Zinc in PDB 4xib: Crystal Structure of the Mzm-Rep Domains of Mind Bomb 1 in Complex with Fly Delta N-Box Peptide

The structure of Crystal Structure of the Mzm-Rep Domains of Mind Bomb 1 in Complex with Fly Delta N-Box Peptide, PDB code: 4xib 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)	45.05 / 2.15
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.131, 74.131, 170.174, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.4

The binding sites of Zinc atom in the Crystal Structure of the Mzm-Rep Domains of Mind Bomb 1 in Complex with Fly Delta N-Box Peptide (pdb code 4xib). 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 in Complex with Fly Delta N-Box Peptide, PDB code: 4xib:
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 in Complex with Fly Delta N-Box Peptide


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 in Complex with Fly Delta N-Box Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:32.0 occ:1.00 SG A:CYS112 2.3 28.8 1.0 SG A:CYS85 2.4 27.0 1.0 SG A:CYS109 2.4 27.4 1.0 SG A:CYS88 2.4 35.7 1.0 HB3 A:CYS88 2.9 39.0 1.0 HB2 A:CYS112 2.9 30.4 1.0 H A:CYS88 3.0 36.0 1.0 H A:CYS109 3.1 28.6 1.0 CB A:CYS88 3.2 32.5 1.0 CB A:CYS112 3.2 25.3 1.0 HB3 A:CYS85 3.2 37.3 1.0 CB A:CYS85 3.3 31.1 1.0 HB2 A:CYS85 3.4 37.3 1.0 HB3 A:CYS109 3.5 31.6 1.0 CB A:CYS109 3.5 26.3 1.0 H A:CYS112 3.6 30.6 1.0 N A:CYS88 3.7 30.0 1.0 HB A:THR87 3.8 38.0 1.0 HB3 A:CYS112 3.8 30.4 1.0 N A:CYS109 3.9 23.8 1.0 HB2 A:CYS88 4.0 39.0 1.0 CA A:CYS88 4.0 35.7 1.0 N A:CYS112 4.2 25.5 1.0 CA A:CYS109 4.2 24.8 1.0 CA A:CYS112 4.3 29.6 1.0 HB2 A:CYS109 4.3 31.6 1.0 H A:GLN90 4.3 40.1 1.0 HB A:VAL111 4.4 38.4 1.0 H A:THR87 4.4 37.3 1.0 HB3 A:GLN90 4.5 46.0 1.0 HA A:LEU108 4.5 27.3 1.0 H A:ARG89 4.6 44.7 1.0 HB2 A:GLN90 4.6 46.0 1.0 HD22 A:LEU108 4.7 28.1 1.0 CA A:CYS85 4.7 30.1 1.0 C A:CYS88 4.7 35.8 1.0 HA A:CYS112 4.7 35.5 1.0 CB A:THR87 4.7 31.6 1.0 HA A:CYS88 4.8 42.9 1.0 C A:CYS109 4.8 23.2 1.0 HB3 A:LEU108 4.8 30.6 1.0 C A:THR87 4.8 35.8 1.0 N A:ARG89 4.9 37.2 1.0 O A:CYS109 4.9 27.0 1.0 C A:LEU108 5.0 23.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Mzm-Rep Domains of Mind Bomb 1 in Complex with Fly Delta N-Box Peptide


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 in Complex with Fly Delta N-Box Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:26.1 occ:1.00 NE2 A:HIS118 2.0 25.4 1.0 ND1 A:HIS122 2.1 30.6 1.0 SG A:CYS103 2.2 33.0 1.0 SG A:CYS100 2.2 22.4 1.0 CE1 A:HIS122 3.0 29.0 1.0 CE1 A:HIS118 3.0 26.6 1.0 HB2 A:CYS103 3.0 34.5 1.0 CD2 A:HIS118 3.0 26.5 1.0 HE1 A:HIS122 3.1 34.8 1.0 HE1 A:HIS118 3.1 31.9 1.0 CG A:HIS122 3.1 23.9 1.0 HB3 A:HIS122 3.2 30.7 1.0 CB A:CYS103 3.2 28.7 1.0 HD2 A:HIS118 3.3 31.8 1.0 CB A:CYS100 3.4 26.3 1.0 HB3 A:CYS100 3.5 31.5 1.0 HB2 A:CYS100 3.5 31.5 1.0 CB A:HIS122 3.6 25.6 1.0 HB2 A:HIS122 3.7 30.7 1.0 HB2 A:GLU102 3.7 27.9 1.0 H A:CYS103 3.8 30.4 1.0 N A:CYS103 3.9 25.3 1.0 HB3 A:CYS103 4.0 34.5 1.0 ND1 A:HIS118 4.1 26.6 1.0 NE2 A:HIS122 4.1 25.9 1.0 CA A:CYS103 4.1 24.7 1.0 CG A:HIS118 4.2 27.1 1.0 H A:GLU102 4.2 26.6 1.0 CD2 A:HIS122 4.2 22.9 1.0 C A:GLU102 4.3 27.0 1.0 HB2 A:HIS119 4.4 39.7 1.0 HA A:CYS103 4.5 29.6 1.0 HB3 A:TYR106 4.6 36.7 1.0 CB A:GLU102 4.6 23.2 1.0 ND1 A:HIS119 4.7 48.6 1.0 H A:HIS119 4.7 39.8 1.0 O A:GLU102 4.7 33.5 1.0 CA A:CYS100 4.8 24.7 1.0 CA A:GLU102 4.8 19.8 1.0 N A:GLU102 4.8 22.2 1.0 HD1 A:HIS118 4.9 31.9 1.0 HE2 A:HIS122 4.9 31.1 1.0 HE1 A:PHE124 4.9 28.1 1.0 HA A:CYS100 5.0 29.7 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