Magnesium in PDB 4o1p: Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp

The structure of Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp, PDB code: 4o1p was solved by H.Huang, E.Zeqiraj, D.F.Ceccarelli, F.Sicheri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.20 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.197, 267.392, 110.210, 90.00, 90.04, 90.00
R / Rfree (%)	19.6 / 23.1

The binding sites of Magnesium atom in the Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp (pdb code 4o1p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp, PDB code: 4o1p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp


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 Rnase L in Complex with 2-5A and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:27.7 occ:1.00 OD2 A:ASP500 2.4 35.6 1.0 O2B A:ANP901 2.4 40.5 1.0 OD1 A:ASP502 2.4 37.5 1.0 OD2 A:ASP502 2.5 41.1 1.0 OD1 A:ASP500 2.5 38.9 1.0 CG A:ASP502 2.8 35.1 1.0 CG A:ASP500 2.8 37.6 1.0 PB A:ANP901 3.7 37.8 1.0 MG A:MG903 3.7 25.0 1.0 OD2 A:ASP482 3.8 37.5 1.0 O1B A:ANP901 4.1 36.1 1.0 CB A:ASP502 4.3 31.9 1.0 CB A:ASP500 4.3 35.5 1.0 O3A A:ANP901 4.4 39.0 1.0 O3G A:ANP901 4.5 51.9 1.0 O1A A:ANP901 4.5 35.3 1.0 NZ A:LYS390 4.6 39.0 1.0 CE A:LYS503 4.8 46.2 1.0 NZ A:LYS503 4.8 52.7 1.0 O A:ASP500 4.8 34.1 1.0 CD A:LYS503 4.8 41.2 1.0 CG A:ASP482 4.8 36.5 1.0 N A:ASP502 4.8 29.6 1.0 O A:HOH1206 4.8 39.2 1.0 N3B A:ANP901 4.9 43.4 1.0 CG A:LYS503 5.0 39.1 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp


