Magnesium in PDB 4k98: Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg

The structure of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg, PDB code: 4k98 was solved by P.Gao, Y.Wu, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.45 / 1.94
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	85.375, 97.877, 133.465, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 19.9

The structure of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg (pdb code 4k98). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg, PDB code: 4k98:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:16.5 occ:1.00 OE1 A:GLU211 2.0 56.4 1.0 O3G A:GTP604 2.1 22.6 1.0 OD2 A:ASP213 2.2 28.0 1.0 O2B A:GTP604 2.3 22.2 1.0 O2A A:GTP604 2.5 34.8 1.0 O A:HOH722 2.5 25.0 1.0 CD A:GLU211 3.0 51.4 1.0 CG A:ASP213 3.1 28.0 1.0 PB A:GTP604 3.2 27.7 0.8 PG A:GTP604 3.3 28.9 0.8 OD1 A:ASP213 3.3 31.3 1.0 OE2 A:GLU211 3.3 51.0 1.0 PA A:GTP604 3.4 33.3 0.8 O3A A:GTP604 3.5 42.1 1.0 O3B A:GTP604 3.5 45.7 1.0 MG A:MG603 3.7 26.9 1.0 OG A:SER199 4.0 23.2 1.0 O2G A:GTP604 4.1 27.1 1.0 O1A A:GTP604 4.2 30.4 1.0 N A:SER199 4.3 16.2 1.0 O1G A:GTP604 4.4 27.3 1.0 O A:HOH710 4.4 17.3 1.0 CG A:GLU211 4.4 42.2 1.0 O1B A:GTP604 4.4 27.2 1.0 O5' A:GTP604 4.5 35.9 1.0 CB A:ASP213 4.5 20.6 1.0 O A:GLU211 4.6 27.6 1.0 CB A:GLU211 4.8 29.2 1.0 CA A:GLY198 4.9 18.9 1.0 CB A:SER199 4.9 21.0 1.0

Magnesium binding site 2 out of 2 in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:26.9 occ:1.00 OD1 A:ASP213 2.3 31.3 1.0 OD2 A:ASP307 2.3 37.3 1.0 OE2 A:GLU211 2.3 51.0 1.0 O2' A:G605 2.5 42.5 1.0 O2A A:GTP604 2.6 34.8 1.0 O3' A:G605 2.6 68.0 1.0 CD A:GLU211 3.3 51.4 1.0 CG A:ASP213 3.4 28.0 1.0 CG A:ASP307 3.4 27.7 1.0 C3' A:G605 3.4 53.5 1.0 C2' A:G605 3.5 49.1 1.0 MG A:MG602 3.7 16.5 1.0 OE1 A:GLU211 3.7 56.4 1.0 PA A:GTP604 3.7 33.3 0.8 OD2 A:ASP213 3.8 28.0 1.0 O1A A:GTP604 3.9 30.4 1.0 CB A:ASP307 3.9 21.0 1.0 O5' A:GTP604 4.1 35.9 1.0 OD1 A:ASP307 4.4 36.3 1.0 C1' A:G605 4.6 42.0 1.0 CB A:ASP213 4.6 20.6 1.0 CG A:GLU211 4.7 42.2 1.0 C4' A:G605 4.7 49.4 1.0 O3G A:GTP604 4.9 22.6 1.0

P.Gao, M.Ascano, Y.Wu, W.Barchet, B.L.Gaffney, T.Zillinger, A.A.Serganov, Y.Liu, R.A.Jones, G.Hartmann, T.Tuschl, D.J.Patel. Cyclic [G(2',5')Pa(3',5')P] Is the Metazoan Second Messenger Produced By Dna-Activated Cyclic Gmp-Amp Synthase. Cell(Cambridge,Mass.) V. 153 1094 2013.
ISSN: ISSN 0092-8674
PubMed: 23647843
DOI: 10.1016/J.CELL.2013.04.046