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

The structure of Structure of An Active Ligase (Hoip)/Ubiquitin Transfer Complex, PDB code: 4ljo was solved by R.R.Rana, B.Stieglitz, Koliopoulos M.G., 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)	44.34 / 1.56
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	45.950, 45.950, 133.010, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21.2

The binding sites of Zinc atom in the Structure of An Active Ligase (Hoip)/Ubiquitin Transfer Complex (pdb code 4ljo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of An Active Ligase (Hoip)/Ubiquitin Transfer Complex, PDB code: 4ljo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Structure of An Active Ligase (Hoip)/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)/Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:26.4 occ:1.00 SG A:CYS893 2.3 31.4 1.0 SG A:CYS871 2.3 26.1 1.0 SG A:CYS874 2.3 31.1 1.0 SG A:CYS890 2.4 27.5 1.0 CB A:CYS871 3.1 25.8 1.0 CB A:CYS890 3.1 26.6 1.0 CB A:CYS874 3.2 35.5 1.0 CB A:CYS893 3.3 32.9 1.0 N A:CYS874 3.7 30.5 1.0 N A:CYS893 3.9 30.6 1.0 CA A:CYS874 4.0 31.3 1.0 CA A:CYS893 4.1 35.4 1.0 CB A:HIS895 4.5 27.3 1.0 CA A:CYS871 4.6 26.8 1.0 CB A:LYS873 4.6 38.7 1.0 CA A:CYS890 4.6 23.9 1.0 C A:CYS893 4.8 34.2 1.0 C A:CYS874 4.8 31.3 1.0 C A:LYS873 4.8 35.2 1.0 CB A:GLN892 4.8 34.6 1.0 C A:GLN892 4.9 34.9 1.0 N A:HIS895 4.9 27.5 1.0 N A:ARG894 4.9 29.1 1.0 N A:LYS875 5.0 29.3 1.0

Zinc binding site 2 out of 5 in the Structure of An Active Ligase (Hoip)/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)/Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:19.3 occ:1.00 ND1 A:HIS926 2.1 18.1 1.0 SG A:CYS901 2.3 21.9 1.0 SG A:CYS930 2.3 18.9 1.0 SG A:CYS898 2.3 20.0 1.0 CE1 A:HIS926 3.0 17.6 1.0 CG A:HIS926 3.2 20.1 1.0 CB A:CYS901 3.2 22.1 1.0 CB A:CYS898 3.3 18.1 1.0 CB A:CYS930 3.5 21.1 1.0 N A:CYS901 3.6 20.7 1.0 CB A:HIS926 3.6 19.8 1.0 CA A:CYS901 4.0 22.2 1.0 NE2 A:HIS926 4.2 20.4 1.0 CB A:PHE932 4.2 19.8 1.0 C A:GLY900 4.2 24.0 1.0 CD2 A:HIS926 4.3 21.2 1.0 CA A:HIS926 4.4 19.3 1.0 CA A:GLY900 4.4 22.1 1.0 N A:GLY900 4.5 20.8 1.0 CE A:MET886 4.6 28.9 1.0 CA A:CYS898 4.7 18.0 1.0 CD A:PRO927 4.7 20.6 1.0 CA A:CYS930 4.8 17.4 1.0 C A:CYS901 4.9 21.3 1.0

