Zinc in PDB 4ljq: Crystal Structure of the Catalytic Core of E3 Ligase Hoip

The structure of Crystal Structure of the Catalytic Core of E3 Ligase Hoip, PDB code: 4ljq was solved by B.Stieglitz, R.R.Rana, M.G.Koliopoulos, A.C.Morris-Davies, E.Christodoulou, S.Howell, N.R.Brown, K.Rittinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.60 / 2.45
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.209, 47.767, 111.145, 101.39, 90.12, 98.92
R / Rfree (%)	20.6 / 24.3

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Core of E3 Ligase Hoip (pdb code 4ljq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Core of E3 Ligase Hoip, PDB code: 4ljq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in the Crystal Structure of the Catalytic Core of E3 Ligase Hoip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Core of E3 Ligase Hoip within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:49.5 occ:1.00 SG B:CYS893 2.1 48.6 1.0 SG B:CYS874 2.3 52.5 1.0 SG B:CYS890 2.4 43.3 1.0 SG B:CYS871 2.5 41.9 1.0 CB B:CYS893 3.1 48.5 1.0 CB B:CYS890 3.2 39.8 1.0 CB B:CYS874 3.2 47.0 1.0 CB B:CYS871 3.3 37.3 1.0 N B:CYS893 3.5 62.0 1.0 N B:CYS874 3.6 54.9 1.0 CA B:CYS893 3.8 52.6 1.0 CA B:CYS874 4.0 54.5 1.0 CB B:HIS895 4.5 40.2 1.0 CB B:GLN892 4.5 47.0 1.0 C B:CYS893 4.5 50.9 1.0 C B:GLN892 4.6 58.2 1.0 CA B:CYS890 4.7 40.0 1.0 CB B:LYS873 4.7 55.1 1.0 CA B:CYS871 4.8 39.4 1.0 C B:LYS873 4.8 53.1 1.0 N B:ARG894 4.8 54.5 1.0 C B:CYS874 4.9 56.0 1.0 N B:HIS895 4.9 42.5 1.0 OH B:TYR878 4.9 77.0 1.0 CA B:GLN892 5.0 54.9 1.0

Zinc binding site 2 out of 18 in the Crystal Structure of the Catalytic Core of E3 Ligase Hoip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Core of E3 Ligase Hoip within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1102 b:22.9 occ:1.00 ND1 B:HIS926 2.0 21.0 1.0 SG B:CYS898 2.2 26.6 1.0 SG B:CYS901 2.2 21.3 1.0 SG B:CYS930 2.3 20.7 1.0 CE1 B:HIS926 2.9 19.5 1.0 CG B:HIS926 3.1 24.2 1.0 CB B:CYS898 3.1 26.3 1.0 CB B:CYS901 3.2 22.9 1.0 CB B:CYS930 3.4 22.2 1.0 N B:CYS901 3.5 23.3 1.0 CB B:HIS926 3.5 23.3 1.0 CA B:CYS901 3.9 22.7 1.0 NE2 B:HIS926 4.1 20.0 1.0 CB B:PHE932 4.1 26.1 1.0 CD2 B:HIS926 4.2 21.8 1.0 C B:GLY900 4.3 23.7 1.0 CA B:HIS926 4.3 23.0 1.0 CA B:CYS898 4.6 26.3 1.0 CA B:GLY900 4.6 22.5 1.0 N B:GLY900 4.7 24.9 1.0 CD B:PRO927 4.8 19.4 1.0 C B:CYS901 4.8 21.6 1.0 CA B:CYS930 4.8 21.0 1.0 N B:PHE932 5.0 22.9 1.0

Zinc binding site 3 out of 18 in the Crystal Structure of the Catalytic Core of E3 Ligase Hoip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Catalytic Core of E3 Ligase Hoip within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1103 b:35.3 occ:1.00 NE2 B:HIS925 2.0 35.8 1.0 NE2 B:HIS923 2.2 28.3 1.0 SG B:CYS916 2.2 47.8 1.0 SG B:CYS911 2.3 35.0 1.0 CE1 B:HIS925 2.8 34.2 1.0 CD2 B:HIS923 3.1 31.0 1.0 CE1 B:HIS923 3.1 31.8 1.0 CD2 B:HIS925 3.1 34.8 1.0 CB B:CYS916 3.2 54.1 1.0 CB B:CYS911 3.2 38.7 1.0 ND1 B:HIS925 3.9 37.1 1.0 CG B:HIS925 4.1 33.4 1.0 ND1 B:HIS923 4.2 29.4 1.0 CG2 B:VAL918 4.3 52.6 1.0 CG B:HIS923 4.3 30.5 1.0 CA B:CYS916 4.5 56.6 1.0 CA B:CYS911 4.7 40.5 1.0 CB B:GLU913 4.8 58.0 1.0 CD2 B:TYR906 5.0 32.2 1.0

