Sodium in PDB 5vgy: 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;

The structure of Identification of A New Zinc Binding Chemotype By Fragment Screening, PDB code: 5vgy 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)	41.60 / 1.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.454, 41.654, 72.045, 90.00, 104.29, 90.00
R / Rfree (%)	11.3 / 15.6

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

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Identification of A New Zinc Binding Chemotype By Fragment Screening (pdb code 5vgy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Identification of A New Zinc Binding Chemotype By Fragment Screening, PDB code: 5vgy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 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:Na302 b:28.3 occ:1.00 O A:LYS45 2.4 22.0 1.0 OH A:TYR191 2.6 13.0 1.0 O A:HOH584 2.9 19.8 1.0 O A:HOH555 3.1 43.6 1.0 CE2 A:TYR191 3.3 10.2 1.0 CZ A:TYR191 3.3 10.8 1.0 O A:HOH642 3.4 42.6 1.0 C A:LYS45 3.5 23.5 1.0 CB A:LEU44 3.7 19.6 1.0 N A:LEU47 3.9 18.0 1.0 CA A:GLY82 4.0 15.5 1.0 CB A:SER259 4.0 11.5 1.0 CA A:PRO46 4.0 21.2 1.0 C A:LEU44 4.1 24.2 1.0 N A:PRO46 4.2 19.5 1.0 C A:PRO46 4.2 19.2 1.0 O A:LEU44 4.2 25.1 1.0 N A:LYS45 4.2 24.3 1.0 CA A:LYS45 4.5 23.7 1.0 CA A:LEU44 4.5 22.1 1.0 CD2 A:TYR191 4.6 11.2 1.0 CE1 A:TYR191 4.6 10.6 1.0 N A:GLY82 4.6 15.3 1.0 O A:HOH506 4.8 24.1 1.0 OG A:SER259 4.9 10.7 1.0 CB A:LEU47 4.9 20.8 1.0 C A:GLY82 4.9 13.8 1.0 CA A:SER259 4.9 11.4 1.0 CG A:LEU44 4.9 16.1 1.0 CD1 A:LEU44 4.9 15.2 1.0 CA A:LEU47 4.9 16.6 1.0 O A:HOH444 4.9 31.1 1.0

Sodium binding site 2 out of 2 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 2 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:44.7 occ:1.00 O A:HOH536 2.5 34.8 1.0 O A:HOH456 2.5 31.3 1.0 O A:HOH679 2.6 34.4 1.0 NH1 A:ARG27 3.2 16.5 1.0 CD A:ARG27 3.3 17.6 1.0 CZ A:ARG27 4.1 13.3 1.0 NE A:ARG27 4.1 14.3 1.0 CG A:ARG27 4.3 14.5 1.0 CB A:PRO138 4.3 13.7 1.0 O A:GLU205 4.6 10.8 1.0 O A:HOH498 4.9 34.9 1.0 CG A:PRO138 4.9 19.2 1.0

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