Zinc in PDB 3epz: Structure of the Replication Foci-Targeting Sequence of Human Dna Cytosine Methyltransferase DNMT1

All present enzymatic activity of Structure of the Replication Foci-Targeting Sequence of Human Dna Cytosine Methyltransferase DNMT1:
2.1.1.37;

The structure of Structure of the Replication Foci-Targeting Sequence of Human Dna Cytosine Methyltransferase DNMT1, PDB code: 3epz was solved by J.R.Walker, G.V.Avvakumov, S.Xue, Y.Li, C.Bountra, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.11 / 2.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.544, 59.768, 96.286, 90.00, 92.31, 90.00
R / Rfree (%)	21.3 / 26.4

The structure of Structure of the Replication Foci-Targeting Sequence of Human Dna Cytosine Methyltransferase DNMT1 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Structure of the Replication Foci-Targeting Sequence of Human Dna Cytosine Methyltransferase DNMT1 (pdb code 3epz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Replication Foci-Targeting Sequence of Human Dna Cytosine Methyltransferase DNMT1, PDB code: 3epz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Replication Foci-Targeting Sequence of Human Dna Cytosine Methyltransferase DNMT1


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 Replication Foci-Targeting Sequence of Human Dna Cytosine Methyltransferase DNMT1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:35.4 occ:1.00 ND1 A:HIS418 2.1 39.8 1.0 SG A:CYS356 2.2 37.3 1.0 SG A:CYS414 2.3 34.9 1.0 SG A:CYS353 2.4 38.0 1.0 CG A:HIS418 3.1 39.4 1.0 CE1 A:HIS418 3.1 41.4 1.0 CB A:CYS353 3.2 41.6 1.0 CB A:HIS418 3.3 37.7 1.0 CB A:CYS414 3.5 35.0 1.0 CB A:CYS356 3.5 40.6 1.0 N A:CYS356 3.9 41.8 1.0 NE2 A:HIS418 4.2 42.4 1.0 CD2 A:HIS418 4.2 40.5 1.0 CB A:GLN355 4.3 40.6 1.0 CA A:CYS356 4.3 41.9 1.0 CA A:HIS418 4.5 37.9 1.0 CB A:HIS416 4.6 40.2 1.0 N A:HIS418 4.6 38.0 1.0 CD2 A:HIS416 4.7 40.8 1.0 CA A:CYS353 4.7 43.9 1.0 C A:GLN355 4.8 42.7 1.0 CA A:CYS414 4.8 35.1 1.0 CA A:GLN355 4.9 42.6 1.0 NE2 A:GLN358 4.9 42.3 1.0 O A:HIS418 5.0 38.2 1.0 N A:GLN355 5.0 43.4 1.0

Zinc binding site 2 out of 2 in the Structure of the Replication Foci-Targeting Sequence of Human Dna Cytosine Methyltransferase DNMT1


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 Replication Foci-Targeting Sequence of Human Dna Cytosine Methyltransferase DNMT1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:60.5 occ:1.00 ND1 B:HIS418 2.0 66.4 1.0 SG B:CYS353 2.3 64.2 1.0 SG B:CYS414 2.5 58.9 1.0 CB B:CYS356 2.6 65.0 1.0 SG B:CYS356 2.6 67.1 1.0 CE1 B:HIS418 3.0 67.1 1.0 CG B:HIS418 3.0 66.4 1.0 CB B:CYS353 3.1 66.1 1.0 CB B:HIS418 3.3 64.2 1.0 N B:CYS356 3.4 64.6 1.0 CA B:CYS356 3.5 64.9 1.0 CB B:CYS414 3.6 56.5 1.0 NE2 B:HIS418 4.1 69.6 1.0 CD2 B:HIS418 4.1 68.7 1.0 CB B:GLN355 4.4 66.3 1.0 CA B:HIS418 4.5 64.5 1.0 C B:GLN355 4.6 65.3 1.0 CA B:CYS353 4.6 65.9 1.0 N B:HIS418 4.6 64.1 1.0 ND1 B:HIS416 4.6 63.3 1.0 CB B:HIS416 4.7 65.2 1.0 C B:CYS356 4.8 65.1 1.0 O B:HIS418 4.9 61.1 1.0 CA B:GLN355 4.9 65.7 1.0 CA B:CYS414 5.0 55.9 1.0

F.Syeda, R.L.Fagan, M.Wean, G.V.Avvakumov, J.R.Walker, S.Xue, S.Dhe-Paganon, C.Brenner. The Replication Focus Targeting Sequence (Rfts) Domain Is A Dna-Competitive Inhibitor of DNMT1. J.Biol.Chem. V. 286 15344 2011.
ISSN: ISSN 0021-9258
PubMed: 21389349
DOI: 10.1074/JBC.M110.209882