Magnesium in PDB 7d4j: Ddatp Complex of Cyclic Trinucleotide Synthase Cdnd

The structure of Ddatp Complex of Cyclic Trinucleotide Synthase Cdnd, PDB code: 7d4j was solved by C.-S.Yang, M.-H.Hou, C.-L.Tsai, Y.-C.Wang, T.-P.Ko, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.37 / 2.09
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	53.173, 53.173, 345.758, 90, 90, 90
R / Rfree (%)	17.6 / 21

The binding sites of Magnesium atom in the Ddatp Complex of Cyclic Trinucleotide Synthase Cdnd (pdb code 7d4j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ddatp Complex of Cyclic Trinucleotide Synthase Cdnd, PDB code: 7d4j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ddatp Complex of Cyclic Trinucleotide Synthase Cdnd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ddatp Complex of Cyclic Trinucleotide Synthase Cdnd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:34.6 occ:1.00 O2B A:DDS401 2.0 28.7 1.0 O2A A:DDS401 2.1 40.3 1.0 O A:HOH673 2.1 36.2 1.0 O2G A:DDS401 2.3 36.8 1.0 O A:HOH728 2.5 36.5 1.0 OD2 A:ASP71 2.5 57.3 1.0 PB A:DDS401 3.2 29.6 1.0 PA A:DDS401 3.4 43.8 1.0 CG A:ASP71 3.4 56.4 1.0 PG A:DDS401 3.6 48.1 1.0 OD1 A:ASP71 3.6 45.8 1.0 O3A A:DDS401 3.6 35.0 1.0 O3B A:DDS401 3.8 34.5 1.0 O A:HOH593 4.1 25.5 1.0 CA A:GLY52 4.1 19.9 1.0 N A:SER53 4.2 16.9 1.0 O5' A:DDS401 4.2 58.8 1.0 C5' A:DDS401 4.3 54.9 1.0 CB A:ASP69 4.4 39.4 1.0 O3G A:DDS401 4.5 45.4 1.0 OG A:SER53 4.5 24.6 1.0 O A:HOH505 4.5 68.4 1.0 O1B A:DDS401 4.5 34.6 1.0 O1A A:DDS401 4.5 52.9 1.0 OD2 A:ASP69 4.5 52.8 1.0 O1G A:DDS401 4.6 57.5 1.0 C A:GLY52 4.7 18.8 1.0 CB A:ASP71 4.9 41.6 1.0 CG A:ASP69 4.9 46.9 1.0

Magnesium binding site 2 out of 2 in the Ddatp Complex of Cyclic Trinucleotide Synthase Cdnd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ddatp Complex of Cyclic Trinucleotide Synthase Cdnd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:36.1 occ:1.00 O A:HOH532 2.4 14.3 1.0 O A:HOH757 2.4 45.0 1.0 O A:HOH549 2.6 19.2 1.0 O A:ASN258 2.6 14.2 1.0 O A:LEU260 2.6 14.0 1.0 O A:HOH778 2.8 47.8 1.0 C A:LEU260 3.4 22.3 1.0 C A:ASN258 3.6 17.0 1.0 NZ A:LYS217 3.6 22.9 1.0 O A:GLY257 3.9 16.2 1.0 C A:ALA259 4.0 15.1 1.0 O A:ALA259 4.1 15.3 1.0 N A:LEU260 4.1 16.8 1.0 N A:ASP261 4.1 22.9 1.0 OD1 A:ASP261 4.1 32.7 1.0 CA A:ASP261 4.2 23.8 1.0 NH1 A:ARG281 4.3 21.1 1.0 CA A:ASN258 4.3 13.7 1.0 CA A:LEU260 4.4 18.6 1.0 N A:ALA259 4.4 18.7 1.0 NH2 A:ARG281 4.5 15.9 1.0 O A:HOH735 4.5 41.9 1.0 O A:HOH842 4.5 33.6 1.0 CA A:ALA259 4.6 15.0 1.0 O A:HOH731 4.8 38.7 1.0 CE A:LYS217 4.8 20.4 1.0 C A:GLY257 4.9 17.7 1.0 CZ A:ARG281 4.9 21.1 1.0

C.-S.Yang, M.-H.Hou, C.-L.Tsai, Y.-C.Wang, T.-P.Ko, Y.Chen. Crystal Structure and Functional Implication of A Bacterial Cyclic Amp-Amp-Gmp Synthetase Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962