Zinc in PDB 5hj0: Crystal Structure of MIS18 'Yippee-Like' Domain

The structure of Crystal Structure of MIS18 'Yippee-Like' Domain, PDB code: 5hj0 was solved by B.Medina-Pritchard, L.Subramanian, R.Allshire, A.Arockia Jeyaprakash, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.63 / 2.64
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	121.069, 121.069, 73.211, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 26

The binding sites of Zinc atom in the Crystal Structure of MIS18 'Yippee-Like' Domain (pdb code 5hj0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of MIS18 'Yippee-Like' Domain, PDB code: 5hj0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of MIS18 'Yippee-Like' Domain


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 MIS18 'Yippee-Like' Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:63.3 occ:1.00 SG A:CYS25 2.3 65.5 1.0 SG A:CYS82 2.3 61.7 1.0 SG A:CYS28 2.3 63.1 1.0 SG A:CYS79 2.4 61.9 1.0 CB A:CYS25 3.2 63.3 1.0 CB A:CYS79 3.3 63.9 1.0 CB A:CYS82 3.4 64.2 1.0 CB A:CYS28 3.4 65.3 1.0 N A:CYS82 3.7 67.1 1.0 N A:CYS28 3.8 67.9 1.0 CA A:CYS82 4.1 65.4 1.0 CA A:CYS28 4.2 67.3 1.0 O A:CYS28 4.2 74.6 1.0 C A:CYS28 4.4 68.7 1.0 CB A:LYS27 4.4 74.3 1.0 CA A:CYS25 4.6 64.9 1.0 CB A:ARG81 4.7 70.8 1.0 CA A:CYS79 4.7 62.4 1.0 C A:ARG81 4.7 69.2 1.0 C A:CYS82 4.7 65.0 1.0 CB A:GLU84 4.8 70.3 1.0 N A:ASN83 4.9 65.0 1.0 N A:LYS27 4.9 70.9 1.0 C A:LYS27 4.9 69.9 1.0 CA A:LYS27 5.0 72.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of MIS18 'Yippee-Like' Domain


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 MIS18 'Yippee-Like' Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:71.8 occ:1.00 SG B:CYS82 2.3 71.2 1.0 SG B:CYS25 2.3 71.0 1.0 SG B:CYS79 2.3 69.1 1.0 SG B:CYS28 2.3 71.5 1.0 CB B:CYS25 3.1 66.9 1.0 CB B:CYS79 3.2 72.4 1.0 CB B:CYS82 3.3 74.5 1.0 CB B:CYS28 3.5 72.2 1.0 N B:CYS28 3.7 70.4 1.0 O B:CYS28 3.9 79.8 1.0 N B:CYS82 4.0 76.8 1.0 CA B:CYS28 4.1 71.5 1.0 CA B:CYS82 4.2 76.1 1.0 C B:CYS28 4.3 72.9 1.0 CA B:CYS25 4.5 65.6 1.0 CB B:LYS27 4.5 69.9 1.0 CA B:CYS79 4.7 72.2 1.0 CB B:ARG81 4.8 81.6 1.0 C B:LYS27 4.8 70.2 1.0 C B:CYS82 4.9 74.0 1.0 N B:LYS27 4.9 69.0 1.0 CB B:GLU84 4.9 73.5 1.0 CB B:GLN30 4.9 75.9 1.0 CA B:LYS27 4.9 69.8 1.0 C B:ARG81 5.0 79.1 1.0 C B:CYS25 5.0 65.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of MIS18 'Yippee-Like' Domain


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 MIS18 'Yippee-Like' Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:0.5 occ:1.00 SG C:CYS82 2.3 0.5 1.0 SG C:CYS79 2.3 0.4 1.0 SG C:CYS25 2.3 0.2 1.0 SG C:CYS28 2.3 0.9 1.0 CB C:CYS25 3.2 0.2 1.0 CB C:CYS79 3.2 0.9 1.0 N C:CYS82 3.3 0.5 1.0 CB C:CYS82 3.4 0.3 1.0 CB C:CYS28 3.5 0.5 1.0 CA C:CYS82 3.8 0.7 1.0 N C:CYS28 4.0 0.0 1.0 CA C:CYS28 4.2 1.0 1.0 CB C:ARG81 4.3 0.1 1.0 C C:ARG81 4.3 0.6 1.0 O C:CYS28 4.3 0.7 1.0 C C:CYS28 4.5 0.7 1.0 C C:CYS82 4.5 0.8 1.0 CA C:ARG81 4.6 0.5 1.0 CA C:CYS79 4.7 0.8 1.0 CA C:CYS25 4.7 1.0 1.0 N C:ARG81 4.7 0.7 1.0 N C:ASN83 4.9 0.7 1.0 C C:CYS79 5.0 0.8 1.0 O C:CYS79 5.0 0.2 1.0

L.Subramanian, B.Medina-Pritchard, R.Barton, F.Spiller, R.Kulasegaran-Shylini, G.Radaviciute, R.C.Allshire, A.Arockia Jeyaprakash. Centromere Localization and Function of MIS18 Requires Yippee-Like Domain-Mediated Oligomerization. Embo Rep. V. 17 496 2016.
ISSN: ESSN 1469-3178
PubMed: 26921242
DOI: 10.15252/EMBR.201541520