Magnesium in PDB 6zxm: Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp

The structure of Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp, PDB code: 6zxm 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 / 3.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	122.603, 72.917, 125.729, 90, 118.2, 90
R / Rfree (%)	22.5 / 29.9

The binding sites of Magnesium atom in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp (pdb code 6zxm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp, PDB code: 6zxm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp


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 in Complex with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:123.6 occ:1.00 OD1 A:ASP13 2.1 124.6 1.0 OE2 A:GLU12 2.1 120.2 1.0 OD2 A:ASP56 2.1 120.7 1.0 CG A:ASP13 3.0 127.3 1.0 CG A:ASP56 3.3 117.4 1.0 CD A:GLU12 3.3 113.3 1.0 OD2 A:ASP13 3.3 133.1 1.0 O A:GLU58 3.7 115.8 1.0 OD1 A:ASP56 4.0 113.8 1.0 OE1 A:GLU12 4.0 110.6 1.0 NE2 A:GLN17 4.3 108.8 1.0 N A:ASP13 4.3 115.9 1.0 CB A:ASP56 4.4 117.4 1.0 N A:SER14 4.4 109.6 1.0 OE1 A:GLN17 4.4 103.7 1.0 CB A:ASP13 4.4 124.0 1.0 CG A:GLU12 4.4 111.5 1.0 CD A:GLN17 4.6 105.7 1.0 CB A:SER14 4.6 108.6 1.0 NZ A:LYS108 4.7 112.6 1.0 CA A:ASP13 4.8 118.2 1.0 C A:GLU58 4.9 118.6 1.0 CB A:GLU58 4.9 123.5 1.0

Magnesium binding site 2 out of 6 in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp


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 in Complex with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:135.6 occ:1.00 OD2 B:ASP56 2.1 134.0 1.0 OE2 B:GLU12 2.1 133.6 1.0 OD1 B:ASP13 2.1 133.8 1.0 O F:GLY87 2.9 144.7 1.0 CG B:ASP13 3.1 134.1 1.0 CG B:ASP56 3.2 133.5 1.0 CD B:GLU12 3.3 129.7 1.0 OD2 B:ASP13 3.4 137.0 1.0 O B:GLU58 3.6 151.6 1.0 OD1 B:ASP56 3.9 132.8 1.0 C F:GLY87 4.0 142.4 1.0 OE1 B:GLU12 4.0 124.3 1.0 NE2 B:GLN17 4.3 133.3 1.0 N B:ASP13 4.3 127.9 1.0 CB B:ASP56 4.4 130.8 1.0 N B:SER14 4.4 126.7 1.0 CG B:GLU12 4.4 129.0 1.0 CB B:ASP13 4.4 132.7 1.0 OE1 B:GLN17 4.5 128.0 1.0 CG B:GLU58 4.6 142.8 1.0 NZ B:LYS108 4.6 113.4 1.0 CB B:SER14 4.6 130.2 1.0 CA F:GLY87 4.7 142.6 1.0 CD B:GLN17 4.7 129.9 1.0 C B:GLU58 4.7 154.3 1.0 CA B:ASP13 4.8 129.5 1.0 N F:HIS88 4.9 137.8 1.0 CA F:HIS88 5.0 136.0 1.0

Magnesium binding site 3 out of 6 in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp


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 in Complex with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:114.3 occ:1.00 OD1 C:ASP13 2.1 113.5 1.0 OE2 C:GLU12 2.1 111.5 1.0 OD2 C:ASP56 2.1 115.6 1.0 CG C:ASP13 3.0 116.4 1.0 CG C:ASP56 3.3 112.9 1.0 OD2 C:ASP13 3.3 121.1 1.0 CD C:GLU12 3.3 106.4 1.0 O C:GLU58 3.6 137.1 1.0 OD1 C:ASP56 3.9 111.1 1.0 OE1 C:GLU12 3.9 104.9 1.0 NZ C:LYS108 4.1 113.2 1.0 N C:ASP13 4.3 106.8 1.0 CB C:ASP13 4.4 115.3 1.0 CB C:ASP56 4.4 111.0 1.0 N C:SER14 4.4 106.0 1.0 OE1 C:GLN17 4.4 101.3 1.0 CG C:GLU12 4.5 103.5 1.0 NE2 C:GLN17 4.5 103.9 1.0 CG C:GLU58 4.6 135.0 1.0 CB C:SER14 4.7 103.7 1.0 CD C:GLN17 4.8 101.8 1.0 CA C:ASP13 4.8 110.5 1.0 C C:GLU58 4.8 137.4 1.0