Zinc binding site 4 out of 18 in the Crystal Structure of the Catalytic Core of E3 Ligase Hoip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Catalytic Core of E3 Ligase Hoip within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1104 b:29.5 occ:1.00 ND1 B:HIS1001 2.0 33.9 1.0 SG B:CYS998 2.2 26.9 1.0 SG B:CYS969 2.3 26.5 1.0 SG B:CYS986 2.3 38.4 1.0 CE1 B:HIS1001 2.9 32.9 1.0 CB B:CYS969 3.0 30.8 1.0 CB B:CYS986 3.1 38.9 1.0 CG B:HIS1001 3.1 31.5 1.0 CB B:CYS998 3.3 27.5 1.0 CB B:HIS1001 3.6 28.3 1.0 N B:CYS998 3.8 26.6 1.0 NE2 B:HIS1001 4.1 34.7 1.0 CA B:CYS998 4.2 27.6 1.0 CD2 B:HIS1001 4.2 32.7 1.0 CA B:CYS969 4.5 34.1 1.0 CA B:CYS986 4.6 38.7 1.0 N B:HIS1001 4.7 23.4 1.0 CA B:HIS1001 4.7 24.7 1.0 CB B:VAL971 4.7 44.4 1.0 CB B:LYS988 4.8 39.3 1.0 CG2 B:VAL971 4.9 42.0 1.0 C B:CYS998 4.9 25.6 1.0 CD B:LYS988 4.9 37.4 1.0 O B:CYS998 5.0 31.3 1.0 C B:LEU997 5.0 25.3 1.0

Zinc binding site 5 out of 18 in the Crystal Structure of the Catalytic Core of E3 Ligase Hoip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Catalytic Core of E3 Ligase Hoip within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1105 b:30.6 occ:1.00 NE2 C:HIS889 1.9 31.9 1.0 NE2 B:HIS889 2.0 33.2 1.0 NE2 C:HIS887 2.0 35.8 1.0 NE2 B:HIS887 2.1 27.4 1.0 CE1 C:HIS889 2.7 31.6 1.0 CE1 B:HIS889 2.7 30.1 1.0 CD2 C:HIS887 2.9 30.7 1.0 CD2 B:HIS887 3.0 27.3 1.0 CE1 C:HIS887 3.1 33.3 1.0 CD2 C:HIS889 3.1 36.5 1.0 CE1 B:HIS887 3.1 26.3 1.0 CD2 B:HIS889 3.2 38.5 1.0 ND1 C:HIS889 3.9 33.6 1.0 ND1 B:HIS889 3.9 32.5 1.0 CG C:HIS887 4.1 31.6 1.0 CG C:HIS889 4.1 35.1 1.0 ND1 C:HIS887 4.1 33.5 1.0 CG B:HIS889 4.2 34.0 1.0 CG B:HIS887 4.2 24.9 1.0 ND1 B:HIS887 4.2 28.9 1.0

Zinc binding site 6 out of 18 in the Crystal Structure of the Catalytic Core of E3 Ligase Hoip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Catalytic Core of E3 Ligase Hoip within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:60.8 occ:1.00 SG A:CYS893 2.0 47.9 1.0 SG A:CYS874 2.3 78.3 1.0 SG A:CYS890 2.4 62.7 1.0 SG A:CYS871 2.5 65.6 1.0 CB A:CYS893 3.1 65.7 1.0 CB A:CYS890 3.2 70.1 1.0 CB A:CYS874 3.2 80.7 1.0 CB A:CYS871 3.4 52.5 1.0 N A:CYS893 3.4 73.5 1.0 N A:CYS874 3.6 74.0 1.0 CA A:CYS893 3.7 68.0 1.0 CA A:CYS874 3.9 77.3 1.0 O A:CYS893 4.0 78.8 1.0 C A:CYS893 4.2 74.0 1.0 CB A:HIS895 4.4 57.7 1.0 CB A:GLN892 4.5 77.7 1.0 C A:GLN892 4.5 72.8 1.0 CB A:LYS873 4.7 77.0 1.0 CA A:CYS890 4.7 65.2 1.0 C A:LYS873 4.8 78.2 1.0 CA A:CYS871 4.8 55.5 1.0 CA A:GLN892 4.9 75.7 1.0 OH A:TYR878 4.9 67.9 1.0 N A:HIS895 5.0 57.5 1.0

