Magnesium in PDB 6zxc: Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State

The structure of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State, PDB code: 6zxc was solved by R.D.Teixeira, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	132.812, 247.368, 41.539, 90, 90, 90
R / Rfree (%)	23.7 / 28.8

The structure of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State (pdb code 6zxc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State, PDB code: 6zxc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg300 b:128.5 occ:1.00 OD2 A:BFD56 1.7 46.9 1.0 F3 A:BFD56 2.0 57.0 1.0 OD1 A:ASP13 2.0 51.9 1.0 CG A:BFD56 2.7 45.8 1.0 O A:GLU58 2.7 53.1 1.0 CG A:ASP13 3.0 53.5 1.0 OE2 A:GLU12 3.0 52.5 1.0 OD1 A:BFD56 3.2 47.0 1.0 OD2 A:ASP13 3.2 53.3 1.0 BE A:BFD56 3.3 50.2 1.0 CD A:GLU12 3.7 51.5 1.0 F1 A:BFD56 3.8 53.2 1.0 OE1 A:GLU12 3.8 53.3 1.0 NZ A:LYS108 3.8 52.9 1.0 C A:GLU58 4.0 52.0 1.0 CB A:BFD56 4.1 44.0 1.0 CB A:ASP13 4.3 53.5 1.0 N A:ASP13 4.3 51.9 1.0 F2 A:BFD56 4.5 51.0 1.0 CA A:GLU58 4.8 53.4 1.0 N A:GLU58 4.8 49.9 1.0 CB A:GLU58 4.8 57.2 1.0 CA A:ASP13 4.9 53.0 1.0 N A:SER14 5.0 52.2 1.0 N A:LEU59 5.0 49.4 1.0

Magnesium binding site 2 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:46.0 occ:1.00 O1A A:GH3301 2.2 60.7 1.0 OD2 A:ASP174 2.3 50.6 1.0 OE2 A:GLU217 2.4 56.1 1.0 OE1 A:GLU218 2.5 77.3 1.0 CD A:GLU218 3.0 78.5 1.0 CG A:GLU218 3.2 71.3 1.0 CD A:GLU217 3.3 53.5 1.0 CG A:ASP174 3.4 46.2 1.0 CG A:GLU217 3.5 51.0 1.0 PA A:GH3301 3.6 59.9 1.0 OE2 A:GLU218 3.9 82.7 1.0 OD1 A:ASP174 4.0 47.1 1.0 MG A:MG303 4.2 23.1 1.0 O3A A:GH3301 4.2 55.5 1.0 OE1 A:GLU217 4.4 53.2 1.0 O5' A:GH3301 4.5 61.5 1.0 CB A:ASP174 4.6 44.5 1.0 O2A A:GH3301 4.6 60.9 1.0 C5' A:GH3301 4.6 59.2 1.0 CB A:GLU218 4.8 64.2 1.0

Magnesium binding site 3 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:23.1 occ:1.00 O3A A:GH3301 2.1 55.5 1.0 O3G A:GH3301 2.1 50.0 1.0 OE2 A:GLU217 2.2 56.1 1.0 OD1 A:ASP174 2.2 47.1 1.0 O A:ILE175 2.4 43.0 1.0 O2B A:GH3301 2.5 50.9 1.0 OE1 A:GLU217 2.5 53.2 1.0 CD A:GLU217 2.7 53.5 1.0 PB A:GH3301 2.8 53.0 1.0 PG A:GH3301 3.2 53.2 1.0 CG A:ASP174 3.2 46.2 1.0 O3B A:GH3301 3.3 52.9 1.0 PA A:GH3301 3.4 59.9 1.0 O1A A:GH3301 3.5 60.7 1.0 OD2 A:ASP174 3.5 50.6 1.0 C A:ILE175 3.6 43.5 1.0 O1G A:GH3301 4.0 53.1 1.0 NZ A:LYS289 4.1 52.5 1.0 N A:ILE175 4.1 42.9 1.0 CG A:GLU217 4.2 51.0 1.0 MG A:MG302 4.2 46.0 1.0 O5' A:GH3301 4.2 61.5 1.0 O1B A:GH3301 4.2 52.9 1.0 C5' A:GH3301 4.3 59.2 1.0 CE A:LYS289 4.3 51.5 1.0 O2G A:GH3301 4.4 53.0 1.0 CA A:ILE175 4.4 43.3 1.0 C A:ASP174 4.5 43.2 1.0 O2A A:GH3301 4.5 60.9 1.0 CB A:ASP174 4.6 44.5 1.0 CB A:PHE178 4.6 52.6 1.0 N A:ASP176 4.6 44.1 1.0 N A:LYS177 4.7 53.5 1.0 N A:PHE178 4.7 51.1 1.0 CA A:ASP176 4.8 46.4 1.0 CB A:ILE175 4.9 43.8 1.0 O A:ASP174 5.0 42.6 1.0

