Magnesium in PDB 1yqt: Rnase-L Inhibitor

The structure of Rnase-L Inhibitor, PDB code: 1yqt was solved by A.Karcher, K.Buttner, B.Martens, R.P.Jansen, K.P.Hopfner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.680, 74.640, 123.690, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22.5

The binding sites of Magnesium atom in the Rnase-L Inhibitor (pdb code 1yqt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rnase-L Inhibitor, PDB code: 1yqt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rnase-L Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rnase-L Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg591 b:15.3 occ:1.00 O1B A:ADP593 2.0 15.2 1.0 O A:HOH597 2.1 14.7 1.0 OG1 A:THR378 2.1 16.4 1.0 O A:HOH595 2.1 15.0 1.0 NE2 A:GLN406 2.1 12.1 1.0 O A:HOH596 2.2 14.3 1.0 CB A:THR378 3.2 14.9 1.0 CD A:GLN406 3.2 15.3 1.0 PB A:ADP593 3.3 17.5 1.0 O3B A:ADP593 3.4 14.9 1.0 OE1 A:GLN406 3.6 18.2 1.0 OE1 A:GLU479 3.8 19.2 1.0 N A:THR378 3.9 14.5 1.0 O2A A:ADP593 4.0 16.9 1.0 CA A:THR378 4.0 15.6 1.0 OD1 A:ASP478 4.1 16.7 1.0 OD2 A:ASP478 4.1 13.9 1.0 O3A A:ADP593 4.2 18.8 1.0 CG2 A:THR378 4.3 14.5 1.0 O2B A:ADP593 4.3 16.1 1.0 OH A:TYR407 4.3 38.7 1.0 CG A:GLN406 4.5 13.7 1.0 CG A:ASP478 4.5 18.3 1.0 CD A:GLU479 4.6 20.2 1.0 PA A:ADP593 4.6 17.4 1.0 CB A:GLN406 4.7 14.7 1.0 OD1 A:ASN373 4.7 18.0 1.0 O A:HOH681 4.8 26.5 1.0 O A:HOH805 4.8 44.1 1.0 NZ A:LYS377 4.9 15.8 1.0 CB A:LYS377 4.9 17.0 1.0 C A:LYS377 5.0 15.6 1.0

Magnesium binding site 2 out of 2 in the Rnase-L Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rnase-L Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg592 b:17.4 occ:1.00 OG A:SER113 2.0 20.0 1.0 O A:HOH598 2.1 18.2 1.0 O1B A:ADP594 2.1 17.6 1.0 O A:HOH600 2.1 16.8 1.0 OE1 A:GLN165 2.1 20.5 1.0 O A:HOH599 2.2 18.6 1.0 CD A:GLN165 3.1 19.5 1.0 CB A:SER113 3.1 20.2 1.0 PB A:ADP594 3.3 20.3 1.0 NE2 A:GLN165 3.5 18.5 1.0 O3B A:ADP594 3.6 18.4 1.0 OE2 A:GLU236 3.7 21.1 1.0 N A:SER113 3.8 19.3 1.0 O2A A:ADP594 4.0 23.3 1.0 CA A:SER113 4.0 19.5 1.0 OD2 A:ASP235 4.1 22.1 1.0 OD1 A:ASP235 4.1 21.5 1.0 O3A A:ADP594 4.2 21.3 1.0 O2B A:ADP594 4.4 18.4 1.0 CD A:GLU236 4.5 22.7 1.0 CG A:GLN165 4.5 18.1 1.0 CG A:ASP235 4.5 22.1 1.0 PA A:ADP594 4.6 22.7 1.0 OH A:TYR166 4.6 40.9 1.0 O A:HOH660 4.7 31.4 1.0 CB A:GLN165 4.8 18.4 1.0 OD1 A:ASN108 4.8 18.7 1.0 CB A:LYS112 4.9 17.0 1.0 C A:LYS112 4.9 18.4 1.0

A.Karcher, K.Buttner, B.Martens, R.P.Jansen, K.P.Hopfner. X-Ray Structure of Rli, An Essential Twin Cassette Abc Atpase Involved in Ribosome Biogenesis and Hiv Capsid Assembly. Structure V. 13 649 2005.
ISSN: ISSN 0969-2126
PubMed: 15837203
DOI: 10.1016/J.STR.2005.02.008