Zinc in PDB 1ml9: Structure of the Neurospora Set Domain Protein Dim-5, A Histone Lysine Methyltransferase

All present enzymatic activity of Structure of the Neurospora Set Domain Protein Dim-5, A Histone Lysine Methyltransferase:
2.1.1.43;

The structure of Structure of the Neurospora Set Domain Protein Dim-5, A Histone Lysine Methyltransferase, PDB code: 1ml9 was solved by X.Zhang, H.Tamaru, S.I.Khan, J.R.Horton, L.J.Keefe, E.U.Selker, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.83 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.730, 81.560, 101.270, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.8

The binding sites of Zinc atom in the Structure of the Neurospora Set Domain Protein Dim-5, A Histone Lysine Methyltransferase (pdb code 1ml9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of the Neurospora Set Domain Protein Dim-5, A Histone Lysine Methyltransferase, PDB code: 1ml9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of the Neurospora Set Domain Protein Dim-5, A Histone Lysine Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Neurospora Set Domain Protein Dim-5, A Histone Lysine Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:37.6 occ:1.00 SG A:CYS132 2.2 37.0 1.0 SG A:CYS81 2.3 42.2 1.0 SG A:CYS66 2.3 43.3 1.0 SG A:CYS128 2.4 41.7 1.0 CB A:CYS66 3.2 42.0 1.0 CB A:CYS132 3.3 41.4 1.0 CB A:CYS128 3.3 36.2 1.0 CB A:CYS81 3.5 41.5 1.0 CA A:CYS128 3.6 33.7 1.0 N A:CYS66 3.7 41.4 1.0 ZN A:ZN3 3.7 45.3 1.0 ZN A:ZN2 3.9 42.9 1.0 SG A:CYS79 4.0 46.6 1.0 CA A:CYS66 4.0 41.5 1.0 CA A:CYS132 4.4 42.0 1.0 SG A:CYS134 4.5 39.4 1.0 SG A:CYS74 4.5 45.6 1.0 N A:CYS128 4.6 32.1 1.0 N A:HIS129 4.7 31.6 1.0 CA A:CYS81 4.7 43.2 1.0 C A:CYS128 4.7 33.5 1.0 N A:CYS81 4.7 46.7 1.0 CE1 A:HIS129 4.7 27.8 1.0 C A:GLY65 4.8 40.6 1.0 C A:CYS66 4.9 42.2 1.0 O A:CYS66 4.9 40.7 1.0

Zinc binding site 2 out of 3 in the Structure of the Neurospora Set Domain Protein Dim-5, A Histone Lysine Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Neurospora Set Domain Protein Dim-5, A Histone Lysine Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:42.9 occ:1.00 SG A:CYS134 2.3 39.4 1.0 SG A:CYS74 2.3 45.6 1.0 SG A:CYS128 2.3 41.7 1.0 SG A:CYS138 2.3 45.6 1.0 CB A:CYS134 3.1 44.5 1.0 CB A:CYS74 3.2 48.1 1.0 CB A:CYS128 3.3 36.2 1.0 CB A:CYS138 3.3 41.2 1.0 ZN A:ZN1 3.9 37.6 1.0 ZN A:ZN3 3.9 45.3 1.0 SG A:CYS66 4.1 43.3 1.0 NE A:ARG141 4.3 33.9 1.0 CA A:CYS134 4.5 47.0 1.0 CA A:CYS74 4.6 51.5 1.0 CA A:CYS138 4.7 40.9 1.0 CB A:CYS132 4.7 41.4 1.0 CA A:CYS128 4.7 33.7 1.0 NH2 A:ARG141 4.9 34.4 1.0 CB A:ASN140 4.9 36.9 1.0 N A:CYS134 4.9 47.9 1.0

Zinc binding site 3 out of 3 in the Structure of the Neurospora Set Domain Protein Dim-5, A Histone Lysine Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Neurospora Set Domain Protein Dim-5, A Histone Lysine Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:45.3 occ:1.00 SG A:CYS79 2.3 46.6 1.0 SG A:CYS66 2.3 43.3 1.0 SG A:CYS68 2.3 50.6 1.0 SG A:CYS74 2.4 45.6 1.0 CB A:CYS66 3.2 42.0 1.0 CB A:CYS68 3.2 48.4 1.0 CB A:CYS74 3.3 48.1 1.0 CB A:CYS79 3.4 48.9 1.0 CA A:CYS74 3.4 51.5 1.0 ZN A:ZN1 3.7 37.6 1.0 ZN A:ZN2 3.9 42.9 1.0 CA A:CYS79 4.0 49.1 1.0 N A:CYS74 4.1 54.2 1.0 SG A:CYS128 4.1 41.7 1.0 N A:CYS68 4.3 51.4 1.0 CA A:CYS68 4.3 51.5 1.0 C A:CYS74 4.6 51.5 1.0 CA A:CYS66 4.6 41.5 1.0 O A:CYS74 4.7 53.5 1.0 N A:GLN80 4.7 48.6 1.0 C A:CYS79 4.8 48.9 1.0 C A:GLU73 4.9 55.3 1.0 C A:CYS66 4.9 42.2 1.0

X.Zhang, H.Tamaru, S.I.Khan, J.R.Horton, L.J.Keefe, E.U.Selker, X.Cheng. Structure of the Neurospora Set Domain Protein Dim-5, A Histone H3 Lysine Methyltransferase Cell(Cambridge,Mass.) V. 111 117 2002.
ISSN: ISSN 0092-8674
PubMed: 12372305
DOI: 10.1016/S0092-8674(02)00999-6