Zinc binding site 3 out of 5 in the Structure of An Active Ligase (Hoip)/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)/Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1103 b:34.4 occ:1.00 NE2 A:HIS923 2.1 31.0 1.0 SG A:CYS911 2.1 69.7 1.0 NE2 A:HIS925 2.2 39.4 1.0 SG A:CYS916 2.4 87.3 1.0 CE1 A:HIS925 2.7 46.1 1.0 CB A:CYS916 2.9 67.5 1.0 CE1 A:HIS923 3.1 35.0 1.0 CD2 A:HIS923 3.1 28.2 1.0 CB A:CYS911 3.3 51.0 1.0 CD2 A:HIS925 3.4 37.2 1.0 ND1 A:HIS925 3.8 42.4 1.0 ND1 A:HIS923 4.2 30.0 1.0 CG A:HIS925 4.2 29.4 1.0 CG A:HIS923 4.2 29.6 1.0 CA A:CYS916 4.4 70.6 1.0 CB A:GLU913 4.6 67.6 1.0 CA A:CYS911 4.7 51.0 1.0 CD2 A:TYR906 4.8 39.4 1.0 O A:GLU913 4.8 73.8 1.0 N A:GLU913 4.8 71.1 1.0 CG1 A:VAL918 4.9 38.2 1.0 CG A:GLU913 5.0 65.0 1.0

Zinc binding site 4 out of 5 in the Structure of An Active Ligase (Hoip)/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)/Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1104 b:28.3 occ:1.00 ND1 A:HIS1001 2.1 23.3 1.0 SG A:CYS998 2.2 26.8 1.0 SG A:CYS986 2.3 29.2 1.0 SG A:CYS969 2.4 33.4 1.0 CE1 A:HIS1001 3.0 27.5 1.0 CB A:CYS969 3.0 36.5 1.0 CG A:HIS1001 3.1 21.0 1.0 CB A:CYS986 3.2 30.3 1.0 CB A:CYS998 3.3 32.3 1.0 CB A:HIS1001 3.5 22.5 1.0 N A:CYS998 4.0 25.2 1.0 O A:HOH1241 4.1 41.3 1.0 NE2 A:HIS1001 4.1 25.8 1.0 CD2 A:HIS1001 4.2 21.9 1.0 CA A:CYS998 4.2 33.1 1.0 CA A:CYS969 4.5 37.3 1.0 CB A:VAL971 4.5 28.5 1.0 N A:HIS1001 4.6 23.9 1.0 CG2 A:VAL971 4.6 30.8 1.0 O A:HOH1368 4.6 47.4 1.0 CB A:LYS988 4.6 34.1 1.0 CA A:CYS986 4.6 33.7 1.0 CA A:HIS1001 4.7 20.6 1.0 CD A:LYS988 4.8 43.0 1.0 C A:CYS969 5.0 38.0 1.0 CG A:LYS988 5.0 40.5 1.0 C A:CYS998 5.0 30.1 1.0

Zinc binding site 5 out of 5 in the Structure of An Active Ligase (Hoip)/Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of An Active Ligase (Hoip)/Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1106 b:21.5 occ:0.75 N1 A:IMD1105 2.0 27.7 1.0 N B:MET1 2.0 28.1 1.0 ND1 A:HIS887 2.1 25.4 1.0 SG A:CYS885 2.2 26.5 1.0 C5 A:IMD1105 2.8 35.2 1.0 CE1 A:HIS887 3.0 25.3 1.0 CA B:MET1 3.0 32.3 1.0 C2 A:IMD1105 3.1 38.4 1.0 CG A:HIS887 3.2 23.5 1.0 CB A:CYS885 3.3 27.7 1.0 CB A:HIS887 3.6 22.6 1.0 CB B:MET1 3.6 38.1 1.0 O B:VAL17 3.9 24.6 1.0 OE1 B:GLU16 4.0 33.9 1.0 C4 A:IMD1105 4.0 34.1 1.0 NE2 A:HIS887 4.1 25.7 1.0 N3 A:IMD1105 4.2 41.0 1.0 CD2 A:HIS887 4.2 25.9 1.0 N A:HIS887 4.3 21.1 1.0 C B:MET1 4.3 26.4 1.0 O A:HOH1363 4.5 41.4 1.0 CA A:HIS887 4.6 21.8 1.0 CA A:CYS885 4.7 25.6 1.0 O A:HOH1260 4.8 37.1 1.0 O B:MET1 4.8 28.5 1.0 N A:MET886 4.8 23.0 1.0 C A:CYS885 5.0 21.5 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