Magnesium in PDB 5yv5: Crystal Structure of the Complex of Archaeal Ribosomal Stalk Protein AP1 and Archaeal Ribosome Recycling Factor AABCE1.

The structure of Crystal Structure of the Complex of Archaeal Ribosomal Stalk Protein AP1 and Archaeal Ribosome Recycling Factor AABCE1., PDB code: 5yv5 was solved by H.Imai, T.Abe, T.Miyoshi, S.Nishikawa, K.Ito, T.Uchiumi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.011, 64.731, 147.073, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.4

The binding sites of Magnesium atom in the Crystal Structure of the Complex of Archaeal Ribosomal Stalk Protein AP1 and Archaeal Ribosome Recycling Factor AABCE1. (pdb code 5yv5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Complex of Archaeal Ribosomal Stalk Protein AP1 and Archaeal Ribosome Recycling Factor AABCE1., PDB code: 5yv5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Complex of Archaeal Ribosomal Stalk Protein AP1 and Archaeal Ribosome Recycling Factor AABCE1.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Complex of Archaeal Ribosomal Stalk Protein AP1 and Archaeal Ribosome Recycling Factor AABCE1. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:17.4 occ:1.00 O3B A:ADP601 2.0 16.0 1.0 O A:HOH721 2.0 15.2 1.0 OG A:SER113 2.1 17.5 1.0 OE1 A:GLN165 2.1 20.3 1.0 O A:HOH826 2.1 14.1 1.0 O A:HOH720 2.2 14.0 1.0 CB A:SER113 3.1 17.5 1.0 CD A:GLN165 3.1 21.0 1.0 PB A:ADP601 3.3 15.5 1.0 O2B A:ADP601 3.5 16.3 1.0 NE2 A:GLN165 3.6 20.2 1.0 OE2 A:GLU236 3.6 16.3 1.0 N A:SER113 3.8 16.8 1.0 O2A A:ADP601 4.0 16.9 1.0 OD2 A:ASP235 4.0 16.0 1.0 CA A:SER113 4.0 17.3 1.0 OD1 A:ASP235 4.1 15.9 1.0 O1B A:ADP601 4.3 15.8 1.0 CD A:GLU236 4.4 16.4 1.0 O3A A:ADP601 4.4 16.7 1.0 CG A:ASP235 4.4 16.0 1.0 CG A:GLN165 4.5 21.4 1.0 PA A:ADP601 4.6 17.6 1.0 CB A:GLN165 4.7 21.9 1.0 CB A:LYS112 4.8 15.7 1.0 OD1 A:ASN108 4.8 16.2 1.0 O A:HOH725 4.8 30.7 1.0 C A:LYS112 4.9 16.0 1.0 OE1 A:GLU236 5.0 15.9 1.0 NZ A:LYS112 5.0 15.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Complex of Archaeal Ribosomal Stalk Protein AP1 and Archaeal Ribosome Recycling Factor AABCE1.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Complex of Archaeal Ribosomal Stalk Protein AP1 and Archaeal Ribosome Recycling Factor AABCE1. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:14.2 occ:1.00 O A:HOH728 2.0 10.1 1.0 O A:HOH821 2.0 8.8 1.0 O1B A:ADP602 2.0 14.2 1.0 OE1 A:GLN406 2.1 14.1 1.0 OG1 A:THR378 2.1 12.5 1.0 O A:HOH744 2.2 9.5 1.0 CD A:GLN406 3.1 14.1 1.0 CB A:THR378 3.2 13.2 1.0 PB A:ADP602 3.2 15.1 1.0 O3B A:ADP602 3.5 14.5 1.0 NE2 A:GLN406 3.5 12.9 1.0 OE1 A:GLU479 3.7 14.9 1.0 N A:THR378 3.9 13.5 1.0 O2A A:ADP602 3.9 16.2 1.0 CA A:THR378 4.1 13.1 1.0 OD1 A:ASP478 4.1 12.2 1.0 OD2 A:ASP478 4.2 11.6 1.0 CG2 A:THR378 4.3 13.2 1.0 O3A A:ADP602 4.3 15.6 1.0 O2B A:ADP602 4.3 15.2 1.0 OH A:TYR407 4.3 27.6 1.0 CG A:GLN406 4.4 14.2 1.0 CD A:GLU479 4.5 14.4 1.0 CG A:ASP478 4.5 12.2 1.0 PA A:ADP602 4.6 16.5 1.0 O A:HOH715 4.7 19.7 1.0 CB A:GLN406 4.7 14.6 1.0 OD1 A:ASN373 4.7 14.4 1.0 CB A:LYS377 4.9 13.6 1.0

H.Imai, T.Abe, T.Miyoshi, S.I.Nishikawa, K.Ito, T.Uchiumi. The Ribosomal Stalk Protein Is Crucial For the Action of the Conserved Atpase ABCE1 Nucleic Acids Res. V. 46 7820 2018.
ISSN: ESSN 1362-4962
PubMed: 30010948
DOI: 10.1093/NAR/GKY619