Zinc in PDB 6kc5: Hoip-HOIPIN1 Complex

All present enzymatic activity of Hoip-HOIPIN1 Complex:
2.3.2.31;

The structure of Hoip-HOIPIN1 Complex, PDB code: 6kc5 was solved by Y.Sato, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.14 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.350, 60.227, 92.280, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 21.7

The binding sites of Zinc atom in the Hoip-HOIPIN1 Complex (pdb code 6kc5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Hoip-HOIPIN1 Complex, PDB code: 6kc5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Hoip-HOIPIN1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hoip-HOIPIN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:34.5 occ:0.50 ZN B:ZN1101 0.0 34.5 0.5 ZN B:ZN1101 1.6 38.9 0.5 SG B:CYS871 2.2 41.0 1.0 SG B:CYS890 2.3 35.9 0.5 SG B:CYS874 2.3 40.2 0.5 SG B:CYS893 2.3 32.1 0.5 SG B:CYS890 2.3 38.1 0.5 SG B:CYS874 2.4 39.5 0.5 CB B:CYS871 2.5 37.3 1.0 CB B:CYS874 2.8 46.0 0.5 CB B:CYS890 3.1 39.5 0.5 CB B:CYS890 3.1 40.8 0.5 CB B:CYS874 3.1 47.4 0.5 N B:CYS874 3.6 48.0 1.0 CA B:CYS874 3.8 47.8 0.5 CB B:CYS893 3.9 50.4 0.5 CA B:CYS874 3.9 47.4 0.5 SG B:CYS893 3.9 42.4 0.5 CA B:CYS871 4.0 50.6 1.0 CB B:CYS893 4.2 52.0 0.5 N B:CYS893 4.2 51.2 1.0 CA B:CYS890 4.5 46.4 0.5 CA B:CYS890 4.5 47.5 0.5 CB B:GLN892 4.6 68.4 1.0 N B:LYS875 4.6 54.8 1.0 C B:CYS871 4.6 50.6 1.0 C B:CYS874 4.6 55.3 1.0 CA B:CYS893 4.7 49.8 0.5 CB B:PHE876 4.7 62.2 1.0 O B:CYS871 4.8 48.5 1.0 N B:CYS871 4.8 51.8 1.0 N B:PHE876 4.8 59.0 1.0 C B:LYS873 4.8 50.1 1.0 CA B:CYS893 4.8 49.6 0.5 CB B:LYS873 5.0 51.9 1.0

Zinc binding site 2 out of 5 in the Hoip-HOIPIN1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hoip-HOIPIN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:38.9 occ:0.50 ZN B:ZN1101 0.0 38.9 0.5 SG B:CYS893 0.7 32.1 0.5 ZN B:ZN1101 1.6 34.5 0.5 SG B:CYS874 2.3 39.5 0.5 SG B:CYS890 2.3 38.1 0.5 SG B:CYS893 2.3 42.4 0.5 SG B:CYS871 2.4 41.0 1.0 CB B:CYS893 2.5 50.4 0.5 CB B:CYS893 2.9 52.0 0.5 CB B:CYS874 3.3 46.0 0.5 SG B:CYS890 3.4 35.9 0.5 CB B:CYS890 3.4 39.5 0.5 CB B:CYS874 3.4 47.4 0.5 SG B:CYS874 3.4 40.2 0.5 CB B:CYS890 3.5 40.8 0.5 N B:CYS893 3.5 51.2 1.0 CA B:CYS893 3.5 49.8 0.5 CB B:CYS871 3.6 37.3 1.0 CA B:CYS893 3.6 49.6 0.5 N B:CYS874 3.7 48.0 1.0 CB B:HIS895 3.9 41.8 1.0 CA B:CYS874 4.1 47.8 0.5 C B:CYS893 4.1 53.0 1.0 CB B:LYS873 4.1 51.9 1.0 CA B:CYS874 4.2 47.4 0.5 N B:HIS895 4.3 46.0 1.0 N B:ARG894 4.3 51.7 1.0 C B:LYS873 4.6 50.1 1.0 C B:GLN892 4.7 60.6 1.0 CA B:HIS895 4.7 43.5 1.0 CA B:CYS890 4.8 46.4 0.5 CA B:LYS873 4.8 48.9 1.0 CA B:CYS890 4.8 47.5 0.5 CB B:GLN892 4.9 68.4 1.0 O B:CYS893 4.9 52.5 1.0 O B:CYS890 4.9 61.9 1.0