Magnesium binding site 4 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg300 b:48.1 occ:1.00 F3 B:BFD56 2.0 46.0 1.0 OD1 B:ASP13 2.2 46.7 1.0 OD2 B:BFD56 2.3 49.5 1.0 O B:GLU58 2.3 46.5 1.0 OD2 B:ASP13 2.7 46.9 1.0 CG B:ASP13 2.8 46.1 1.0 CG B:BFD56 3.4 44.4 1.0 OE2 B:GLU12 3.6 47.8 1.0 C B:GLU58 3.6 48.0 1.0 BE B:BFD56 3.6 46.6 1.0 OD1 B:BFD56 3.8 44.2 1.0 F1 B:BFD56 4.2 53.7 1.0 CB B:GLU58 4.3 50.7 1.0 CB B:ASP13 4.3 46.2 1.0 CA B:GLU58 4.4 48.1 1.0 CD B:GLU12 4.4 45.8 1.0 NZ B:LYS108 4.5 44.5 1.0 N B:LEU59 4.6 48.2 1.0 OE1 B:GLU12 4.6 45.3 1.0 F2 B:BFD56 4.6 47.6 1.0 N B:GLU58 4.7 44.1 1.0 N B:ASP13 4.7 44.1 1.0 CB B:BFD56 4.8 41.1 1.0 CA B:LEU59 4.9 48.5 1.0

Magnesium binding site 5 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:76.7 occ:1.00 O1A B:GH3301 2.0 63.6 1.0 OE2 B:GLU218 2.1 80.5 1.0 OE2 B:GLU217 2.5 70.6 1.0 OD2 B:ASP174 2.5 48.6 1.0 CD B:GLU218 3.1 79.8 1.0 CD B:GLU217 3.3 68.1 1.0 PA B:GH3301 3.4 49.8 1.0 CG B:GLU217 3.4 62.7 1.0 CG B:GLU218 3.6 75.6 1.0 CG B:ASP174 3.6 48.7 1.0 O5' B:GH3301 3.9 55.2 1.0 O3A B:GH3301 4.1 40.9 1.0 C5' B:GH3301 4.1 53.6 1.0 OD1 B:ASP174 4.1 49.4 1.0 OE1 B:GLU218 4.2 78.9 1.0 MG B:MG303 4.3 29.4 1.0 OE1 B:GLU217 4.4 70.8 1.0 O2A B:GH3301 4.6 51.3 1.0 CB B:ASP174 4.8 47.2 1.0 CB B:GLU217 4.9 60.7 1.0