Zinc binding site 7 out of 18 in the Crystal Structure of the Catalytic Core of E3 Ligase Hoip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Catalytic Core of E3 Ligase Hoip within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:27.6 occ:1.00 ND1 A:HIS926 2.1 27.0 1.0 SG A:CYS898 2.2 31.6 1.0 SG A:CYS930 2.2 28.6 1.0 SG A:CYS901 2.3 27.9 1.0 CE1 A:HIS926 3.0 25.1 1.0 CB A:CYS898 3.1 27.8 1.0 CG A:HIS926 3.2 29.8 1.0 CB A:CYS901 3.2 23.0 1.0 CB A:CYS930 3.4 26.8 1.0 N A:CYS901 3.4 26.8 1.0 CB A:HIS926 3.6 26.9 1.0 CA A:CYS901 3.9 27.0 1.0 CB A:PHE932 4.1 31.8 1.0 NE2 A:HIS926 4.1 26.6 1.0 C A:GLY900 4.3 30.1 1.0 CD2 A:HIS926 4.3 28.2 1.0 CA A:HIS926 4.4 29.8 1.0 CA A:GLY900 4.5 30.0 1.0 CA A:CYS898 4.6 28.6 1.0 N A:GLY900 4.6 32.7 1.0 C A:CYS901 4.7 28.3 1.0 CD A:PRO927 4.8 27.1 1.0 CA A:CYS930 4.8 26.4 1.0 N A:TYR902 4.9 34.7 1.0 N A:PHE932 4.9 28.4 1.0

Zinc binding site 8 out of 18 in the Crystal Structure of the Catalytic Core of E3 Ligase Hoip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Catalytic Core of E3 Ligase Hoip within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1103 b:55.0 occ:1.00 NE2 A:HIS925 2.1 52.5 1.0 SG A:CYS916 2.1 63.9 1.0 SG A:CYS911 2.2 68.8 1.0 NE2 A:HIS923 2.3 53.6 1.0 CE1 A:HIS925 2.7 50.6 1.0 CB A:CYS911 3.1 75.3 1.0 CE1 A:HIS923 3.2 57.3 1.0 CD2 A:HIS925 3.3 44.0 1.0 CD2 A:HIS923 3.3 52.8 1.0 CB A:CYS916 3.3 89.2 1.0 ND1 A:HIS925 3.9 50.8 1.0 CG A:HIS925 4.2 43.6 1.0 ND1 A:HIS923 4.3 56.4 1.0 CB A:GLU913 4.4 87.0 1.0 CG A:HIS923 4.4 48.8 1.0 CA A:CYS916 4.4 88.6 1.0 CA A:CYS911 4.6 70.6 1.0

Zinc binding site 9 out of 18 in the Crystal Structure of the Catalytic Core of E3 Ligase Hoip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Catalytic Core of E3 Ligase Hoip within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1104 b:41.6 occ:1.00 ND1 A:HIS1001 1.9 39.0 1.0 SG A:CYS998 2.2 38.7 1.0 SG A:CYS969 2.3 42.0 1.0 SG A:CYS986 2.3 51.5 1.0 CE1 A:HIS1001 2.8 43.8 1.0 CG A:HIS1001 3.1 39.8 1.0 CB A:CYS969 3.1 50.4 1.0 CB A:CYS986 3.1 48.0 1.0 CB A:CYS998 3.4 37.4 1.0 CB A:HIS1001 3.5 35.9 1.0 N A:CYS998 3.9 38.7 1.0 NE2 A:HIS1001 4.0 43.8 1.0 CD2 A:HIS1001 4.1 40.8 1.0 CA A:CYS998 4.2 36.2 1.0 CA A:CYS969 4.5 52.4 1.0 CA A:CYS986 4.6 51.2 1.0 N A:HIS1001 4.7 35.3 1.0 CB A:VAL971 4.7 57.8 1.0 CA A:HIS1001 4.7 34.5 1.0 CG2 A:VAL971 4.8 57.6 1.0 CB A:LYS988 4.8 51.0 1.0 CD A:LYS988 4.9 54.6 1.0 C A:CYS998 5.0 36.6 1.0 CE A:LYS988 5.0 54.8 1.0

Zinc binding site 10 out of 18 in the Crystal Structure of the Catalytic Core of E3 Ligase Hoip


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Catalytic Core of E3 Ligase Hoip within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1105 b:39.9 occ:1.00 CE1 A:HIS889 2.0 37.5 1.0 CE1 A:HIS887 2.1 42.5 1.0 NE2 A:HIS889 2.6 37.1 1.0 NE2 A:HIS887 2.7 37.2 1.0 ND1 A:HIS889 3.2 43.0 1.0 ND1 A:HIS887 3.3 43.4 1.0 CD2 A:HIS889 3.9 42.4 1.0 CD2 A:HIS887 4.0 38.9 1.0 CG A:HIS889 4.2 42.1 1.0 CG A:HIS887 4.3 42.3 1.0

B.Stieglitz, R.R.Rana, M.G.Koliopoulos, A.C.Morris-Davies, V.Schaeffer, E.Christodoulou, S.Howell, N.R.Brown, I.Dikic, K.Rittinger. Structural Basis For Ligase-Specific Conjugation of Linear Ubiquitin Chains By Hoip. Nature V. 503 422 2013.
ISSN: ISSN 0028-0836
PubMed: 24141947
DOI: 10.1038/NATURE12638