.5
CA A:ASP34 4.3 10.8 0.5
NE2 A:HIS36 4.4 23.1 0.5
C A:ASP110 4.5 9.2 1.0
CE1 A:HIS36 4.6 21.7 0.5
OD2 A:ASP110 4.6 15.4 1.0
O A:ASP110 4.8 10.7 1.0
N A:ASP110 4.9 8.8 1.0
N A:THR35 4.9 12.0 1.0
OD2 A:ASP32 4.9 10.6 1.0

Reference:

P.K.Chrysanthopoulos, P.Mujumdar, L.A.Woods, O.Dolezal, B.Ren, T.S.Peat, S.A.Poulsen. Identification of A New Zinc Binding Chemotype By Fragment Screening. J. Med. Chem. V. 60 7333 2017.
ISSN: ISSN 1520-4804
PubMed: 28817930
DOI: 10.1021/ACS.JMEDCHEM.7B00606
Page generated: Tue Dec 15 11:39:11 2020

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