Magnesium in PDB 7x4t: Lpcdne Umpnpp Mg Complex

The structure of Lpcdne Umpnpp Mg Complex, PDB code: 7x4t 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)	28.92 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.495, 72.91, 66.28, 90, 90, 90
R / Rfree (%)	15.9 / 19.7

The binding sites of Magnesium atom in the Lpcdne Umpnpp Mg Complex (pdb code 7x4t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Lpcdne Umpnpp Mg Complex, PDB code: 7x4t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Lpcdne Umpnpp 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 Umpnpp Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:17.8 occ:1.00 O1A A:2KH401 2.0 24.7 1.0 OD2 A:ASP67 2.1 18.3 1.0 O2B A:2KH401 2.1 24.5 1.0 O2G A:2KH401 2.1 23.9 1.0 O A:HOH552 2.1 19.8 1.0 O A:HOH545 2.2 16.2 1.0 CG A:ASP67 3.1 20.4 1.0 PB A:2KH401 3.1 20.9 1.0 PA A:2KH401 3.3 21.4 1.0 MG A:MG404 3.3 27.4 1.0 PG A:2KH401 3.4 23.1 1.0 OD1 A:ASP67 3.5 18.4 1.0 N3A A:2KH401 3.6 17.7 1.0 O3B A:2KH401 3.6 21.7 1.0 OG A:SER53 3.9 23.2 1.0 O A:HOH630 4.0 38.2 1.0 O A:ASP65 4.0 19.7 1.0 OG A:SER64 4.0 35.0 1.0 O A:HOH582 4.0 20.1 1.0 C5' A:2KH401 4.1 23.7 1.0 O3G A:2KH401 4.1 20.9 1.0 O5' A:2KH401 4.2 22.5 1.0 N A:SER53 4.2 18.6 1.0 O2A A:2KH401 4.4 19.8 1.0 O A:HOH688 4.4 28.2 1.0 CB A:ASP67 4.4 18.1 1.0 O1B A:2KH401 4.4 19.7 1.0 O1G A:2KH401 4.5 24.2 1.0 CB A:SER53 4.7 20.2 1.0 CA A:GLY52 4.7 20.1 1.0 O A:HOH538 4.8 48.9 1.0

Magnesium binding site 2 out of 5 in the Lpcdne Umpnpp 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 Umpnpp Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:27.4 occ:1.00 O3' A:2KH402 2.2 21.8 1.0 OD1 A:ASP67 2.3 18.4 1.0 OD2 A:ASP139 2.4 27.1 1.0 O1A A:2KH401 2.4 24.7 1.0 O A:HOH545 2.4 16.2 1.0 O A:HOH688 2.5 28.2 1.0 CG A:ASP67 3.3 20.4 1.0 MG A:MG403 3.3 17.8 1.0 CG A:ASP139 3.4 26.6 1.0 O2' A:2KH402 3.5 25.6 1.0 OD2 A:ASP67 3.5 18.3 1.0 PA A:2KH401 3.5 21.4 1.0 C3' A:2KH402 3.6 25.2 1.0 O2A A:2KH401 3.8 19.8 1.0 CB A:ASP139 3.8 21.0 1.0 C2' A:2KH402 3.8 28.3 1.0 O A:HOH519 3.8 26.2 1.0 O5' A:2KH401 4.0 22.5 1.0 O A:HOH630 4.1 38.2 1.0 O2G A:2KH401 4.5 23.9 1.0 O A:HOH538 4.5 48.9 1.0 OD1 A:ASP139 4.5 24.5 1.0 O A:ASP65 4.5 19.7 1.0 C5' A:2KH401 4.6 23.7 1.0 CB A:ASP67 4.7 18.1 1.0 C4' A:2KH402 4.7 29.2 1.0 O3B A:2KH402 4.7 47.5 1.0 O1B A:2KH402 4.7 41.1 1.0 O A:HOH674 4.9 36.9 1.0 O2B A:2KH401 4.9 24.5 1.0 N3A A:2KH401 5.0 17.7 1.0 O A:HOH552 5.0 19.8 1.0

