Calcium in PDB 7vg3: Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 30-Bp Rna

The structure of Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 30-Bp Rna also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 30-Bp Rna (pdb code 7vg3). 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 Arabidopsis DCL3 in Complex with A 30-Bp Rna, PDB code: 7vg3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 30-Bp Rna


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 Arabidopsis DCL3 in Complex with A 30-Bp Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:38.6 occ:1.00 OP1 D:A9 2.2 44.0 1.0 OE2 A:GLU1015 2.2 38.6 1.0 CD A:GLU1015 2.9 38.6 1.0 OE1 A:GLU1015 3.4 38.6 1.0 P D:A9 3.6 44.0 1.0 CB A:ASP1133 3.8 34.6 1.0 OE1 A:GLU1136 3.9 38.3 1.0 CG A:GLU1015 3.9 38.6 1.0 OD2 A:ASP1133 4.1 34.6 1.0 O5' D:A9 4.2 44.0 1.0 OP2 D:A9 4.2 44.0 1.0 C5' D:A9 4.3 44.0 1.0 ND2 A:ASN1052 4.5 36.9 1.0 CG A:ASP1133 4.5 34.6 1.0 OP2 D:U10 4.7 40.9 1.0 O3' D:G8 4.7 48.8 1.0 CD A:GLU1136 4.9 38.3 1.0 OP1 D:U10 5.0 40.9 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 30-Bp Rna


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 Arabidopsis DCL3 in Complex with A 30-Bp Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:55.5 occ:1.00 OP1 C:U25 1.9 60.1 1.0 OE2 A:GLU1224 2.2 61.7 1.0 OD1 A:ASP1316 2.5 69.6 1.0 CD A:GLU1224 3.2 61.7 1.0 OE1 A:GLU1319 3.2 61.0 1.0 P C:U25 3.4 60.1 1.0 CG A:ASP1316 3.5 69.6 1.0 OD2 A:ASP1316 3.9 69.6 1.0 OE1 A:GLU1224 3.9 61.7 1.0 CG A:GLU1224 4.0 61.7 1.0 CD A:GLU1319 4.1 61.0 1.0 O3' C:C24 4.2 49.3 1.0 O5' C:U25 4.3 60.1 1.0 OP2 C:U25 4.3 60.1 1.0 OE2 A:GLU1319 4.3 61.0 1.0 C5' C:U25 4.4 60.1 1.0 CB A:ASP1316 4.6 69.6 1.0 ND2 A:ASN1261 4.8 55.1 1.0 OD2 A:ASP1228 4.8 53.9 1.0 OD1 A:ASN1261 5.0 55.1 1.0

Q.Wang, Y.Xue, L.Zhang, Z.Zhong, S.Feng, C.Wang, L.Xiao, Z.Yang, C.J.Harris, Z.Wu, J.Zhai, M.Yang, S.Li, S.E.Jacobsen, J.Du. Mechanism of Sirna Production By A Plant Dicer-Rna Complex in Dicing-Competent Conformation. Science L4546 2021.
ISSN: ESSN 1095-9203
PubMed: 34648373
DOI: 10.1126/SCIENCE.ABL4546