Magnesium binding site 6 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:29.4 occ:1.00 O3G B:GH3301 1.8 55.7 1.0 OE2 B:GLU217 2.0 70.6 1.0 OE1 B:GLU217 2.1 70.8 1.0 O B:ILE175 2.2 40.6 1.0 OD1 B:ASP174 2.2 49.4 1.0 O3A B:GH3301 2.4 40.9 1.0 CD B:GLU217 2.4 68.1 1.0 O2B B:GH3301 3.1 45.0 1.0 CG B:ASP174 3.2 48.7 1.0 PG B:GH3301 3.2 44.5 1.0 PB B:GH3301 3.3 42.5 1.0 C B:ILE175 3.4 43.4 1.0 PA B:GH3301 3.6 49.8 1.0 OD2 B:ASP174 3.6 48.6 1.0 O1A B:GH3301 3.7 63.6 1.0 O3B B:GH3301 3.7 42.6 1.0 N B:ILE175 3.8 45.0 1.0 CG B:GLU217 3.9 62.7 1.0 NZ B:LYS289 4.1 49.7 1.0 O1G B:GH3301 4.1 43.4 1.0 CA B:ILE175 4.1 44.5 1.0 C5' B:GH3301 4.2 53.6 1.0 O2G B:GH3301 4.2 47.2 1.0 MG B:MG302 4.3 76.7 1.0 C B:ASP174 4.3 45.0 1.0 CB B:PHE178 4.4 45.3 1.0 O5' B:GH3301 4.4 55.2 1.0 N B:ASP176 4.5 42.5 1.0 CB B:ASP174 4.5 47.2 1.0 N B:PHE178 4.6 45.9 1.0 CE B:LYS289 4.6 51.8 1.0 CB B:ILE175 4.6 43.9 1.0 N B:LYS177 4.6 47.9 1.0 O1B B:GH3301 4.7 38.0 1.0 CA B:ASP176 4.7 44.6 1.0 CB B:GLU217 4.8 60.7 1.0 O B:ASP174 4.8 45.6 1.0 CA B:ASP174 4.8 45.9 1.0 O2A B:GH3301 4.9 51.3 1.0 C B:ASP176 4.9 46.4 1.0

Magnesium binding site 7 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg300 b:50.4 occ:1.00 F3 C:BFD56 1.8 68.6 1.0 OD2 C:BFD56 1.9 69.0 1.0 OD1 C:ASP13 2.1 67.1 1.0 O C:GLU58 2.3 68.8 1.0 CG C:ASP13 2.9 67.9 1.0 CG C:BFD56 2.9 65.5 1.0 OD2 C:ASP13 3.0 72.0 1.0 BE C:BFD56 3.3 70.4 1.0 OD1 C:BFD56 3.4 64.7 1.0 C C:GLU58 3.6 69.7 1.0 OE2 C:GLU12 3.6 63.6 1.0 F1 C:BFD56 3.8 73.7 1.0 NZ C:LYS108 4.1 61.1 1.0 CD C:GLU12 4.3 62.6 1.0 CB C:BFD56 4.3 64.3 1.0 OE1 C:GLU12 4.3 64.4 1.0 CA C:GLU58 4.3 71.3 1.0 CB C:ASP13 4.4 66.2 1.0 F2 C:BFD56 4.4 80.7 1.0 CB C:GLU58 4.4 72.1 1.0 N C:GLU58 4.5 71.3 1.0 N C:LEU59 4.6 69.2 1.0 N C:ASP13 4.7 61.8 1.0 CA C:LEU59 4.9 69.9 1.0

Magnesium binding site 8 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:47.0 occ:1.00 OE2 C:GLU217 2.5 58.7 1.0 OD2 C:ASP174 2.7 51.9 1.0 OE2 C:GLU218 2.8 77.8 1.0 O1A C:GH3301 2.9 47.0 1.0 CD C:GLU218 3.4 76.4 1.0 CD C:GLU217 3.4 54.9 1.0 CG C:GLU218 3.6 72.1 1.0 PA C:GH3301 3.6 49.7 1.0 CG C:GLU217 3.6 55.2 1.0 O2A C:GH3301 3.8 56.9 1.0 O5' C:GH3301 3.8 55.1 1.0 CG C:ASP174 3.8 51.0 1.0 NH2 B:ARG23 4.0 54.9 1.0 C5' C:GH3301 4.1 56.6 1.0 OD1 C:ASP174 4.3 55.7 1.0 OE1 C:GLU218 4.5 79.7 1.0 MG C:MG303 4.5 28.4 1.0 OE1 C:GLU217 4.6 51.2 1.0 NH1 B:ARG23 4.9 53.5 1.0 CZ B:ARG23 4.9 52.4 1.0

