Sodium in PDB 6gzy: Hoip-FRAGMENT5 Complex

All present enzymatic activity of Hoip-FRAGMENT5 Complex:
2.3.2.27;

The structure of Hoip-FRAGMENT5 Complex, PDB code: 6gzy was solved by H.Johansson, Y.C.I.Tsai, K.Fantom, C.W.Chung, L.Martino, D.House, K.Rittinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.69 / 2.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.202, 117.249, 37.940, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.6

The structure of Hoip-FRAGMENT5 Complex also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Sodium atom in the Hoip-FRAGMENT5 Complex (pdb code 6gzy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hoip-FRAGMENT5 Complex, PDB code: 6gzy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hoip-FRAGMENT5 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hoip-FRAGMENT5 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4013 b:48.1 occ:1.00 O A:HOH4210 3.4 43.3 1.0 HE1 A:TYR1033 3.4 32.6 1.0 HB3 A:HIS925 3.4 32.8 1.0 O A:HIS926 3.7 18.8 1.0 HA A:PRO927 3.8 25.9 1.0 O2 A:SO44006 3.8 31.7 1.0 C A:HIS926 3.8 20.0 1.0 N A:PRO927 4.0 17.1 1.0 HD1 A:TYR1033 4.1 28.3 1.0 CE1 A:TYR1033 4.2 27.2 1.0 HD3 A:PRO927 4.2 20.3 1.0 CB A:HIS925 4.2 27.4 1.0 HB2 A:HIS925 4.2 32.8 1.0 O1 A:SO44006 4.3 31.7 1.0 N A:HIS926 4.3 20.2 1.0 HD21 A:ASN903 4.3 23.8 1.0 CA A:PRO927 4.4 21.6 1.0 H A:HIS926 4.4 24.2 1.0 C A:HIS925 4.4 23.2 1.0 HB3 A:PRO927 4.5 23.5 1.0 CA A:HIS926 4.5 19.4 1.0 CD1 A:TYR1033 4.6 23.6 1.0 O A:HOH4161 4.6 41.3 1.0 HA A:HIS926 4.6 23.3 1.0 HD22 A:ASN903 4.7 23.8 1.0 O A:HIS925 4.7 19.7 1.0 S A:SO44006 4.7 28.0 1.0 CD A:PRO927 4.7 16.9 1.0 ND2 A:ASN903 4.7 19.9 1.0 HH A:TYR1033 5.0 29.1 1.0 CA A:HIS925 5.0 20.8 1.0 CB A:PRO927 5.0 19.6 1.0

Sodium binding site 2 out of 2 in the Hoip-FRAGMENT5 Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hoip-FRAGMENT5 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na4011 b:44.9 occ:1.00 HB3 B:HIS925 3.4 33.9 1.0 O2 B:SO44006 3.5 31.0 1.0 HE1 B:TYR1033 3.6 32.3 1.0 HA B:PRO927 4.0 20.6 1.0 O B:HIS926 4.0 16.2 1.0 HD1 B:TYR1033 4.1 31.8 1.0 C B:HIS926 4.1 24.6 1.0 HD21 B:ASN903 4.1 28.7 1.0 HB2 B:HIS925 4.2 33.9 1.0 CB B:HIS925 4.2 28.3 1.0 N B:PRO927 4.3 16.8 1.0 O3 B:SO44006 4.3 38.2 1.0 CE1 B:TYR1033 4.4 27.0 1.0 HD3 B:PRO927 4.4 17.9 1.0 OE2 B:GLU913 4.5 80.5 1.0 N B:HIS926 4.5 22.7 1.0 S B:SO44006 4.5 29.4 1.0 C B:HIS925 4.6 23.6 1.0 HD22 B:ASN903 4.6 28.7 1.0 ND2 B:ASN903 4.6 24.0 1.0 CA B:PRO927 4.6 17.2 1.0 CD1 B:TYR1033 4.6 26.6 1.0 H B:HIS926 4.7 27.2 1.0 HB3 B:PRO927 4.7 18.8 1.0 O B:HIS925 4.7 22.2 1.0 CA B:HIS926 4.8 23.9 1.0 HA B:HIS926 4.8 28.6 1.0 CD B:PRO927 4.9 14.9 1.0

H.Johansson, Y.C.Isabella Tsai, K.Fantom, C.W.Chung, S.Kumper, L.Martino, D.A.Thomas, H.C.Eberl, M.Muelbaier, D.House, K.Rittinger. Fragment-Based Covalent Ligand Screening Enables Rapid Discovery of Inhibitors For the Rbr E3 Ubiquitin Ligase Hoip. J. Am. Chem. Soc. V. 141 2703 2019.
ISSN: ESSN 1520-5126
PubMed: 30657686
DOI: 10.1021/JACS.8B13193