Zinc in PDB 1mvh: Structure of the Set Domain Histone Lysine Methyltransferase CLR4

The structure of Structure of the Set Domain Histone Lysine Methyltransferase CLR4, PDB code: 1mvh was solved by J.R.Min, X.Zhang, X.D.Cheng, S.I.S.Grewal, R.-M.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.070, 75.070, 190.590, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 26.9

The structure of Structure of the Set Domain Histone Lysine Methyltransferase CLR4 also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Zinc atom in the Structure of the Set Domain Histone Lysine Methyltransferase CLR4 (pdb code 1mvh). 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 Set Domain Histone Lysine Methyltransferase CLR4, PDB code: 1mvh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of the Set Domain Histone Lysine Methyltransferase CLR4


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 Set Domain Histone Lysine Methyltransferase CLR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:62.7 occ:1.00 SG A:CYS278 2.2 68.9 1.0 SG A:CYS307 2.3 66.2 1.0 SG A:CYS311 2.4 74.0 1.0 SG A:CYS260 2.4 0.0 1.0 CB A:CYS260 2.8 0.8 1.0 CB A:CYS307 3.1 63.3 1.0 CA A:CYS307 3.4 62.7 1.0 CB A:CYS311 3.5 79.7 1.0 N A:CYS260 3.6 0.6 1.0 SG A:CYS276 3.7 68.3 1.0 CA A:CYS260 3.7 0.3 1.0 CB A:CYS278 3.7 79.5 1.0 ZN A:ZN503 3.8 80.6 1.0 ZN A:ZN502 3.8 64.6 1.0 O A:CYS260 4.1 0.3 1.0 N A:ASN308 4.3 66.3 1.0 C A:CYS260 4.3 0.6 1.0 C A:CYS307 4.4 64.5 1.0 N A:CYS307 4.4 57.5 1.0 SG A:CYS268 4.6 87.3 1.0 CA A:CYS311 4.8 80.5 1.0 C A:GLY259 4.8 93.9 1.0 CA A:CYS278 4.9 83.9 1.0 N A:CYS278 4.9 88.5 1.0

Zinc binding site 2 out of 3 in the Structure of the Set Domain Histone Lysine Methyltransferase CLR4


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 Set Domain Histone Lysine Methyltransferase CLR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:64.6 occ:1.00 SG A:CYS307 2.1 66.2 1.0 SG A:CYS313 2.3 79.2 1.0 SG A:CYS268 2.4 87.3 1.0 SG A:CYS317 2.6 57.0 1.0 CB A:CYS307 2.9 63.3 1.0 CB A:CYS313 3.6 79.5 1.0 ZN A:ZN501 3.8 62.7 1.0 CB A:CYS268 3.9 94.5 1.0 CB A:CYS317 3.9 61.6 1.0 ZN A:ZN503 4.0 80.6 1.0 SG A:CYS260 4.0 0.0 1.0 CA A:CYS307 4.4 62.7 1.0 CB A:CYS311 4.5 79.7 1.0 CB A:ASN319 4.6 50.4 1.0 N A:CYS268 4.7 95.5 1.0 NE A:ARG320 4.7 60.0 1.0 SG A:CYS311 4.8 74.0 1.0 CA A:CYS268 4.8 95.2 1.0 C A:GLY267 4.8 96.4 1.0 CA A:CYS313 4.9 81.2 1.0 NH2 A:ARG320 4.9 58.8 1.0 N A:CYS313 4.9 81.0 1.0 CZ A:ARG320 5.0 60.6 1.0 N A:CYS307 5.0 57.5 1.0

Zinc binding site 3 out of 3 in the Structure of the Set Domain Histone Lysine Methyltransferase CLR4


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 Set Domain Histone Lysine Methyltransferase CLR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:80.6 occ:1.00 SG A:CYS276 2.2 68.3 1.0 SG A:CYS262 2.4 0.4 1.0 SG A:CYS260 2.4 0.0 1.0 SG A:CYS268 2.4 87.3 1.0 CB A:CYS268 2.9 94.5 1.0 CB A:CYS276 3.5 86.8 1.0 CB A:CYS260 3.5 0.8 1.0 SG A:CYS307 3.8 66.2 1.0 ZN A:ZN501 3.8 62.7 1.0 ZN A:ZN502 4.0 64.6 1.0 CA A:CYS276 4.0 90.0 1.0 CB A:CYS262 4.1 0.4 1.0 CA A:CYS268 4.3 95.2 1.0 CZ A:PHE288 4.3 78.1 1.0 O A:CYS262 4.5 0.0 1.0 CE2 A:PHE288 4.6 80.2 1.0 C A:CYS262 4.6 0.2 1.0 N A:CYS262 4.6 0.2 1.0 CA A:CYS262 4.7 0.4 1.0 N A:CYS276 4.8 94.1 1.0 O A:CYS268 4.8 96.7 1.0 CA A:CYS260 4.9 0.3 1.0 SG A:CYS278 5.0 68.9 1.0

J.Min, X.Zhang, X.Cheng, S.I.Grewal, R.M.Xu. Structure of the Set Domain Histone Lysine Methyltransferase CLR4. Nat.Struct.Biol. V. 9 828 2002.
ISSN: ISSN 1072-8368
PubMed: 12389037