Magnesium in PDB 6r5k: Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase

All present enzymatic activity of Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase:
3.1.13.4;

The binding sites of Magnesium atom in the Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase (pdb code 6r5k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase, PDB code: 6r5k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:0.4 occ:1.00 MG E:MG102 1.3 1.0 1.0 N3 E:A65 2.2 0.7 1.0 C5' E:A66 2.5 0.1 1.0 C1' E:A65 2.5 0.7 1.0 O3' E:A65 2.7 0.7 1.0 O2' E:A65 3.0 0.7 1.0 C4 E:A65 3.0 0.7 1.0 C2' E:A65 3.2 0.7 1.0 N9 E:A65 3.2 0.7 1.0 C2 E:A65 3.3 0.7 1.0 O5' E:A66 3.4 0.1 1.0 O A:LEU1047 3.4 0.4 1.0 O4' E:A65 3.5 0.7 1.0 C3' E:A65 3.5 0.7 1.0 C4' E:A66 3.5 0.1 1.0 P E:A66 3.5 0.1 1.0 C3' E:A66 3.6 0.1 1.0 NE2 A:HIS1015 3.6 0.3 1.0 OP2 E:A66 3.7 0.1 1.0 CA A:SER1048 3.9 0.1 1.0 C2' E:A66 3.9 0.1 1.0 CD2 A:HIS1015 4.0 0.3 1.0 C4' E:A65 4.0 0.7 1.0 O4' E:A66 4.2 0.1 1.0 C A:LEU1047 4.3 0.4 1.0 C5 E:A65 4.4 0.7 1.0 N A:LEU1049 4.4 0.5 1.0 N A:SER1048 4.5 0.1 1.0 CB A:SER1048 4.5 0.1 1.0 N1 E:A65 4.6 0.7 1.0 C8 E:A65 4.6 0.7 1.0 CD2 A:LEU1049 4.6 0.5 1.0 C1' E:A66 4.7 0.1 1.0 OP2 E:A67 4.7 0.0 1.0 C A:SER1048 4.7 0.1 1.0 O A:TYR1046 4.8 0.6 1.0 CE1 A:HIS1015 4.9 0.3 1.0 OP1 E:A66 4.9 0.1 1.0 O3' E:A66 4.9 0.1 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of A Poly(A) Rnp Bound to the PAN2-PAN3 Deadenylase within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg102 b:1.0 occ:1.00 MG E:MG101 1.3 0.4 1.0 O2' E:A65 2.1 0.7 1.0 N3 E:A65 2.2 0.7 1.0 O A:LEU1047 2.6 0.4 1.0 CA A:SER1048 2.6 0.1 1.0 C1' E:A65 2.7 0.7 1.0 C2' E:A65 2.8 0.7 1.0 C4 E:A65 2.9 0.7 1.0 O3' E:A65 3.0 0.7 1.0 N9 E:A65 3.1 0.7 1.0 C A:LEU1047 3.2 0.4 1.0 C2 E:A65 3.2 0.7 1.0 N A:SER1048 3.2 0.1 1.0 CB A:SER1048 3.3 0.1 1.0 C3' E:A65 3.5 0.7 1.0 NE2 A:HIS1015 3.7 0.3 1.0 C A:SER1048 3.7 0.1 1.0 N A:LEU1049 3.7 0.5 1.0 C5' E:A66 3.8 0.1 1.0 O4' E:A65 3.9 0.7 1.0 O A:TYR1046 4.1 0.6 1.0 C5 E:A65 4.1 0.7 1.0 P E:A66 4.2 0.1 1.0 OP2 E:A66 4.2 0.1 1.0 N1 E:A65 4.3 0.7 1.0 C8 E:A65 4.4 0.7 1.0 C4' E:A65 4.4 0.7 1.0 CD2 A:HIS1015 4.4 0.3 1.0 O5' E:A66 4.4 0.1 1.0 CA A:LEU1047 4.6 0.4 1.0 OG A:SER1048 4.7 0.1 1.0 CE1 A:HIS1015 4.7 0.3 1.0 C6 E:A65 4.7 0.7 1.0 C4' E:A66 4.8 0.1 1.0 C3' E:A66 4.8 0.1 1.0 CD2 A:LEU1049 4.8 0.5 1.0 O A:SER1048 4.9 0.1 1.0 C A:TYR1046 4.9 0.6 1.0 N7 E:A65 4.9 0.7 1.0 N A:LEU1047 5.0 0.4 1.0 C2' E:A66 5.0 0.1 1.0

I.B.Schafer, M.Yamashita, J.M.Schuller, S.Schussler, P.Reichelt, M.Strauss, E.Conti. Molecular Basis For Poly(A) Rnp Architecture and Recognition By the PAN2-PAN3 Deadenylase. Cell V. 177 1619 2019.
ISSN: ISSN 1097-4172
PubMed: 31104843
DOI: 10.1016/J.CELL.2019.04.013