Zinc in PDB 6kc6: Hoip-HOIPIN8 Complex

All present enzymatic activity of Hoip-HOIPIN8 Complex:
2.3.2.31;

The structure of Hoip-HOIPIN8 Complex, PDB code: 6kc6 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)	46.59 / 2.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.586, 88.793, 104.438, 90.00, 101.08, 90.00
R / Rfree (%)	21.1 / 26.7

The structure of Hoip-HOIPIN8 Complex also contains other interesting chemical elements:

Fluorine	(F)	12 atoms
Chlorine	(Cl)	9 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Hoip-HOIPIN8 Complex (pdb code 6kc6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Hoip-HOIPIN8 Complex, PDB code: 6kc6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hoip-HOIPIN8 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:60.4 occ:1.00 SG A:CYS893 2.2 58.1 1.0 SG A:CYS890 2.2 55.5 1.0 SG A:CYS874 2.3 59.3 1.0 SG A:CYS871 2.4 59.5 1.0 CB A:CYS890 3.1 53.4 1.0 CB A:CYS893 3.1 64.5 1.0 CB A:CYS871 3.2 48.8 1.0 CB A:CYS874 3.3 60.4 1.0 N A:CYS874 3.6 60.0 1.0 N A:CYS893 3.7 67.8 1.0 CA A:CYS893 3.9 64.6 1.0 CA A:CYS874 4.0 64.8 1.0 CB A:HIS895 4.4 54.1 1.0 C A:CYS893 4.5 67.7 1.0 CA A:CYS890 4.6 50.7 1.0 CB A:LYS873 4.6 66.6 1.0 CB A:GLN892 4.6 60.3 1.0 CA A:CYS871 4.7 51.0 1.0 C A:CYS874 4.7 65.8 1.0 C A:LYS873 4.7 65.0 1.0 N A:HIS895 4.8 53.4 1.0 C A:GLN892 4.8 71.2 1.0 N A:ARG894 4.8 67.2 1.0 N A:LYS875 4.8 66.4 1.0 O A:CYS890 5.0 59.5 1.0 N A:LYS873 5.0 58.3 1.0

Zinc binding site 2 out of 24 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hoip-HOIPIN8 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:40.1 occ:1.00 ND1 A:HIS926 2.0 33.2 1.0 SG A:CYS930 2.3 36.5 1.0 SG A:CYS901 2.3 39.1 1.0 SG A:CYS898 2.4 37.8 1.0 CE1 A:HIS926 2.9 39.3 1.0 CG A:HIS926 3.2 40.8 1.0 CB A:CYS898 3.2 30.7 1.0 CB A:CYS901 3.2 32.4 1.0 CB A:CYS930 3.4 35.6 1.0 N A:CYS901 3.5 38.9 1.0 CB A:HIS926 3.6 34.5 1.0 CB A:PHE932 4.0 35.1 1.0 CA A:CYS901 4.0 37.0 1.0 NE2 A:HIS926 4.1 40.2 1.0 CD2 A:HIS926 4.2 37.0 1.0 C A:GLY900 4.2 42.6 1.0 CA A:HIS926 4.3 38.8 1.0 CA A:GLY900 4.4 38.3 1.0 N A:GLY900 4.6 41.9 1.0 CD A:PRO927 4.7 32.5 1.0 CA A:CYS898 4.7 39.3 1.0 CA A:CYS930 4.8 39.4 1.0 N A:PHE932 4.8 32.0 1.0 C A:CYS901 4.8 38.2 1.0 CG A:PHE932 4.9 38.4 1.0 C A:CYS898 5.0 39.3 1.0

Zinc binding site 3 out of 24 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hoip-HOIPIN8 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1103 b:47.0 occ:1.00 NE2 A:HIS923 2.1 40.9 1.0 NE2 A:HIS925 2.1 45.9 1.0 SG A:CYS911 2.2 48.8 1.0 SG A:CYS916 2.4 46.7 1.0 CE1 A:HIS923 2.9 43.0 1.0 CD2 A:HIS925 3.0 40.9 1.0 CB A:CYS911 3.1 50.9 1.0 CE1 A:HIS925 3.1 50.3 1.0 CD2 A:HIS923 3.2 43.2 1.0 CB A:CYS916 3.2 45.0 1.0 ND1 A:HIS923 4.1 44.6 1.0 CG A:HIS925 4.2 42.7 1.0 ND1 A:HIS925 4.2 41.0 1.0 CG A:HIS923 4.2 42.1 1.0 CA A:CYS916 4.4 49.1 1.0 CA A:CYS911 4.6 52.6 1.0 CB A:GLU913 4.6 53.1 1.0 CG2 A:VAL918 4.6 40.2 1.0 CD2 A:TYR906 4.9 51.2 1.0

