Magnesium in PDB 4jrn: ROP18 Kinase Domain in Complex with Amp-Pnp and Sucrose

The structure of ROP18 Kinase Domain in Complex with Amp-Pnp and Sucrose, PDB code: 4jrn was solved by D.Lim, D.A.Gold, J.Lindsay, E.E.Rosowski, W.Niedelman, M.B.Yaffe, J.P.J.Saeij, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.55 / 2.71
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	48.650, 48.650, 293.746, 90.00, 90.00, 120.00
R / Rfree (%)	23.2 / 28.9

The binding sites of Magnesium atom in the ROP18 Kinase Domain in Complex with Amp-Pnp and Sucrose (pdb code 4jrn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the ROP18 Kinase Domain in Complex with Amp-Pnp and Sucrose, PDB code: 4jrn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the ROP18 Kinase Domain in Complex with Amp-Pnp and Sucrose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of ROP18 Kinase Domain in Complex with Amp-Pnp and Sucrose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:61.9 occ:1.00 O3G A:ANP601 3.0 57.4 1.0 O2A A:ANP601 3.3 73.3 1.0 OD1 A:ASN414 3.4 51.6 1.0 NZ A:LYS411 3.6 69.6 1.0 CB A:ALA413 3.8 65.2 1.0 O1A A:ANP601 4.1 55.5 1.0 O3' A:ANP601 4.3 72.7 1.0 PA A:ANP601 4.4 51.0 1.0 MG A:MG603 4.4 69.8 1.0 PG A:ANP601 4.5 68.3 1.0 CG A:ASN414 4.6 41.5 1.0 C A:ALA413 4.6 54.7 1.0 C3' A:ANP601 4.6 55.7 1.0 O A:ALA413 4.6 56.6 1.0 O2G A:ANP601 4.8 76.0 1.0 CA A:ALA413 4.8 63.0 1.0 N A:ASN414 4.9 56.9 1.0 O A:HOH705 5.0 54.6 1.0

Magnesium binding site 2 out of 2 in the ROP18 Kinase Domain in Complex with Amp-Pnp and Sucrose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of ROP18 Kinase Domain in Complex with Amp-Pnp and Sucrose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:69.8 occ:1.00 O3G A:ANP601 2.0 57.4 1.0 OD2 A:ASP427 2.3 67.7 1.0 OD1 A:ASP427 2.4 64.7 1.0 O1G A:ANP601 2.5 51.4 1.0 CG A:ASP427 2.6 61.8 1.0 O2B A:ANP601 2.6 69.0 1.0 PG A:ANP601 2.7 68.3 1.0 PB A:ANP601 3.6 51.0 1.0 N3B A:ANP601 3.6 72.5 1.0 O1A A:ANP601 3.7 55.5 1.0 CB A:ASP427 4.0 40.9 1.0 O2G A:ANP601 4.1 76.0 1.0 O2A A:ANP601 4.1 73.3 1.0 PA A:ANP601 4.3 51.0 1.0 O3A A:ANP601 4.3 55.6 1.0 MG A:MG602 4.4 61.9 1.0 OD1 A:ASN414 4.8 51.6 1.0 O1B A:ANP601 4.9 72.8 1.0 OD1 A:ASP409 5.0 75.8 1.0

D.Lim, D.A.Gold, L.Julien, E.E.Rosowski, W.Niedelman, M.B.Yaffe, J.P.Saeij. Structure of the Toxoplasma Gondii ROP18 Kinase Domain Reveals A Second Ligand Binding Pocket Required For Acute Virulence. J.Biol.Chem. V. 288 34968 2013.
ISSN: ISSN 0021-9258
PubMed: 24129568
DOI: 10.1074/JBC.M113.523266