Magnesium in PDB 4k99: Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppdg(2 , 5 )Pdg

The structure of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppdg(2 , 5 )Pdg, PDB code: 4k99 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)	39.18 / 1.95
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	85.124, 97.613, 131.372, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.2

The structure of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppdg(2 , 5 )Pdg 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 -Pppdg(2 , 5 )Pdg (pdb code 4k99). 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 -Pppdg(2 , 5 )Pdg, PDB code: 4k99:
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 -Pppdg(2 , 5 )Pdg


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 -Pppdg(2 , 5 )Pdg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:19.9 occ:1.00 OD2 A:ASP213 2.0 26.4 1.0 OE1 A:GLU211 2.1 31.7 1.0 O3G A:GH3604 2.1 22.2 1.0 O2A A:GH3604 2.1 26.7 1.0 O2B A:GH3604 2.2 20.4 1.0 O A:HOH703 2.2 22.9 1.0 CG A:ASP213 3.0 30.4 1.0 PB A:GH3604 3.1 27.0 0.9 CD A:GLU211 3.2 36.5 1.0 PA A:GH3604 3.3 28.7 0.9 PG A:GH3604 3.3 24.7 0.9 OD1 A:ASP213 3.4 36.0 1.0 O3A A:GH3604 3.4 41.2 1.0 MG A:MG603 3.4 63.6 1.0 O3B A:GH3604 3.6 33.2 1.0 OE2 A:GLU211 3.7 35.5 1.0 OG A:SER199 3.9 21.6 1.0 O1A A:GH3604 4.0 48.5 1.0 O2G A:GH3604 4.1 24.2 1.0 N A:SER199 4.3 19.1 1.0 O A:HOH710 4.3 20.2 1.0 O5' A:GH3604 4.3 38.8 1.0 O1B A:GH3604 4.4 25.0 1.0 O1G A:GH3604 4.4 32.1 1.0 CB A:ASP213 4.4 24.4 1.0 CG A:GLU211 4.5 29.3 1.0 O A:GLU211 4.5 24.6 1.0 CB A:GLU211 4.8 27.9 1.0 CB A:SER199 4.8 23.1 1.0 CA A:GLY198 4.9 22.3 1.0 C A:GLU211 4.9 26.1 1.0

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


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 -Pppdg(2 , 5 )Pdg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:63.6 occ:1.00 O2A A:GH3604 2.3 26.7 1.0 OD1 A:ASP213 2.4 36.0 1.0 OE2 A:GLU211 2.5 35.5 1.0 OD2 A:ASP307 2.6 37.0 1.0 O2' A:GDO605 3.1 56.5 1.0 CD A:GLU211 3.1 36.5 1.0 OE1 A:GLU211 3.3 31.7 1.0 CG A:ASP213 3.4 30.4 1.0 PA A:GH3604 3.4 28.7 0.9 MG A:MG602 3.4 19.9 1.0 CG A:ASP307 3.6 32.7 1.0 O1A A:GH3604 3.6 48.5 1.0 O5' A:GH3604 3.6 38.8 1.0 OD2 A:ASP213 3.7 26.4 1.0 C2' A:GDO605 3.8 48.8 1.0 C3' A:GDO605 3.8 50.1 1.0 O A:HOH905 4.0 52.3 1.0 CB A:ASP307 4.3 27.1 1.0 CG A:GLU211 4.3 29.3 1.0 OD1 A:ASP307 4.5 32.7 1.0 O A:HOH966 4.5 53.2 1.0 O3G A:GH3604 4.6 22.2 1.0 C4' A:GDO605 4.7 50.2 1.0 CB A:ASP213 4.7 24.4 1.0 O3A A:GH3604 4.7 41.2 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