Zinc binding site 4 out of 24 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hoip-HOIPIN8 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1104 b:45.4 occ:1.00 ND1 A:HIS1001 2.0 33.8 1.0 SG A:CYS969 2.3 40.2 1.0 SG A:CYS998 2.3 44.3 1.0 SG A:CYS986 2.4 49.9 1.0 CB A:CYS969 3.0 47.3 1.0 CE1 A:HIS1001 3.0 42.5 1.0 CG A:HIS1001 3.1 38.8 1.0 CB A:CYS986 3.2 51.6 1.0 CB A:CYS998 3.3 32.4 1.0 CB A:HIS1001 3.5 36.9 1.0 N A:CYS998 3.8 39.0 1.0 NE2 A:HIS1001 4.1 43.3 1.0 CA A:CYS998 4.2 34.3 1.0 CD2 A:HIS1001 4.2 41.2 1.0 CB A:LYS988 4.4 39.0 1.0 CA A:CYS969 4.4 46.6 1.0 CB A:VAL971 4.6 50.5 1.0 CA A:CYS986 4.6 49.1 1.0 N A:HIS1001 4.7 43.3 1.0 CA A:HIS1001 4.7 41.8 1.0 CD A:LYS988 4.7 43.1 1.0 C A:CYS998 4.9 38.4 1.0 CG2 A:VAL971 4.9 48.7 1.0 C A:CYS969 4.9 51.3 1.0 N A:LYS988 5.0 43.7 1.0

Zinc binding site 5 out of 24 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Hoip-HOIPIN8 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1101 b:59.1 occ:1.00 SG C:CYS893 2.1 55.5 1.0 SG C:CYS890 2.3 56.1 1.0 SG C:CYS874 2.4 56.6 1.0 SG C:CYS871 2.5 62.0 1.0 CB C:CYS890 3.1 67.5 1.0 CB C:CYS874 3.1 49.6 1.0 CB C:CYS871 3.2 53.0 1.0 CB C:CYS893 3.2 64.3 1.0 N C:CYS874 3.6 60.4 1.0 N C:CYS893 3.7 71.0 1.0 CA C:CYS874 3.9 57.2 1.0 CA C:CYS893 4.0 66.3 1.0 CB C:HIS895 4.4 48.0 1.0 CA C:CYS890 4.5 61.9 1.0 CB C:LYS873 4.5 65.7 1.0 CB C:GLN892 4.6 63.7 1.0 C C:CYS893 4.6 67.2 1.0 CA C:CYS871 4.6 55.2 1.0 C C:GLN892 4.6 71.4 1.0 C C:CYS874 4.6 63.6 1.0 C C:LYS873 4.7 63.1 1.0 N C:LYS875 4.8 64.4 1.0 N C:HIS895 4.9 54.0 1.0 O C:CYS890 4.9 65.0 1.0 C C:CYS890 5.0 67.6 1.0 N C:ARG894 5.0 67.6 1.0 CA C:LYS873 5.0 64.0 1.0

Zinc binding site 6 out of 24 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Hoip-HOIPIN8 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1102 b:40.5 occ:1.00 ND1 C:HIS926 2.1 32.5 1.0 SG C:CYS901 2.3 39.0 1.0 SG C:CYS930 2.3 37.3 1.0 SG C:CYS898 2.4 40.3 1.0 CE1 C:HIS926 3.1 39.0 1.0 CG C:HIS926 3.2 36.2 1.0 CB C:CYS901 3.2 38.5 1.0 CB C:CYS898 3.2 32.9 1.0 CB C:CYS930 3.4 38.3 1.0 CB C:HIS926 3.5 34.4 1.0 N C:CYS901 3.6 39.6 1.0 CB C:PHE932 4.0 38.8 1.0 CA C:CYS901 4.0 40.0 1.0 NE2 C:HIS926 4.2 36.1 1.0 CA C:HIS926 4.2 37.6 1.0 C C:GLY900 4.3 42.0 1.0 CD2 C:HIS926 4.3 32.0 1.0 CA C:GLY900 4.5 40.9 1.0 N C:GLY900 4.6 43.1 1.0 CA C:CYS898 4.7 37.4 1.0 CD C:PRO927 4.7 34.7 1.0 CA C:CYS930 4.8 36.8 1.0 C C:CYS901 4.8 41.0 1.0 CG C:PHE932 4.9 38.2 1.0 N C:PHE932 4.9 32.7 1.0 CE C:MET886 5.0 41.6 1.0

Zinc binding site 7 out of 24 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Hoip-HOIPIN8 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1103 b:54.3 occ:1.00 NE2 C:HIS925 1.9 53.5 1.0 NE2 C:HIS923 2.0 46.1 1.0 SG C:CYS911 2.2 54.0 1.0 SG C:CYS916 2.4 59.8 1.0 CE1 C:HIS925 2.7 54.6 1.0 CE1 C:HIS923 2.8 46.7 1.0 CD2 C:HIS923 3.1 46.6 1.0 CD2 C:HIS925 3.1 55.8 1.0 CB C:CYS911 3.2 61.3 1.0 CB C:CYS916 3.2 59.0 1.0 ND1 C:HIS925 3.9 59.7 1.0 ND1 C:HIS923 4.0 48.2 1.0 CG C:HIS925 4.1 54.8 1.0 CG C:HIS923 4.1 47.9 1.0 CA C:CYS916 4.4 62.5 1.0 CB C:GLU913 4.5 88.7 1.0 CG2 C:VAL918 4.6 52.2 1.0 CA C:CYS911 4.6 64.3 1.0 CD2 C:TYR906 5.0 56.4 1.0

