Magnesium in PDB 4rv7: Characterization of An Essential Diadenylate Cyclase

All present enzymatic activity of Characterization of An Essential Diadenylate Cyclase:
2.7.7.85;

The structure of Characterization of An Essential Diadenylate Cyclase, PDB code: 4rv7 was solved by A.Dickmanns, P.Neumann, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.86 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	130.680, 130.680, 178.150, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 25.6

The binding sites of Magnesium atom in the Characterization of An Essential Diadenylate Cyclase (pdb code 4rv7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Characterization of An Essential Diadenylate Cyclase, PDB code: 4rv7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Characterization of An Essential Diadenylate Cyclase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Characterization of An Essential Diadenylate Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:0.0 occ:1.00 O2A A:ATP1001 2.1 96.7 0.8 O1B A:ATP1001 2.4 0.5 0.8 OE2 A:GLU124 2.7 0.6 1.0 PA A:ATP1001 3.2 95.1 0.8 PB A:ATP1001 3.6 99.3 0.8 O3G A:ATP1001 3.6 89.3 0.8 O3A A:ATP1001 3.6 0.7 0.8 O1A A:ATP1001 3.9 95.1 0.8 CD A:GLU124 3.9 0.9 1.0 O3B A:ATP1001 4.2 0.9 0.8 PG A:ATP1001 4.6 87.5 0.8 O5' A:ATP1001 4.6 87.5 0.8 CG A:GLU124 4.7 0.8 1.0 OE1 A:GLU124 4.8 0.1 1.0 CA A:GLY101 4.8 94.9 1.0 O2B A:ATP1001 4.9 97.1 0.8

Magnesium binding site 2 out of 4 in the Characterization of An Essential Diadenylate Cyclase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Characterization of An Essential Diadenylate Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:0.3 occ:1.00 O1B B:ATP1001 2.3 92.1 0.8 OE2 B:GLU124 2.4 99.2 1.0 O2A B:ATP1001 2.9 93.6 0.8 PB B:ATP1001 3.6 90.1 0.8 CD B:GLU124 3.6 99.3 1.0 PA B:ATP1001 3.9 91.1 0.8 O3A B:ATP1001 3.9 0.6 0.8 O3G B:ATP1001 4.2 95.9 0.8 OE1 B:GLU124 4.3 0.4 1.0 CA B:GLY101 4.4 79.4 1.0 O1A B:ATP1001 4.4 88.9 0.8 O3B B:ATP1001 4.6 0.3 0.8 CG B:GLU124 4.7 97.3 1.0 N B:GLY101 4.7 80.3 1.0 O2B B:ATP1001 4.7 89.2 0.8 PG B:ATP1001 4.9 95.5 0.8 O1G B:ATP1001 4.9 95.6 0.8

Magnesium binding site 3 out of 4 in the Characterization of An Essential Diadenylate Cyclase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Characterization of An Essential Diadenylate Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:0.2 occ:0.86 O2A C:ATP1001 2.1 0.2 0.8 OE2 C:GLU124 2.3 0.4 1.0 O1B C:ATP1001 2.3 0.8 0.8 O3G C:ATP1001 2.5 0.0 0.8 CD C:GLU124 3.4 0.8 1.0 PB C:ATP1001 3.4 0.3 0.8 PA C:ATP1001 3.4 0.9 0.8 PG C:ATP1001 3.5 1.0 0.8 O3B C:ATP1001 3.6 0.7 0.8 CG C:GLU124 3.8 0.4 1.0 O3A C:ATP1001 3.8 0.4 0.8 O1G C:ATP1001 3.9 0.2 0.8 O5' C:ATP1001 4.4 87.9 0.8 O1A C:ATP1001 4.5 0.8 0.8 OE1 C:GLU124 4.5 0.9 1.0 O2B C:ATP1001 4.8 0.0 0.8 O2G C:ATP1001 4.9 0.6 0.8

Magnesium binding site 4 out of 4 in the Characterization of An Essential Diadenylate Cyclase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Characterization of An Essential Diadenylate Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:0.8 occ:1.00 O2A D:ATP1001 2.0 0.9 0.8 O1B D:ATP1001 2.2 0.3 0.8 OE2 D:GLU124 2.4 0.1 1.0 O3G D:ATP1001 2.9 0.5 0.8 PA D:ATP1001 3.3 0.7 0.8 PB D:ATP1001 3.4 0.2 0.8 CD D:GLU124 3.5 0.3 1.0 O3A D:ATP1001 3.7 0.0 0.8 O3B D:ATP1001 3.8 0.4 0.8 PG D:ATP1001 4.0 0.6 0.8 CG D:GLU124 4.1 0.6 1.0 O1A D:ATP1001 4.3 0.4 0.8 O5' D:ATP1001 4.5 0.0 0.8 O1G D:ATP1001 4.5 0.1 0.8 OE1 D:GLU124 4.5 0.7 1.0 O2B D:ATP1001 4.8 0.4 0.8

J.Rosenberg, A.Dickmanns, P.Neumann, K.Gunka, J.Arens, V.Kaever, J.Stulke, R.Ficner, F.M.Commichau. Structural and Biochemical Analysis of the Essential Diadenylate Cyclase Cdaa From Listeria Monocytogenes J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X