Magnesium binding site 9 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:28.4 occ:1.00 O2B C:GH3301 1.9 42.6 1.0 O C:ILE175 2.1 49.0 1.0 OE1 C:GLU217 2.1 51.2 1.0 O3G C:GH3301 2.1 36.1 1.0 OE2 C:GLU217 2.2 58.7 1.0 OD1 C:ASP174 2.3 55.7 1.0 O1A C:GH3301 2.4 47.0 1.0 CD C:GLU217 2.5 54.9 1.0 PB C:GH3301 3.2 40.1 1.0 C C:ILE175 3.3 47.5 1.0 PG C:GH3301 3.3 45.1 1.0 CG C:ASP174 3.4 51.0 1.0 O3B C:GH3301 3.6 41.7 1.0 PA C:GH3301 3.7 49.7 1.0 OD2 C:ASP174 3.8 51.9 1.0 O3A C:GH3301 3.8 45.1 1.0 N C:ILE175 3.9 47.7 1.0 NH2 B:ARG23 3.9 54.9 1.0 CG C:GLU217 4.0 55.2 1.0 O1G C:GH3301 4.1 40.6 1.0 NZ C:LYS289 4.1 60.3 1.0 CA C:ILE175 4.1 48.0 1.0 CB C:PHE178 4.2 42.7 1.0 C5' C:GH3301 4.3 56.6 1.0 N C:ASP176 4.3 45.8 1.0 C C:ASP174 4.3 46.8 1.0 N C:PHE178 4.4 45.7 1.0 CE C:LYS289 4.4 64.3 1.0 O1B C:GH3301 4.5 39.9 1.0 MG C:MG302 4.5 47.0 1.0 O5' C:GH3301 4.5 55.1 1.0 N C:LYS177 4.5 46.4 1.0 CB C:ILE175 4.6 49.0 1.0 O2G C:GH3301 4.6 47.5 1.0 CA C:ASP176 4.6 46.8 1.0 CB C:ASP174 4.6 48.5 1.0 C C:ASP176 4.7 45.2 1.0 O C:ASP174 4.9 45.8 1.0 CB C:GLU217 4.9 54.4 1.0 O2A C:GH3301 4.9 56.9 1.0 CA C:ASP174 4.9 47.3 1.0 CA C:PHE178 4.9 43.5 1.0

Magnesium binding site 10 out of 12 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Activated State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg300 b:72.0 occ:1.00 F3 D:BFD56 2.0 78.1 1.0 OD1 D:ASP13 2.4 78.4 1.0 OD2 D:BFD56 2.7 83.7 1.0 OD2 D:ASP13 2.7 85.3 1.0 O D:GLU58 2.8 89.2 1.0 CG D:ASP13 2.9 84.8 1.0 BE D:BFD56 3.6 74.0 1.0 CG D:BFD56 3.7 77.4 1.0 OE2 D:GLU12 3.7 89.2 1.0 F1 D:BFD56 3.9 74.3 1.0 OD1 D:BFD56 4.0 73.3 1.0 C D:GLU58 4.0 89.5 1.0 CB D:GLU58 4.4 91.3 1.0 CB D:ASP13 4.4 87.5 1.0 CD D:GLU12 4.6 83.3 1.0 CA D:GLU58 4.7 88.8 1.0 F2 D:BFD56 4.7 73.4 1.0 OE1 D:GLU12 4.7 82.1 1.0 N D:GLU58 5.0 85.3 1.0

R.D.Teixeira, T.Schirmer. Dgcr Structure in Activated State To Be Published.