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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 3epz:

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

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Structure of the Replication Foci-Targeting Sequence of Human Dna Cytosine Methyltransferase DNMT1, PDB code: 3epz:

Sodium binding site 1 out of 1 in 3epz

Go back to Sodium Binding Sites List in 3epz
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na1

b:51.0
occ:1.00
 O A:LEU540 2.4 46.2 1.0
O A:GLY500 2.4 43.9 1.0
O A:MSE502 2.7 41.7 1.0
O A:ASN541 3.1 47.8 1.0
C A:GLY500 3.4 43.3 1.0
C A:ASN541 3.6 47.1 1.0
C A:LEU540 3.6 45.8 1.0
CD2 A:LEU542 3.6 41.9 1.0
N A:MSE502 3.7 41.2 1.0
C A:MSE502 3.7 41.1 1.0
CB A:ASN541 3.8 49.5 1.0
C A:LEU501 3.8 42.0 1.0
CG A:LEU542 3.8 43.3 1.0
CA A:LEU501 3.9 43.1 1.0
CA A:ASN541 4.1 48.1 1.0
N A:LEU501 4.1 42.7 1.0
CA A:MSE502 4.1 40.8 1.0
CB A:MSE502 4.2 40.9 1.0
N A:ASN541 4.3 46.7 1.0
N A:LEU542 4.3 45.8 1.0
O A:LEU501 4.5 42.2 1.0
CA A:GLY500 4.5 42.9 1.0
CA A:LEU542 4.6 44.9 1.0
CA A:LEU540 4.7 45.0 1.0
CB A:LEU542 4.8 43.7 1.0
N A:GLN503 4.9 40.2 1.0
CD1 A:LEU542 4.9 42.0 1.0
CG A:ASN541 5.0 53.4 1.0

Reference:

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
Page generated: Mon Oct 7 08:54:27 2024

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