Magnesium binding site 4 out of 6 in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp


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 in Complex with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:157.5 occ:1.00 OD2 D:ASP56 2.1 161.3 1.0 OD1 D:ASP13 2.1 162.1 1.0 OE2 D:GLU12 2.1 156.8 1.0 N D:ASP13 2.6 159.0 1.0 CG D:ASP13 2.8 164.9 1.0 CG D:ASP56 3.0 161.6 1.0 CD D:GLU12 3.2 154.1 1.0 CB D:ASP56 3.3 159.0 1.0 CB D:ASP13 3.4 166.2 1.0 C D:GLU12 3.4 157.3 1.0 CA D:GLU12 3.4 153.3 1.0 CA D:ASP13 3.5 163.7 1.0 OD2 D:ASP13 3.8 166.2 1.0 O D:GLU58 3.8 164.0 1.0 CG D:GLU12 3.9 154.1 1.0 OE1 D:GLU12 4.1 152.8 1.0 OD1 D:ASP56 4.1 162.6 1.0 CB D:GLU12 4.2 153.2 1.0 CD1 D:LEU59 4.2 173.8 1.0 N D:SER14 4.3 162.5 1.0 CD2 D:LEU59 4.3 165.9 1.0 C D:ASP13 4.5 164.4 1.0 N D:GLU12 4.6 149.4 1.0 O D:GLU12 4.7 157.9 1.0 CA D:ASP56 4.8 155.3 1.0 C D:GLU58 4.8 166.3 1.0 CG D:LEU59 4.9 172.2 1.0

Magnesium binding site 5 out of 6 in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp


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 in Complex with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg303 b:153.7 occ:1.00 OD2 E:ASP56 2.1 156.8 1.0 OD1 E:ASP13 2.1 153.0 1.0 OE2 E:GLU12 2.1 146.5 1.0 CG E:ASP13 3.0 154.3 1.0 CG E:ASP56 3.2 157.6 1.0 CD E:GLU12 3.3 143.1 1.0 OD2 E:ASP13 3.3 156.0 1.0 O E:GLU58 3.5 170.6 1.0 OD1 E:ASP56 3.9 157.0 1.0 OE1 E:GLU12 3.9 141.1 1.0 NZ E:LYS108 4.2 142.7 1.0 N E:ASP13 4.3 148.7 1.0 CB E:ASP56 4.3 156.2 1.0 CB E:ASP13 4.4 153.8 1.0 CG E:GLU12 4.4 142.4 1.0 N E:SER14 4.5 150.8 1.0 CG E:GLU58 4.6 164.5 1.0 C E:GLU58 4.8 169.7 1.0 CA E:ASP13 4.8 151.2 1.0 CB E:SER14 4.8 151.0 1.0

Magnesium binding site 6 out of 6 in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp


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 in Complex with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg303 b:148.2 occ:1.00 OE2 F:GLU12 2.1 144.8 1.0 OD2 F:ASP56 2.1 146.2 1.0 OD1 F:ASP13 2.1 144.3 1.0 CG F:ASP13 3.1 143.1 1.0 CG F:ASP56 3.2 145.0 1.0 CD F:GLU12 3.3 141.6 1.0 OD2 F:ASP13 3.4 145.6 1.0 NE2 F:GLN17 3.5 144.9 1.0 O F:GLU58 3.7 159.6 1.0 OD1 F:ASP56 3.9 145.5 1.0 OE1 F:GLU12 3.9 140.9 1.0 NZ F:LYS108 4.1 130.6 1.0 N F:ASP13 4.3 135.5 1.0 CB F:ASP56 4.4 141.2 1.0 OD1 B:ASN63 4.4 174.2 1.0 N F:SER14 4.4 136.4 1.0 CG F:GLU12 4.4 139.7 1.0 CB F:ASP13 4.5 141.5 1.0 CB B:ASN63 4.5 173.4 1.0 CD F:GLN17 4.6 144.9 1.0 CB F:SER14 4.7 140.2 1.0 CG F:GLU58 4.7 156.8 1.0 CG B:ASN63 4.7 172.3 1.0 CA F:ASP13 4.8 138.1 1.0 C F:GLU58 4.9 158.7 1.0 OE1 F:GLN17 4.9 143.0 1.0

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