Zinc binding site 3 out of 5 in the Hoip-HOIPIN1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hoip-HOIPIN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1102 b:24.1 occ:1.00 ND1 B:HIS926 2.1 25.1 1.0 SG B:CYS898 2.3 24.5 1.0 SG B:CYS901 2.3 24.6 1.0 SG B:CYS930 2.3 24.1 1.0 CE1 B:HIS926 3.0 25.5 1.0 CG B:HIS926 3.2 23.6 1.0 CB B:CYS901 3.2 23.9 1.0 CB B:CYS898 3.3 22.2 1.0 CB B:CYS930 3.5 21.5 1.0 CB B:HIS926 3.5 21.6 1.0 N B:CYS901 3.5 26.4 1.0 CA B:CYS901 4.0 24.6 1.0 CB B:PHE932 4.0 25.1 1.0 NE2 B:HIS926 4.2 24.6 1.0 CD2 B:HIS926 4.2 24.7 1.0 CA B:HIS926 4.3 22.8 1.0 C B:GLY900 4.3 35.0 1.0 CA B:GLY900 4.5 30.7 1.0 N B:GLY900 4.6 30.7 1.0 CA B:CYS898 4.7 25.7 1.0 CD B:PRO927 4.7 23.5 1.0 C B:CYS901 4.8 23.9 1.0 CA B:CYS930 4.8 23.9 1.0 CE B:MET886 4.8 33.3 1.0 N B:PHE932 4.9 21.7 1.0 CG B:PHE932 4.9 24.6 1.0 N B:TYR902 5.0 24.7 1.0

Zinc binding site 4 out of 5 in the Hoip-HOIPIN1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hoip-HOIPIN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1103 b:31.8 occ:1.00 NE2 B:HIS925 2.0 30.0 1.0 NE2 B:HIS923 2.1 28.6 1.0 SG B:CYS911 2.2 36.8 1.0 SG B:CYS916 2.5 38.8 1.0 CE1 B:HIS925 2.9 39.2 1.0 CD2 B:HIS923 3.1 27.1 1.0 CE1 B:HIS923 3.1 31.9 1.0 CD2 B:HIS925 3.1 35.0 1.0 CB B:CYS916 3.2 34.2 1.0 CB B:CYS911 3.2 32.2 1.0 O B:VAL918 3.8 49.4 1.0 ND1 B:HIS925 4.0 43.6 1.0 CG B:HIS925 4.2 31.1 1.0 ND1 B:HIS923 4.2 27.1 1.0 CG B:HIS923 4.2 26.1 1.0 CB B:GLU913 4.5 41.7 1.0 NZ B:LYS919 4.5 48.3 1.0 CA B:CYS911 4.6 35.2 1.0 CA B:CYS916 4.7 39.0 1.0 C B:VAL918 4.9 39.2 1.0 CG B:GLU913 4.9 49.3 1.0 CD2 B:TYR906 5.0 36.7 1.0

Zinc binding site 5 out of 5 in the Hoip-HOIPIN1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Hoip-HOIPIN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1104 b:33.7 occ:1.00 ND1 B:HIS1001 2.0 33.5 1.0 SG B:CYS986 2.3 36.9 1.0 SG B:CYS969 2.3 34.5 1.0 SG B:CYS998 2.4 35.7 1.0 CE1 B:HIS1001 2.9 34.6 1.0 CG B:HIS1001 3.1 30.8 1.0 CB B:CYS986 3.1 42.5 1.0 CB B:CYS969 3.1 35.7 1.0 CB B:CYS998 3.4 34.3 1.0 CB B:HIS1001 3.5 27.3 1.0 N B:CYS998 4.0 30.6 1.0 NE2 B:HIS1001 4.0 35.0 1.0 CD2 B:HIS1001 4.2 38.1 1.0 CA B:CYS998 4.3 34.3 1.0 OE2 B:GLU973 4.5 72.7 1.0 N B:HIS1001 4.5 27.9 1.0 CA B:CYS986 4.5 48.0 1.0 CA B:CYS969 4.5 43.7 1.0 CB B:VAL971 4.6 42.0 1.0 CB B:LYS988 4.6 51.6 1.0 CA B:HIS1001 4.7 27.1 1.0 CG2 B:VAL971 4.9 38.1 1.0 C B:CYS998 5.0 34.3 1.0 C B:CYS969 5.0 46.6 1.0

D.Oikawa, Y.Sato, F.Ohtake, K.Komakura, K.Hanada, K.Sugawara, S.Terawaki, Y.Mizukami, H.T.Phuong, K.Iio, S.Obika, M.Fukushi, T.Irie, D.Tsuruta, S.Sakamoto, K.Tanaka, Y.Saeki, S.Fukai, F.Tokunaga. Molecular Bases For Hoipins-Mediated Inhibition of Lubac and Innate Immune Responses. Commun Biol V. 3 163 2020.
ISSN: ESSN 2399-3642
PubMed: 32246052
DOI: 10.1038/S42003-020-0882-8