Calcium in PDB 7xw2: Cryo-Em Structure of Human Dicer-Pre-Mirna in A Dicing State

All present enzymatic activity of Cryo-Em Structure of Human Dicer-Pre-Mirna in A Dicing State:
3.1.26.3;

The binding sites of Calcium atom in the Cryo-Em Structure of Human Dicer-Pre-Mirna in A Dicing State (pdb code 7xw2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Human Dicer-Pre-Mirna in A Dicing State, PDB code: 7xw2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Human Dicer-Pre-Mirna in A Dicing State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Human Dicer-Pre-Mirna in A Dicing State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:30.0 occ:1.00 OP1 C:C52 2.0 73.2 1.0 OE1 A:GLU1564 2.6 39.2 1.0 OE2 A:GLU1564 2.9 39.2 1.0 CD A:GLU1564 3.0 39.2 1.0 OD1 A:ASP1561 3.1 41.1 1.0 P C:C52 3.4 73.2 1.0 O5' C:C52 4.1 73.2 1.0 OD1 A:ASP1320 4.1 40.6 1.0 CG A:ASP1561 4.2 41.1 1.0 OP2 C:C52 4.3 73.2 1.0 O3' C:G51 4.4 75.1 1.0 CG A:GLU1564 4.5 39.2 1.0 C5' C:C52 4.5 73.2 1.0 OD1 A:ASN1353 4.6 49.3 1.0 O A:ALA1560 4.8 38.2 1.0 CA A:ASP1561 4.8 41.1 1.0 OE1 A:GLU1316 4.8 46.2 1.0 CG A:ASP1320 4.8 40.6 1.0 OD2 A:ASP1320 4.8 40.6 1.0 CB A:ASP1561 4.9 41.1 1.0 CD A:GLU1316 4.9 46.2 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Human Dicer-Pre-Mirna in A Dicing State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Human Dicer-Pre-Mirna in A Dicing State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:30.0 occ:1.00 OE2 A:GLU1705 1.9 62.8 1.0 OP1 C:U23 2.0 87.2 1.0 CD A:GLU1705 2.4 62.8 1.0 OE1 A:GLU1705 2.4 62.8 1.0 OD1 A:ASP1810 2.7 69.4 1.0 P C:U23 3.5 87.2 1.0 OD2 A:ASP1810 3.5 69.4 1.0 CG A:ASP1810 3.5 69.4 1.0 OE1 A:GLU1813 3.7 56.5 1.0 CG A:GLU1705 3.9 62.8 1.0 OP2 C:U23 4.2 87.2 1.0 O5' C:U23 4.3 87.2 1.0 C5' C:U23 4.4 87.2 1.0 O3' C:U22 4.4 75.1 1.0 ND2 A:ASN1742 4.5 59.2 1.0 OD2 A:ASP1709 4.6 48.0 1.0 CD A:GLU1813 4.6 56.5 1.0 CB A:GLU1705 4.8 62.8 1.0 CB A:ASP1810 5.0 69.4 1.0

Y.Y.Lee, H.Lee, H.Kim, V.N.Kim, S.H.Roh. Structure of the Human Dicer-Pre-Mirna Complex in A Dicing State. Nature 2023.
ISSN: ESSN 1476-4687
PubMed: 36813958
DOI: 10.1038/S41586-023-05723-3