Zinc in PDB 4xi6: Crystal Structure of the Mzm-Rep Domains of Mind Bomb 1

The structure of Crystal Structure of the Mzm-Rep Domains of Mind Bomb 1, PDB code: 4xi6 was solved by B.J.Mcmillan, S.C.Blacklow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.94 / 2.04
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.083, 73.083, 170.959, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.8

The binding sites of Zinc atom in the Crystal Structure of the Mzm-Rep Domains of Mind Bomb 1 (pdb code 4xi6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Mzm-Rep Domains of Mind Bomb 1, PDB code: 4xi6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Mzm-Rep Domains of Mind Bomb 1


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 Mzm-Rep Domains of Mind Bomb 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:22.5 occ:1.00 SG A:CYS109 2.3 15.0 1.0 SG A:CYS88 2.3 19.1 1.0 SG A:CYS112 2.3 16.3 1.0 SG A:CYS85 2.3 16.9 1.0 HB2 A:CYS112 2.9 20.7 1.0 HB3 A:CYS88 3.0 25.0 1.0 H A:CYS88 3.0 23.9 1.0 H A:CYS109 3.0 14.3 1.0 HB3 A:CYS85 3.2 18.5 1.0 CB A:CYS88 3.2 20.8 1.0 CB A:CYS112 3.2 17.3 1.0 CB A:CYS85 3.3 15.4 1.0 HB2 A:CYS85 3.4 18.5 1.0 HB3 A:CYS109 3.4 15.0 1.0 CB A:CYS109 3.5 12.5 1.0 H A:CYS112 3.5 19.1 1.0 N A:CYS88 3.7 19.9 1.0 N A:CYS109 3.8 11.9 1.0 HB A:THR87 3.9 23.4 1.0 HB3 A:CYS112 3.9 20.7 1.0 HB2 A:CYS88 4.0 25.0 1.0 CA A:CYS88 4.0 21.4 1.0 N A:CYS112 4.1 15.9 1.0 CA A:CYS109 4.2 11.7 1.0 HB2 A:CYS109 4.3 15.0 1.0 CA A:CYS112 4.3 17.0 1.0 H A:THR87 4.4 22.5 1.0 H A:GLN90 4.4 23.1 1.0 HB3 A:GLN90 4.4 22.8 1.0 HB A:VAL111 4.4 27.0 1.0 H A:ARG89 4.5 29.8 1.0 O A:HOH768 4.5 52.0 1.0 HA A:LEU108 4.5 15.1 1.0 HD22 A:LEU108 4.6 16.1 1.0 HB2 A:GLN90 4.7 22.8 1.0 HA A:CYS112 4.7 20.4 1.0 CA A:CYS85 4.7 14.5 1.0 CB A:THR87 4.7 19.5 1.0 C A:CYS88 4.8 23.6 1.0 C A:CYS109 4.8 13.8 1.0 HB3 A:LEU108 4.8 15.2 1.0 HA A:CYS88 4.8 25.7 1.0 O A:CYS109 4.8 15.2 1.0 C A:THR87 4.8 20.1 1.0 N A:ARG89 4.9 24.8 1.0 HG22 A:THR87 4.9 23.9 1.0 C A:LEU108 5.0 12.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Mzm-Rep Domains of Mind Bomb 1


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 Mzm-Rep Domains of Mind Bomb 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:18.9 occ:1.00 NE2 A:HIS118 2.0 12.7 1.0 ND1 A:HIS122 2.1 14.3 1.0 SG A:CYS103 2.3 15.1 1.0 SG A:CYS100 2.3 11.8 1.0 HB2 A:CYS103 3.0 14.3 1.0 CE1 A:HIS122 3.0 15.9 1.0 CE1 A:HIS118 3.0 13.4 1.0 CD2 A:HIS118 3.1 13.2 1.0 HE1 A:HIS122 3.1 19.1 1.0 CG A:HIS122 3.2 13.1 1.0 HE1 A:HIS118 3.2 16.1 1.0 HB3 A:HIS122 3.2 12.9 1.0 CB A:CYS103 3.2 11.9 1.0 HD2 A:HIS118 3.2 15.9 1.0 CB A:CYS100 3.4 7.8 1.0 HB3 A:CYS100 3.5 9.4 1.0 HB2 A:CYS100 3.5 9.4 1.0 CB A:HIS122 3.6 10.8 1.0 HB2 A:HIS122 3.7 12.9 1.0 HB2 A:GLU102 3.8 13.7 1.0 H A:CYS103 3.8 15.1 1.0 N A:CYS103 3.9 12.5 1.0 HB3 A:CYS103 4.0 14.3 1.0 ND1 A:HIS118 4.1 14.5 1.0 NE2 A:HIS122 4.1 15.4 1.0 CA A:CYS103 4.1 11.8 1.0 CG A:HIS118 4.2 13.2 1.0 H A:GLU102 4.2 10.7 1.0 CD2 A:HIS122 4.2 14.3 1.0 C A:GLU102 4.3 13.4 1.0 HB2 A:HIS119 4.3 21.0 1.0 HA A:CYS103 4.5 14.2 1.0 HB3 A:TYR106 4.6 14.9 1.0 CB A:GLU102 4.6 11.4 1.0 H A:HIS119 4.7 18.4 1.0 ND1 A:HIS119 4.7 24.7 1.0 CA A:CYS100 4.8 8.9 1.0 N A:GLU102 4.8 8.9 1.0 CA A:GLU102 4.8 10.8 1.0 O A:GLU102 4.8 16.1 1.0 HE1 A:PHE124 4.9 13.0 1.0 HE2 A:HIS122 4.9 18.5 1.0 HD1 A:HIS118 4.9 17.4 1.0 O A:HOH758 4.9 35.8 1.0 HD1 A:TYR106 5.0 16.7 1.0 HB3 A:GLU102 5.0 13.7 1.0 HA A:CYS100 5.0 10.7 1.0

B.J.Mcmillan, N.Ohlenhard, B.Schnute, B.Zimmerman, L.Miles, N.Beglova, T.Klein, S.C.Blacklow. A Tail of Two Sites: A Bipartite Mechanism For Recognition of Notch Ligands By Mind Bomb E3 Ligases Mol.Cell V. 57 2015.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2015.01.019