Magnesium in PDB 6ah3: Cryo-Em Structure of Yeast Ribonuclease P with Pre-Trna Substrate

All present enzymatic activity of Cryo-Em Structure of Yeast Ribonuclease P with Pre-Trna Substrate:
3.1.26.5;

The structure of Cryo-Em Structure of Yeast Ribonuclease P with Pre-Trna Substrate also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Cryo-Em Structure of Yeast Ribonuclease P with Pre-Trna Substrate (pdb code 6ah3). 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 Yeast Ribonuclease P with Pre-Trna Substrate, PDB code: 6ah3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Yeast Ribonuclease P with Pre-Trna Substrate


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 P with Pre-Trna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:30.0 occ:1.00 OP2 A:A91 2.0 75.2 1.0 O4 A:U93 2.1 20.0 1.0 OP1 T:G1 2.1 78.6 1.0 OP2 A:U92 2.1 78.6 1.0 C5' T:G1 2.8 77.9 1.0 P T:G1 3.1 76.9 1.0 C4 A:U93 3.3 20.0 1.0 O5' T:G1 3.4 78.8 1.0 P A:A91 3.4 76.9 1.0 P A:U92 3.6 76.9 1.0 OP2 T:G1 3.8 75.2 1.0 MG A:MG402 4.0 30.0 1.0 OP1 A:A91 4.0 78.6 1.0 O5' A:A91 4.1 78.8 1.0 C5 A:U93 4.1 20.0 1.0 C4' T:G1 4.2 78.7 1.0 OP1 A:U92 4.3 75.2 1.0 N3 A:U93 4.3 20.0 1.0 O3' A:A91 4.4 77.2 1.0 O3' T:A0 4.5 77.2 1.0 C5 A:U92 4.5 20.0 1.0 O5' A:U92 4.5 78.8 1.0 O3' A:A90 4.5 77.2 1.0 OP2 A:A344 4.7 75.2 1.0 C3' A:A91 4.7 78.2 1.0 OP2 T:C2 4.8 0.2 1.0 C5' A:A91 4.8 77.9 1.0 OP1 A:A344 4.8 78.6 1.0 C3' T:G1 4.9 78.2 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Yeast Ribonuclease P with Pre-Trna Substrate


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 P with Pre-Trna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:30.0 occ:1.00 OP1 A:A91 2.0 78.6 1.0 OP1 A:G343 2.1 75.2 1.0 OP2 A:A344 2.1 75.2 1.0 OP1 T:G1 2.1 78.6 1.0 O3' T:A0 2.4 77.2 1.0 P T:G1 2.7 76.9 1.0 P A:A91 3.1 76.9 1.0 C5' A:A91 3.4 77.9 1.0 P A:A344 3.5 76.9 1.0 OP2 A:A91 3.5 75.2 1.0 P A:G343 3.5 76.9 1.0 OP2 T:G1 3.6 75.2 1.0 O5' A:A91 3.7 78.8 1.0 C3' T:A0 3.7 78.2 1.0 MG A:MG401 4.0 30.0 1.0 O5' T:G1 4.0 78.8 1.0 C4' A:G343 4.0 78.7 1.0 C4' T:A0 4.0 78.7 1.0 O5' A:A344 4.2 78.8 1.0 C5' A:G343 4.2 77.9 1.0 OP1 A:A344 4.2 78.6 1.0 O2' A:A90 4.3 79.3 1.0 O3' A:C342 4.4 77.2 1.0 O5' A:G343 4.4 78.8 1.0 OP2 A:G343 4.4 78.6 1.0 O3' A:A90 4.4 77.2 1.0 O2' T:A0 4.4 79.3 1.0 O3' A:G343 4.5 77.2 1.0 C5' T:A0 4.5 77.9 1.0 C4' A:A91 4.5 78.7 1.0 OP2 A:U92 4.5 78.6 1.0 C5' T:G1 4.6 77.9 1.0 C2' A:A90 4.6 79.3 1.0 C3' A:G343 4.7 78.2 1.0 C2' T:A0 4.7 79.3 1.0 C5' A:A344 4.9 77.9 1.0

P.Lan, M.Tan, Y.Zhang, S.Niu, J.Chen, S.Shi, S.Qiu, X.Wang, X.Peng, G.Cai, H.Cheng, J.Wu, G.Li, M.Lei. Structural Insight Into Precursor Trna Processing By Yeast Ribonuclease P. Science V. 362 2018.
ISSN: ESSN 1095-9203
PubMed: 30262633
DOI: 10.1126/SCIENCE.AAT6678