Zinc binding site 8 out of 24 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Hoip-HOIPIN8 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1104 b:42.6 occ:1.00 ND1 C:HIS1001 2.0 31.6 1.0 SG C:CYS969 2.3 37.5 1.0 SG C:CYS998 2.3 40.9 1.0 SG C:CYS986 2.4 42.9 1.0 CE1 C:HIS1001 2.9 38.9 1.0 CB C:CYS969 3.0 32.0 1.0 CG C:HIS1001 3.1 39.3 1.0 CB C:CYS986 3.1 42.1 1.0 CB C:CYS998 3.4 31.7 1.0 CB C:HIS1001 3.5 35.4 1.0 N C:CYS998 3.8 42.7 1.0 NE2 C:HIS1001 4.0 43.0 1.0 CD2 C:HIS1001 4.1 38.1 1.0 CA C:CYS998 4.2 37.9 1.0 CA C:CYS969 4.5 45.0 1.0 CB C:LYS988 4.5 37.6 1.0 N C:HIS1001 4.6 42.6 1.0 CA C:CYS986 4.6 42.6 1.0 CB C:VAL971 4.6 42.0 1.0 CA C:HIS1001 4.7 42.9 1.0 CG2 C:VAL971 4.7 44.7 1.0 C C:CYS998 4.9 38.7 1.0 N C:LYS988 4.9 42.9 1.0 CD C:LYS988 4.9 43.5 1.0

Zinc binding site 9 out of 24 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Hoip-HOIPIN8 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1101 b:63.4 occ:1.00 SG E:CYS890 2.2 63.5 1.0 SG E:CYS893 2.3 66.8 1.0 SG E:CYS871 2.3 66.5 1.0 SG E:CYS874 2.4 57.5 1.0 CB E:CYS871 3.1 51.2 1.0 CB E:CYS874 3.2 62.6 1.0 CB E:CYS890 3.3 72.9 1.0 CB E:CYS893 3.4 57.9 1.0 N E:CYS874 3.5 63.8 1.0 N E:CYS893 3.9 70.0 1.0 CA E:CYS874 3.9 67.4 1.0 CB E:LYS873 4.2 75.3 1.0 CA E:CYS893 4.2 64.5 1.0 CB E:HIS895 4.5 67.2 1.0 C E:LYS873 4.5 64.5 1.0 C E:CYS874 4.6 70.2 1.0 CA E:CYS871 4.6 50.5 1.0 C E:GLN892 4.6 73.0 1.0 CB E:GLN892 4.7 71.5 1.0 CA E:CYS890 4.7 69.7 1.0 N E:LYS875 4.8 65.7 1.0 CG E:LYS873 4.8 86.3 1.0 CA E:LYS873 4.8 69.2 1.0 C E:CYS893 4.9 69.6 1.0 N E:LYS873 5.0 68.9 1.0

Zinc binding site 10 out of 24 in the Hoip-HOIPIN8 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Hoip-HOIPIN8 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1102 b:47.7 occ:1.00 ND1 E:HIS926 2.1 46.8 1.0 SG E:CYS901 2.2 44.1 1.0 SG E:CYS930 2.3 44.1 1.0 SG E:CYS898 2.4 43.1 1.0 CE1 E:HIS926 3.0 47.0 1.0 CB E:CYS898 3.2 43.9 1.0 CG E:HIS926 3.2 46.3 1.0 CB E:CYS901 3.3 50.7 1.0 CB E:CYS930 3.5 40.6 1.0 N E:CYS901 3.6 44.7 1.0 CB E:HIS926 3.6 47.0 1.0 CB E:PHE932 3.9 46.9 1.0 CA E:CYS901 4.0 46.2 1.0 NE2 E:HIS926 4.2 47.6 1.0 C E:GLY900 4.2 46.1 1.0 CD2 E:HIS926 4.3 46.5 1.0 CA E:HIS926 4.3 48.3 1.0 CA E:GLY900 4.4 41.8 1.0 CA E:CYS898 4.6 43.9 1.0 N E:GLY900 4.6 45.4 1.0 CD E:PRO927 4.8 42.2 1.0 CG E:PHE932 4.8 46.5 1.0 C E:CYS901 4.8 44.9 1.0 N E:PHE932 4.8 39.5 1.0 CA E:CYS930 4.8 44.7 1.0 C E:CYS898 4.9 45.4 1.0 O E:CYS898 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