Calcium in PDB 7vg2: Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 40-Bp Rna

The structure of Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 40-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 40-Bp Rna (pdb code 7vg2). 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 40-Bp Rna, PDB code: 7vg2:
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 40-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 40-Bp Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:20.2 occ:1.00 OE1 A:GLU1136 2.1 19.4 1.0 OP1 D:A19 2.2 22.1 1.0 OE1 A:GLU1015 2.4 20.1 1.0 OD1 A:ASP1019 2.7 21.4 1.0 OD1 A:ASP1133 2.9 19.7 1.0 CD A:GLU1136 3.1 19.4 1.0 OE2 A:GLU1136 3.6 19.4 1.0 CD A:GLU1015 3.6 20.1 1.0 CG A:ASP1019 3.6 21.4 1.0 P D:A19 3.7 22.1 1.0 OD2 A:ASP1019 3.8 21.4 1.0 OE2 A:GLU1015 4.0 20.1 1.0 CE A:LYS1129 4.1 21.3 1.0 OD1 A:ASN1052 4.1 20.7 1.0 CG A:ASP1133 4.1 19.7 1.0 C5' D:A19 4.2 22.1 1.0 O5' D:A19 4.3 22.1 1.0 CG A:GLU1136 4.4 19.4 1.0 O3' D:G18 4.4 22.0 1.0 O A:GLU1015 4.4 20.1 1.0 CA A:ASP1133 4.5 19.7 1.0 CB A:GLU1136 4.5 19.4 1.0 OP2 D:A19 4.7 22.1 1.0 CG A:GLU1015 4.8 20.1 1.0 CB A:GLU1015 4.8 20.1 1.0 CB A:ASP1133 4.8 19.7 1.0 N A:ASP1133 4.8 19.7 1.0 O A:SER1132 4.9 19.6 1.0 NZ A:LYS1129 4.9 21.3 1.0 OD2 A:ASP1133 4.9 19.7 1.0 CG A:ASN1052 5.0 20.7 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 40-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 40-Bp Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:35.4 occ:1.00 OD1 A:ASP1316 1.8 35.1 1.0 OP1 C:U25 2.2 29.9 1.0 OE1 A:GLU1319 2.6 32.8 1.0 CG A:ASP1316 3.0 35.1 1.0 ND2 A:ASN1261 3.0 34.2 1.0 OE2 A:GLU1319 3.1 32.8 1.0 CD A:GLU1319 3.2 32.8 1.0 OE2 A:GLU1224 3.4 32.6 1.0 P C:U25 3.4 29.9 1.0 OD2 A:ASP1316 3.6 35.1 1.0 CG A:ASN1261 3.8 34.2 1.0 OP2 C:U25 3.9 29.9 1.0 OD1 A:ASN1261 3.9 34.2 1.0 OD1 A:ASP1228 4.0 28.4 1.0 CA A:ASP1316 4.0 35.1 1.0 CB A:ASP1316 4.0 35.1 1.0 N A:ASP1316 4.1 35.1 1.0 O3' C:C24 4.4 25.3 1.0 CG A:GLU1319 4.5 32.8 1.0 O A:LYS1312 4.5 38.2 1.0 O5' C:U25 4.5 29.9 1.0 C A:GLY1315 4.6 36.3 1.0 CD A:GLU1224 4.6 32.6 1.0 O A:GLY1315 4.8 36.3 1.0 C5' C:U25 4.9 29.9 1.0 CB A:ASN1261 4.9 34.2 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