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 Rnase L in Complex with 2-5A and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:25.0 occ:1.00 O A:HOH1046 2.0 36.6 1.0 O2B A:ANP901 2.2 40.5 1.0 O1A A:ANP901 2.3 35.3 1.0 OD2 A:ASP500 2.4 35.6 1.0 OD1 A:ASN487 2.6 34.1 1.0 O2G A:ANP901 2.7 48.0 1.0 N3B A:ANP901 3.1 43.4 1.0 PB A:ANP901 3.2 37.8 1.0 CG A:ASP500 3.5 37.6 1.0 PG A:ANP901 3.5 49.7 1.0 PA A:ANP901 3.6 36.1 1.0 CG A:ASN487 3.6 33.3 1.0 MG A:MG902 3.7 27.7 1.0 O3G A:ANP901 3.8 51.9 1.0 O3A A:ANP901 3.8 39.0 1.0 ND2 A:ASN487 3.9 33.4 1.0 O5' A:ANP901 4.0 35.5 1.0 CB A:ASP500 4.1 35.5 1.0 OD2 A:ASP482 4.4 37.5 1.0 OD1 A:ASP500 4.4 38.9 1.0 O1B A:ANP901 4.5 36.1 1.0 O2A A:ANP901 4.8 34.2 1.0 O1G A:ANP901 4.8 47.8 1.0 O A:GLN486 4.9 32.1 1.0 CB A:ASN487 5.0 30.6 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:25.3 occ:1.00 OD1 B:ASP502 2.3 45.1 1.0 O1B B:ANP901 2.3 48.9 1.0 OD2 B:ASP500 2.5 37.1 1.0 OD2 B:ASP502 2.5 44.7 1.0 OD1 B:ASP500 2.7 38.5 1.0 CG B:ASP502 2.8 40.7 1.0 CG B:ASP500 3.0 37.0 1.0 NH2 B:ARG398 3.3 68.5 1.0 MG B:MG903 3.5 31.1 1.0 PB B:ANP901 3.7 46.5 1.0 OD2 B:ASP482 3.7 39.1 1.0 O2B B:ANP901 4.2 51.1 1.0 CB B:ASP502 4.3 39.2 1.0 O1G B:ANP901 4.3 66.7 1.0 CB B:ASP500 4.5 35.8 1.0 O2A B:ANP901 4.5 34.1 1.0 CZ B:ARG398 4.6 67.3 1.0 CE B:LYS503 4.6 50.3 1.0 O3A B:ANP901 4.6 38.4 1.0 CD B:LYS503 4.6 45.1 1.0 NZ B:LYS503 4.7 52.0 1.0 NZ B:LYS390 4.7 30.6 1.0 CG B:ASP482 4.7 36.6 1.0 CG B:LYS503 4.8 43.0 1.0 N B:ASP502 4.8 34.9 1.0 O B:ASP500 4.9 34.2 1.0 N3B B:ANP901 4.9 51.7 1.0 CA B:ASP502 5.0 37.7 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:31.1 occ:1.00 OD2 B:ASP500 2.1 37.1 1.0 O2A B:ANP901 2.3 34.1 1.0 O1B B:ANP901 2.5 48.9 1.0 OD1 B:ASN487 2.5 28.5 1.0 O2G B:ANP901 2.6 66.5 1.0 CG B:ASP500 3.2 37.0 1.0 PB B:ANP901 3.4 46.5 1.0 N3B B:ANP901 3.4 51.7 1.0 CG B:ASN487 3.4 28.3 1.0 PG B:ANP901 3.5 60.5 1.0 MG B:MG902 3.5 25.3 1.0 PA B:ANP901 3.6 32.6 1.0 ND2 B:ASN487 3.7 26.7 1.0 O1G B:ANP901 3.8 66.7 1.0 CB B:ASP500 3.9 35.8 1.0 O3A B:ANP901 3.9 38.4 1.0 OD2 B:ASP482 4.1 39.1 1.0 O5' B:ANP901 4.1 33.6 1.0 OD1 B:ASP500 4.1 38.5 1.0 O2B B:ANP901 4.7 51.1 1.0 O1A B:ANP901 4.7 33.0 1.0 CB B:ASN487 4.8 29.0 1.0 O3G B:ANP901 4.8 56.6 1.0 O B:GLN486 5.0 32.0 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg902 b:29.3 occ:1.00 O1B C:ANP901 2.2 43.3 1.0 O C:HOH1011 2.3 44.0 1.0 OD2 C:ASP502 2.4 49.3 1.0 OD2 C:ASP500 2.4 33.2 1.0 OD1 C:ASP502 2.4 48.3 1.0 OD1 C:ASP500 2.6 29.9 1.0 CG C:ASP502 2.8 42.1 1.0 CG C:ASP500 2.8 34.0 1.0 PB C:ANP901 3.5 43.1 1.0 MG C:MG903 3.6 24.3 1.0 OD2 C:ASP482 4.0 47.0 1.0 O2B C:ANP901 4.0 43.0 1.0 CB C:ASP502 4.3 40.9 1.0 O3A C:ANP901 4.3 39.0 1.0 CB C:ASP500 4.3 33.4 1.0 O2A C:ANP901 4.4 39.5 1.0 O1G C:ANP901 