Zinc in PDB 4ljp: Structure of An Active Ligase (Hoip-H889A)/Ubiquitin Transfer Complex

The structure of Structure of An Active Ligase (Hoip-H889A)/Ubiquitin Transfer Complex, PDB code: 4ljp was solved by R.R.Rana, B.Stieglitz, 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)	38.17 / 2.15
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	46.000, 46.000, 133.370, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 21.6

The binding sites of Zinc atom in the Structure of An Active Ligase (Hoip-H889A)/Ubiquitin Transfer Complex (pdb code 4ljp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of An Active Ligase (Hoip-H889A)/Ubiquitin Transfer Complex, PDB code: 4ljp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of An Active Ligase (Hoip-H889A)/Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of An Active Ligase (Hoip-H889A)/Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:38.3 occ:1.00 SG A:CYS890 2.3 34.1 1.0 SG A:CYS893 2.3 40.0 1.0 SG A:CYS871 2.5 38.5 1.0 SG A:CYS874 2.5 39.7 1.0 CB A:CYS890 3.1 45.8 1.0 CB A:CYS871 3.2 38.3 1.0 CB A:CYS874 3.4 42.9 1.0 CB A:CYS893 3.4 41.4 1.0 N A:CYS893 3.8 45.2 1.0 N A:CYS874 3.8 45.3 1.0 CA A:CYS893 4.1 44.5 1.0 CA A:CYS874 4.2 44.8 1.0 CB A:HIS895 4.5 41.1 1.0 CA A:CYS890 4.6 41.5 1.0 CB A:LYS873 4.6 47.8 1.0 CB A:GLN892 4.7 41.3 1.0 CA A:CYS871 4.7 38.4 1.0 C A:CYS893 4.7 44.4 1.0 C A:GLN892 4.7 45.1 1.0 N A:HIS895 4.9 43.3 1.0 N A:ARG894 4.9 44.5 1.0 C A:CYS874 4.9 43.8 1.0 C A:LYS873 4.9 45.2 1.0 N A:LYS875 5.0 37.1 1.0

Zinc binding site 2 out of 4 in the Structure of An Active Ligase (Hoip-H889A)/Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of An Active Ligase (Hoip-H889A)/Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:28.2 occ:1.00 ND1 A:HIS926 2.1 30.9 1.0 SG A:CYS901 2.3 29.3 1.0 SG A:CYS930 2.4 28.5 1.0 SG A:CYS898 2.4 31.2 1.0 CE1 A:HIS926 3.1 32.6 1.0 CG A:HIS926 3.1 29.6 1.0 CB A:CYS901 3.3 28.8 1.0 CB A:CYS898 3.4 21.3 1.0 CB A:HIS926 3.4 27.4 1.0 CB A:CYS930 3.5 24.4 1.0 N A:CYS901 3.5 19.3 1.0 CA A:CYS901 4.0 25.6 1.0 C A:GLY900 4.1 25.7 1.0 CB A:PHE932 4.2 20.1 1.0 NE2 A:HIS926 4.2 32.6 1.0 CD2 A:HIS926 4.2 29.3 1.0 CA A:HIS926 4.3 33.4 1.0 CA A:GLY900 4.3 24.4 1.0 CE A:MET886 4.6 34.7 1.0 N A:GLY900 4.6 27.9 1.0 CD A:PRO927 4.7 31.5 1.0 CA A:CYS898 4.8 23.3 1.0 C A:CYS901 4.8 28.6 1.0 CA A:CYS930 4.9 27.0 1.0 O A:GLY900 4.9 29.8 1.0 CG A:PHE932 5.0 25.7 1.0

Zinc binding site 3 out of 4 in the Structure of An Active Ligase (Hoip-H889A)/Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of An Active Ligase (Hoip-H889A)/Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1103 b:41.3 occ:1.00 NE2 A:HIS925 2.1 47.3 1.0 NE2 A:HIS923 2.1 38.1 1.0 SG A:CYS916 2.2 68.7 1.0 SG A:CYS911 2.3 55.5 1.0 CE1 A:HIS925 2.8 50.1 1.0 CD2 A:HIS923 3.0 33.7 1.0 CE1 A:HIS923 3.2 42.5 1.0 CD2 A:HIS925 3.3 35.1 1.0 CB A:CYS911 3.3 60.1 1.0 CB A:CYS916 3.4 75.4 1.0 ND1 A:HIS925 3.9 45.9 1.0 CG A:HIS923 4.2 33.8 1.0 CG A:HIS925 4.2 38.8 1.0 ND1 A:HIS923 4.3 36.7 1.0 CA A:CYS916 4.6 76.5 1.0 CG2 A:VAL918 4.6 47.7 1.0 CA A:CYS911 4.7 62.6 1.0 CB A:GLU913 4.8 83.6 1.0 O A:GLU913 4.9 96.6 1.0

Zinc binding site 4 out of 4 in the Structure of An Active Ligase (Hoip-H889A)/Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of An Active Ligase (Hoip-H889A)/Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1104 b:40.0 occ:1.00 ND1 A:HIS1001 2.1 45.0 1.0 SG A:CYS986 2.2 41.7 1.0 SG A:CYS969 2.4 43.1 1.0 SG A:CYS998 2.4 40.1 1.0 CB A:CYS969 3.0 42.4 1.0 CE1 A:HIS1001 3.0 32.8 1.0 CB A:CYS986 3.0 45.2 1.0 CG A:HIS1001 3.2 31.8 1.0 CB A:CYS998 3.3 44.4 1.0 CB A:HIS1001 3.5 32.3 1.0 N A:CYS998 3.9 42.2 1.0 CA A:CYS998 4.2 45.8 1.0 NE2 A:HIS1001 4.2 30.9 1.0 CD2 A:HIS1001 4.3 32.4 1.0 CA A:CYS969 4.5 49.8 1.0 CB A:VAL971 4.5 41.8 1.0 CA A:CYS986 4.5 49.0 1.0 CG2 A:VAL971 4.6 40.7 1.0 N A:HIS1001 4.7 35.5 1.0 CB A:LYS988 4.7 49.1 1.0 CA A:HIS1001 4.7 32.6 1.0 CD A:LYS988 4.9 51.6 1.0 C A:CYS998 4.9 43.1 1.0 C A:CYS969 5.0 51.1 1.0 CG A:LYS988 5.0 48.5 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