Magnesium binding site 3 out of 5 in the Lpcdne Umpnpp 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 Umpnpp Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:35.4 occ:1.00 O A:HOH543 2.0 35.3 1.0 OD1 A:ASP139 2.2 24.5 1.0 OD2 A:ASP65 2.2 30.8 1.0 O A:HOH519 2.2 26.2 1.0 OD1 A:ASP128 2.2 31.8 1.0 O2G A:2KH402 2.3 41.5 1.0 CG A:ASP139 3.1 26.6 1.0 CG A:ASP128 3.2 35.3 1.0 OD2 A:ASP139 3.2 27.1 1.0 CG A:ASP65 3.3 31.6 1.0 PG A:2KH402 3.4 57.6 1.0 O3G A:2KH402 3.4 53.7 1.0 OD2 A:ASP128 3.9 38.9 1.0 CB A:ASP65 3.9 28.7 1.0 O A:HOH554 4.0 27.3 1.0 O3B A:2KH402 4.0 47.5 1.0 O A:HOH674 4.1 36.9 1.0 NE2 A:HIS130 4.2 31.5 1.0 CB A:ASP128 4.2 23.1 1.0 OD1 A:ASP65 4.3 30.0 1.0 CB A:ASP139 4.5 21.0 1.0 O1G A:2KH402 4.6 43.6 1.0 CA A:ASP128 4.7 23.8 1.0 CE1 A:HIS130 4.7 37.4 1.0 O A:HOH644 4.8 48.7 1.0 O A:ALA138 4.9 23.3 1.0 CA A:ASP139 4.9 20.0 1.0

Magnesium binding site 4 out of 5 in the Lpcdne Umpnpp 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 Umpnpp Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:23.7 occ:1.00 O2G B:2KH401 2.0 24.1 1.0 O2A B:2KH401 2.0 24.7 1.0 OD2 B:ASP67 2.1 22.0 1.0 O1B B:2KH401 2.1 23.4 1.0 O B:HOH532 2.1 22.4 1.0 O B:HOH574 2.2 19.1 1.0 CG B:ASP67 3.1 23.0 1.0 PB B:2KH401 3.2 28.0 1.0 PG B:2KH401 3.2 27.1 1.0 PA B:2KH401 3.3 26.0 1.0 MG B:MG404 3.3 31.4 1.0 OD1 B:ASP67 3.4 21.8 1.0 O3B B:2KH401 3.6 23.8 1.0 N3A B:2KH401 3.6 24.4 1.0 OG B:SER53 3.9 25.3 1.0 O B:ASP65 4.1 24.4 1.0 O1G B:2KH401 4.1 23.7 1.0 O B:HOH531 4.2 20.4 1.0 O5' B:2KH401 4.2 25.4 1.0 C5' B:2KH401 4.2 24.4 1.0 O3G B:2KH401 4.3 24.2 1.0 N B:SER53 4.3 21.4 1.0 O B:HOH689 4.3 30.7 1.0 O1A B:2KH401 4.4 30.0 1.0 CB B:ASP67 4.4 19.7 1.0 O2B B:2KH401 4.5 26.1 1.0 CB B:SER53 4.7 23.8 1.0 CA B:GLY52 4.9 26.2 1.0

Magnesium binding site 5 out of 5 in the Lpcdne Umpnpp Mg Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Lpcdne Umpnpp Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:31.4 occ:1.00 O3' B:2KH402 2.3 27.2 1.0 OD1 B:ASP67 2.4 21.8 1.0 O B:HOH574 2.4 19.1 1.0 OD2 B:ASP139 2.4 26.0 1.0 O B:HOH689 2.5 30.7 1.0 O2A B:2KH401 2.5 24.7 1.0 CG B:ASP67 3.3 23.0 1.0 MG B:MG403 3.3 23.7 1.0 CG B:ASP139 3.4 28.6 1.0 OD2 B:ASP67 3.6 22.0 1.0 O2' B:2KH402 3.6 30.6 1.0 O B:HOH508 3.6 37.5 1.0 PA B:2KH401 3.6 26.0 1.0 C3' B:2KH402 3.7 24.3 1.0 CB B:ASP139 3.8 23.2 1.0 O1A B:2KH401 3.8 30.0 1.0 C2' B:2KH402 4.0 31.0 1.0 O1B B:2KH402 4.1 57.7 1.0 O5' B:2KH401 4.2 25.4 1.0 O2G B:2KH401 4.5 24.1 1.0 OD1 B:ASP139 4.6 31.8 1.0 O B:ASP65 4.6 24.4 1.0 C4' B:2KH402 4.7 28.0 1.0 CB B:ASP67 4.7 19.7 1.0 C5' B:2KH401 4.8 24.4 1.0 O B:HOH532 5.0 22.4 1.0 O B:HOH674 5.0 47.0 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.