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Sodium in PDB 6gzy: Hoip-FRAGMENT5 Complex

Enzymatic activity of Hoip-FRAGMENT5 Complex

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

Protein crystallography data

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

Other elements in 6gzy:

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

Zinc (Zn) 8 atoms

Sodium Binding Sites:

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 6gzy

Go back to Sodium Binding Sites List in 6gzy
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 6gzy

Go back to Sodium Binding Sites List in 6gzy
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

Reference:

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
Page generated: Tue Dec 15 12:18:44 2020

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