Magnesium in PDB 7x4q: Lpcdne Utp Mg Complex

The structure of Lpcdne Utp Mg Complex, PDB code: 7x4q was solved by Y.Chen, T.P.Ko, C.S.Yang, Y.C.Wang, M.H.Hou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.23 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.584, 74.719, 80.343, 90, 98.23, 90
R / Rfree (%)	16.1 / 18.7

The binding sites of Magnesium atom in the Lpcdne Utp Mg Complex (pdb code 7x4q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Lpcdne Utp Mg Complex, PDB code: 7x4q:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Lpcdne Utp Mg Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Lpcdne Utp Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:12.9 occ:1.00 O3G A:UTP401 2.0 12.4 1.0 O A:HOH550 2.0 12.4 1.0 O2B A:UTP401 2.1 12.8 1.0 O2A A:UTP401 2.1 13.7 1.0 OD2 A:ASP67 2.1 13.7 1.0 O A:HOH552 2.1 10.6 1.0 PB A:UTP401 3.1 12.4 1.0 CG A:ASP67 3.1 11.4 1.0 PG A:UTP401 3.3 13.3 1.0 PA A:UTP401 3.3 12.9 1.0 MG A:MG404 3.4 14.7 1.0 OD1 A:ASP67 3.5 12.9 1.0 O3B A:UTP401 3.5 15.8 1.0 O3A A:UTP401 3.5 15.1 1.0 OG A:SER53 3.8 11.8 1.0 O A:ASP65 3.9 18.3 1.0 O A:HOH684 3.9 25.8 1.0 O1G A:UTP401 4.1 11.8 1.0 C5' A:UTP401 4.1 9.9 1.0 O A:HOH533 4.1 10.0 1.0 N A:SER53 4.2 16.1 1.0 O5' A:UTP401 4.2 12.7 1.0 O2G A:UTP401 4.4 13.7 1.0 CB A:ASP67 4.5 7.3 1.0 O1A A:UTP401 4.5 14.3 1.0 O1B A:UTP401 4.5 12.9 1.0 O A:HOH734 4.6 16.9 1.0 CB A:SER53 4.6 10.4 1.0 CA A:GLY52 4.7 12.8 1.0 O A:HOH626 4.9 21.8 1.0 N A:ASP67 5.0 11.2 1.0 C A:GLY52 5.0 15.5 1.0

Magnesium binding site 2 out of 4 in the Lpcdne Utp Mg Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Lpcdne Utp Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:14.7 occ:1.00 OD1 A:ASP67 2.3 12.9 1.0 O3' A:UTP402 2.4 11.0 1.0 OD2 A:ASP139 2.4 13.8 1.0 O A:HOH734 2.4 16.9 1.0 O2A A:UTP401 2.5 13.7 1.0 O A:HOH552 2.5 10.6 1.0 CG A:ASP67 3.3 11.4 1.0 CG A:ASP139 3.4 15.1 1.0 MG A:MG403 3.4 12.9 1.0 OD2 A:ASP67 3.6 13.7 1.0 PA A:UTP401 3.6 12.9 1.0 C3' A:UTP402 3.7 13.9 1.0 O2' A:UTP402 3.7 13.6 1.0 CB A:ASP139 3.8 10.0 1.0 O A:HOH551 3.9 26.1 1.0 O A:HOH684 4.0 25.8 1.0 O1A A:UTP401 4.1 14.3 1.0 O5' A:UTP401 4.1 12.7 1.0 C2' A:UTP402 4.1 15.7 1.0 O A:HOH553 4.3 41.6 1.0 C5' A:UTP401 4.5 9.9 1.0 O3G A:UTP401 4.5 12.4 1.0 C4' A:UTP402 4.5 15.0 1.0 O A:ASP65 4.5 18.3 1.0 OD1 A:ASP139 4.5 19.7 1.0 CB A:ASP67 4.7 7.3 1.0 CB A:ASP65 4.8 16.2 1.0 O A:HOH655 4.9 34.2 1.0

Magnesium binding site 3 out of 4 in the Lpcdne Utp Mg Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Lpcdne Utp Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:13.5 occ:1.00 O1G B:UTP401 2.0 13.4 1.0 O1A B:UTP401 2.0 15.0 1.0 O2B B:UTP401 2.1 14.0 1.0 OD2 B:ASP67 2.1 14.4 1.0 O B:HOH554 2.1 12.0 1.0 O B:HOH552 2.2 13.1 1.0 CG B:ASP67 3.1 12.0 1.0 PB B:UTP401 3.1 13.6 1.0 PG B:UTP401 3.3 15.2 1.0 PA B:UTP401 3.3 16.2 1.0 MG B:MG404 3.3 16.9 1.0 OD1 B:ASP67 3.5 13.2 1.0 O3A B:UTP401 3.6 18.8 1.0 O3B B:UTP401 3.6 15.6 1.0 OG B:SER53 3.9 10.8 1.0 O B:HOH716 4.0 31.3 1.0 O B:ASP65 4.0 12.5 1.0 C5' B:UTP401 4.1 12.1 1.0 O2G B:UTP401 4.1 17.9 1.0 O B:HOH529 4.2 11.5 1.0 O5' B:UTP401 4.3 13.6 1.0 N B:SER53 4.3 12.2 1.0 O3G B:UTP401 4.4 15.3 1.0 CB B:ASP67 4.4 6.3 1.0 O2A B:UTP401 4.4 17.5 1.0 O1B B:UTP401 4.5 12.9 1.0 O B:HOH648 4.6 19.1 1.0 CB B:SER53 4.7 9.2 1.0 CA B:GLY52 4.8 11.5 1.0 O B:HOH599 4.8 28.1 1.0 N B:ASP67 5.0 7.5 1.0

Magnesium binding site 4 out of 4 in the Lpcdne Utp Mg Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Lpcdne Utp Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:16.9 occ:1.00 OD1 B:ASP67 2.3 13.2 1.0 OD2 B:ASP139 2.4 16.4 1.0 O B:HOH648 2.4 19.1 1.0 O B:HOH554 2.4 12.0 1.0 O3' B:UTP402 2.4 17.4 1.0 O1A B:UTP401 2.5 15.0 1.0 CG B:ASP67 3.2 12.0 1.0 MG B:MG403 3.3 13.5 1.0 CG B:ASP139 3.4 16.6 1.0 OD2 B:ASP67 3.5 14.4 1.0 PA B:UTP401 3.6 16.2 1.0 O2' B:UTP402 3.8 15.7 1.0 C3' B:UTP402 3.8 16.9 1.0 CB B:ASP139 3.8 14.3 1.0 O B:HOH716 3.9 31.3 1.0 O2A B:UTP401 4.1 17.5 1.0 O2B B:UTP402 4.1 24.2 0.5 O5' B:UTP401 4.1 13.6 1.0 O B:HOH602 4.1 25.3 1.0 C2' B:UTP402 4.2 18.6 1.0 O1G B:UTP401 4.5 13.4 1.0 C5' B:UTP401 4.5 12.1 1.0 O B:ASP65 4.5 12.5 1.0 OD1 B:ASP139 4.5 20.1 1.0 C4' B:UTP402 4.6 19.6 1.0 CB B:ASP67 4.6 6.3 1.0 O B:HOH670 4.9 34.9 1.0 CB B:ASP65 5.0 16.5 1.0

Y.Chen, T.P.Ko, C.S.Yang, Y.C.Wang, M.H.Hou. Structure and Function of Cyclic Di-Ump Synthesizing Cgas/Dncv-Like Nucleotidyltransferases To Be Published.