Magnesium in PDB 4yiy: Structure of MRB1590 Bound to Amp-Pnp

The structure of Structure of MRB1590 Bound to Amp-Pnp, PDB code: 4yiy was solved by P.L.R.Shaw, M.A.Schumacher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.82 / 3.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	103.181, 71.522, 103.543, 90.00, 120.03, 90.00
R / Rfree (%)	23.3 / 29.8

The binding sites of Magnesium atom in the Structure of MRB1590 Bound to Amp-Pnp (pdb code 4yiy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of MRB1590 Bound to Amp-Pnp, PDB code: 4yiy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of MRB1590 Bound to Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of MRB1590 Bound to Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:43.1 occ:1.00 MG B:MG703 2.0 37.7 1.0 OG B:SER320 2.2 39.6 1.0 N3B B:ANP701 2.6 40.0 1.0 O3G B:ANP701 2.7 38.9 1.0 PG B:ANP701 3.2 38.9 1.0 O1B B:ANP701 3.5 40.3 1.0 CB B:SER320 3.6 39.1 1.0 PB B:ANP701 3.7 39.1 1.0 O1A B:ANP701 3.8 38.9 1.0 OD1 B:ASP409 3.8 20.0 1.0 O2G B:ANP701 3.9 40.5 1.0 OD2 B:ASP411 3.9 41.4 1.0 N B:SER320 4.0 36.9 1.0 CG1 B:VAL456 4.2 41.5 1.0 CA B:SER320 4.2 37.1 1.0 OD2 B:ASP409 4.4 20.0 1.0 CG B:ASP409 4.5 20.0 1.0 O1G B:ANP701 4.5 39.4 1.0 O3A B:ANP701 4.5 39.2 1.0 CB B:LYS319 4.7 38.9 1.0 PA B:ANP701 4.7 39.0 1.0 OG A:SER386 4.7 20.0 1.0 CG B:ASP411 4.7 41.4 1.0 N A:GLY387 4.9 39.2 1.0 O2B B:ANP701 4.9 40.0 1.0 C B:LYS319 5.0 36.6 1.0

Magnesium binding site 2 out of 4 in the Structure of MRB1590 Bound to Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of MRB1590 Bound to Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:37.7 occ:1.00 OG B:SER320 1.8 39.6 1.0 MG B:MG702 2.0 43.1 1.0 O1A B:ANP701 2.6 38.9 1.0 N3B B:ANP701 2.7 40.0 1.0 CB B:SER320 3.0 39.1 1.0 O3G B:ANP701 3.2 38.9 1.0 N A:GLY387 3.5 39.2 1.0 PG B:ANP701 3.6 38.9 1.0 OG A:SER386 3.6 20.0 1.0 PA B:ANP701 3.7 39.0 1.0 OD1 A:ASP355 3.9 37.1 1.0 PB B:ANP701 4.1 39.1 1.0 O2A B:ANP701 4.1 40.0 1.0 CA B:SER320 4.2 37.1 1.0 CA A:SER386 4.2 37.3 1.0 N B:SER320 4.3 36.9 1.0 O1G B:ANP701 4.3 39.4 1.0 O3A B:ANP701 4.3 39.2 1.0 C A:SER386 4.3 37.4 1.0 CA A:GLY387 4.3 39.2 1.0 CB A:SER386 4.4 20.0 1.0 O1B B:ANP701 4.5 40.3 1.0 OD2 B:ASP411 4.7 41.4 1.0 NH2 B:ARG324 4.8 36.5 1.0 O2G B:ANP701 4.8 40.5 1.0 CG A:ASP355 4.8 36.8 1.0 OD2 B:ASP409 4.9 20.0 1.0 OD2 A:ASP355 5.0 37.1 1.0

Magnesium binding site 3 out of 4 in the Structure of MRB1590 Bound to Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of MRB1590 Bound to Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:45.6 occ:1.00 OG A:SER320 1.7 20.0 1.0 O2G A:ANP701 1.7 45.7 1.0 MG A:MG703 2.1 79.5 1.0 O1B A:ANP701 2.8 44.4 1.0 CB A:SER320 3.1 20.0 1.0 PG A:ANP701 3.2 43.9 1.0 O3G A:ANP701 3.9 43.4 1.0 PB A:ANP701 3.9 42.7 1.0 OD1 A:ASP409 3.9 41.0 1.0 OD2 A:ASP411 4.0 41.4 1.0 N3B A:ANP701 4.0 44.2 1.0 CA A:SER320 4.1 40.5 1.0 N A:SER320 4.2 40.6 1.0 O1G A:ANP701 4.2 43.3 1.0 OD2 A:ASP409 4.2 40.2 1.0 N B:GLY387 4.3 42.5 1.0 CG A:ASP409 4.4 40.4 1.0 O2B A:ANP701 4.5 42.2 1.0 OD1 B:ASP355 4.5 42.1 1.0 CG A:ASP411 4.6 41.6 1.0 O1A A:ANP701 4.7 40.5 1.0 CA B:GLY387 4.8 41.7 1.0 CB A:ASP411 4.9 40.5 1.0

Magnesium binding site 4 out of 4 in the Structure of MRB1590 Bound to Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of MRB1590 Bound to Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:79.5 occ:1.00 MG A:MG702 2.1 45.6 1.0 O1B A:ANP701 2.1 44.4 1.0 OG A:SER320 2.1 20.0 1.0 O2G A:ANP701 2.3 45.7 1.0 CB A:SER320 2.8 20.0 1.0 O1A A:ANP701 2.9 40.5 1.0 PB A:ANP701 3.4 42.7 1.0 PG A:ANP701 3.4 43.9 1.0 N B:GLY387 3.4 42.5 1.0 OD1 B:ASP355 3.6 42.1 1.0 N3B A:ANP701 3.7 44.2 1.0 CA B:SER386 3.7 41.6 1.0 PA A:ANP701 3.9 41.1 1.0 CB B:SER386 4.0 42.1 1.0 O1G A:ANP701 4.0 43.3 1.0 C B:SER386 4.0 41.4 1.0 OG B:SER386 4.1 42.3 1.0 O3A A:ANP701 4.2 43.1 1.0 CA A:SER320 4.2 40.5 1.0 NH2 A:ARG324 4.3 37.9 1.0 O2A A:ANP701 4.4 41.6 1.0 N A:SER320 4.4 40.6 1.0 CG B:ASP355 4.5 40.8 1.0 CA B:GLY387 4.5 41.7 1.0 O2B A:ANP701 4.5 42.2 1.0 OD2 B:ASP355 4.6 40.4 1.0 O3G A:ANP701 4.6 43.4 1.0 N B:SER386 4.8 40.0 1.0 O B:ALA385 4.9 38.8 1.0

P.L.Shaw, N.M.Mcadams, M.A.Hast, M.L.Ammerman, L.K.Read, M.A.Schumacher. Structures of the T. Brucei Krna Editing Factor MRB1590 Reveal Unique Rna-Binding Pore Motif Contained Within An Abc-Atpase Fold. Nucleic Acids Res. V. 43 7096 2015.
ISSN: ESSN 1362-4962
PubMed: 26117548
DOI: 10.1093/NAR/GKV647