4.4 53.7 1.0 NZ C:LYS390 4.4 32.5 1.0 O2G C:ANP901 4.5 53.7 1.0 N3B C:ANP901 4.7 46.2 1.0 N C:ASP502 4.9 35.6 1.0 PG C:ANP901 4.9 54.2 1.0 PA C:ANP901 4.9 34.3 1.0 O C:ASP500 4.9 34.9 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg903 b:24.3 occ:1.00 O2A C:ANP901 1.9 39.5 1.0 O1G C:ANP901 2.2 53.7 1.0 OD2 C:ASP500 2.3 33.2 1.0 O1B C:ANP901 2.3 43.3 1.0 OD1 C:ASN487 2.6 28.3 1.0 PB C:ANP901 3.1 43.1 1.0 N3B C:ANP901 3.2 46.2 1.0 PA C:ANP901 3.2 34.3 1.0 CG C:ASP500 3.3 34.0 1.0 PG C:ANP901 3.4 54.2 1.0 O3A C:ANP901 3.6 39.0 1.0 CG C:ASN487 3.6 28.6 1.0 MG C:MG902 3.6 29.3 1.0 O C:HOH1011 3.6 44.0 1.0 O5' C:ANP901 3.8 35.9 1.0 CB C:ASP500 3.9 33.4 1.0 ND2 C:ASN487 4.0 27.8 1.0 O2G C:ANP901 4.2 53.7 1.0 OD1 C:ASP500 4.2 29.9 1.0 O1A C:ANP901 4.4 37.4 1.0 O C:HOH1072 4.4 31.9 1.0 O3G C:ANP901 4.4 53.8 1.0 O2B C:ANP901 4.5 43.0 1.0 OD2 C:ASP482 4.6 47.0 1.0 O C:GLN486 4.8 31.6 1.0 CB C:ASN487 4.9 28.0 1.0 O3' C:ANP901 5.0 27.9 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg902 b:53.7 occ:1.00 O1A D:ANP901 2.3 41.5 1.0 O2G D:ANP901 2.5 63.1 1.0 OD1 D:ASN487 2.6 32.0 1.0 MG D:MG903 2.9 55.5 1.0 O5' D:ANP901 3.2 39.3 1.0 N3B D:ANP901 3.4 49.7 1.0 PA D:ANP901 3.4 35.9 1.0 PG D:ANP901 3.5 57.7 1.0 O3' D:ANP901 3.6 36.0 1.0 OD2 D:ASP500 3.6 50.6 1.0 O D:GLN486 3.7 31.7 1.0 CG D:ASN487 3.8 31.7 1.0 O2B D:ANP901 3.8 52.8 1.0 PB D:ANP901 4.0 43.8 1.0 O1G D:ANP901 4.0 52.9 1.0 O3A D:ANP901 4.1 44.0 1.0 C3' D:ANP901 4.2 36.9 1.0 C D:GLN486 4.2 33.0 1.0 CB D:GLN486 4.3 38.4 1.0 C5' D:ANP901 4.4 39.2 1.0 ND2 D:ASN487 4.5 31.5 1.0 CG D:ASP500 4.5 43.4 1.0 C4' D:ANP901 4.6 37.2 1.0 N D:ASN487 4.6 31.5 1.0 O2A D:ANP901 4.7 38.5 1.0 CB D:ASP500 4.7 41.8 1.0 O3G D:ANP901 4.7 57.9 1.0 CA D:ASN487 4.8 32.3 1.0 CB D:ASN487 4.9 32.4 1.0 CA D:GLN486 4.9 35.4 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Rnase L in Complex with 2-5A and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg903 b:55.5 occ:1.00 O2G D:ANP901 2.5 63.1 1.0 OD2 D:ASP500 2.8 50.6 1.0 OD2 D:ASP482 2.9 42.8 1.0 MG D:MG902 2.9 53.7 1.0 OD1 D:ASN487 3.0 32.0 1.0 ND2 D:ASN487 3.2 31.5 1.0 CG D:ASN487 3.5 31.7 1.0 O2B D:ANP901 3.6 52.8 1.0 PG D:ANP901 3.9 57.7 1.0 CG D:ASP482 4.0 37.8 1.0 O1A D:ANP901 4.0 41.5 1.0 CG D:ASP500 4.0 43.4 1.0 OD1 D:ASP482 4.2 35.3 1.0 NE2 D:GLN484 4.4 51.0 1.0 O3G D:ANP901 4.5 57.9 1.0 N3B D:ANP901 4.5 49.7 1.0 CD D:GLN484 4.5 51.0 1.0 PB D:ANP901 4.6 43.8 1.0 CG D:GLN484 4.6 43.9 1.0 CB D:ASP500 4.8 41.8 1.0 OD1 D:ASP500 4.8 45.8 1.0 CB D:ASN487 5.0 32.4 1.0

H.Huang, E.Zeqiraj, F.Sicheri. Dimeric Structure of Pseudokinase Rnase L Bound to 2-5A Reveals A Basis For Interferon Induced Antiviral Activity Mol.Cell V. 53 221 2014.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2013.12.025