Magnesium in PDB 7c7a: Cryo-Em Structure of Yeast Ribonuclease Mrp with Substrate ITS1

All present enzymatic activity of Cryo-Em Structure of Yeast Ribonuclease Mrp with Substrate ITS1:
3.1.26.5;

The structure of Cryo-Em Structure of Yeast Ribonuclease Mrp with Substrate ITS1 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Cryo-Em Structure of Yeast Ribonuclease Mrp with Substrate ITS1 (pdb code 7c7a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryo-Em Structure of Yeast Ribonuclease Mrp with Substrate ITS1, PDB code: 7c7a:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of Yeast Ribonuclease Mrp with Substrate ITS1


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 Yeast Ribonuclease Mrp with Substrate ITS1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:67.1 occ:1.00 OP2 A:A86 2.2 70.9 1.0 OP1 R:A1 2.5 79.5 1.0 OP2 A:G87 2.5 76.5 1.0 P A:A86 3.5 70.9 1.0 P R:A1 3.7 79.5 1.0 C5' R:A1 3.7 79.5 1.0 O5' R:A1 3.8 79.5 1.0 P A:G87 3.8 76.5 1.0 MG A:MG402 4.0 75.3 1.0 OP1 A:A86 4.1 70.9 1.0 O5' A:A86 4.3 70.9 1.0 OP1 A:G87 4.4 76.5 1.0 OP1 R:C2 4.4 85.4 1.0 O5' A:G87 4.6 76.5 1.0 O3' A:A85 4.6 72.8 1.0 OP2 A:A306 4.7 65.6 1.0 OP2 R:A1 4.7 79.5 1.0 OP1 A:A306 4.7 65.6 1.0 O3' R:A0 4.7 77.1 1.0 O3' R:A1 4.9 79.5 1.0 C4' R:A1 4.9 79.5 1.0 C5' A:A86 4.9 70.9 1.0 O3' A:A86 5.0 70.9 1.0 P R:C2 5.0 85.4 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of Yeast Ribonuclease Mrp with Substrate ITS1


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 Yeast Ribonuclease Mrp with Substrate ITS1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:75.3 occ:1.00 OP1 A:A86 2.2 70.9 1.0 O3' R:A0 2.2 77.1 1.0 OP1 R:A1 2.4 79.5 1.0 P R:A1 2.8 79.5 1.0 OP1 A:A305 2.9 64.0 1.0 OP2 A:A306 2.9 65.6 1.0 O5' A:A305 3.2 64.0 1.0 P A:A86 3.3 70.9 1.0 C3' R:A0 3.5 77.1 1.0 P A:A305 3.6 64.0 1.0 C5' A:A86 3.6 70.9 1.0 OP2 A:A86 3.7 70.9 1.0 O2' R:A0 3.7 77.1 1.0 O5' R:A1 3.9 79.5 1.0 C5' R:A1 3.9 79.5 1.0 C4' R:A0 3.9 77.1 1.0 O5' A:A86 3.9 70.9 1.0 OP2 R:A1 4.0 79.5 1.0 MG A:MG401 4.0 67.1 1.0 P A:A306 4.1 65.6 1.0 C2' R:A0 4.2 77.1 1.0 C4' A:A305 4.2 64.0 1.0 O3' A:C304 4.3 69.3 1.0 OP2 A:G87 4.3 76.5 1.0 C5' A:A305 4.3 64.0 1.0 O3' A:A305 4.5 64.0 1.0 C5' R:A0 4.6 77.1 1.0 O3' A:A85 4.6 72.8 1.0 C3' A:A305 4.7 64.0 1.0 OP1 A:A306 4.7 65.6 1.0 C4' A:A86 4.9 70.9 1.0 OP1 A:G87 4.9 76.5 1.0 P A:G87 5.0 76.5 1.0 OP2 A:A305 5.0 64.0 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of Yeast Ribonuclease Mrp with Substrate ITS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Yeast Ribonuclease Mrp with Substrate ITS1 within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg101 b:80.1 occ:1.00 OP1 A:G87 2.2 76.5 1.0 OP2 R:A1 2.3 79.5 1.0 P R:A1 3.5 79.5 1.0 P A:G87 3.6 76.5 1.0 OP1 R:A1 3.9 79.5 1.0 OP1 A:U88 4.3 98.6 1.0 O5' A:G87 4.3 76.5 1.0 O5' R:A1 4.3 79.5 1.0 OP2 A:G87 4.4 76.5 1.0 O3' A:A86 4.6 70.9 1.0 C5' A:G87 4.6 76.5 1.0 O3' R:A0 4.7 77.1 1.0 OP1 R:A0 4.7 77.1 1.0 O5' R:A0 4.9 77.1 1.0

P.Lan, B.Zhou, M.Tan, S.Li, M.Cao, J.Wu, M.Lei. Structural Insight Into Precursor Ribosomal Rna Processing By Ribonuclease Mrp. Science V. 369 656 2020.
ISSN: ESSN 1095-9203
PubMed: 32586950
DOI: 10.1126/SCIENCE.ABC0149