Magnesium in PDB 7d4s: Apo-Form Cyclic Trinucleotide Synthase Cdnd

The structure of Apo-Form Cyclic Trinucleotide Synthase Cdnd, PDB code: 7d4s 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)	33.50 / 1.93
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	66.316, 116.432, 107.41, 90, 90, 90
R / Rfree (%)	15.2 / 19.2

The binding sites of Magnesium atom in the Apo-Form Cyclic Trinucleotide Synthase Cdnd (pdb code 7d4s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Apo-Form Cyclic Trinucleotide Synthase Cdnd, PDB code: 7d4s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Apo-Form 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 Apo-Form Cyclic Trinucleotide Synthase Cdnd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:13.6 occ:1.00 OD2 A:ASP69 2.1 18.1 1.0 O2B A:APC401 2.1 14.6 1.0 O2G A:APC401 2.1 15.3 1.0 O A:HOH555 2.1 15.4 1.0 O2A A:APC401 2.1 15.0 1.0 OD2 A:ASP71 2.1 14.3 1.0 CG A:ASP71 3.1 16.2 1.0 PB A:APC401 3.2 15.5 1.0 CG A:ASP69 3.3 18.8 1.0 PA A:APC401 3.3 16.4 1.0 PG A:APC401 3.3 17.6 1.0 MG A:MG404 3.3 17.6 1.0 OD1 A:ASP71 3.5 13.2 1.0 O3B A:APC401 3.6 16.0 1.0 C3A A:APC401 3.7 16.0 1.0 O A:HOH543 3.8 23.3 1.0 O3G A:APC401 3.9 14.5 1.0 C5' A:APC401 4.0 11.5 1.0 OG A:SER53 4.0 14.7 1.0 CB A:ASP69 4.0 16.8 1.0 O5' A:APC401 4.1 15.9 1.0 O A:HOH577 4.1 13.2 1.0 O A:ASP69 4.1 14.8 1.0 OD1 A:ASP69 4.2 17.8 1.0 O1A A:APC401 4.4 16.2 1.0 CB A:ASP71 4.5 14.2 1.0 O1B A:APC401 4.5 15.2 1.0 O A:HOH768 4.5 27.6 1.0 C A:ASP69 4.5 15.3 1.0 O1G A:APC401 4.5 17.1 1.0 N A:SER53 4.5 12.1 1.0 O A:HOH592 4.7 21.4 1.0 N A:ASP71 4.8 13.5 1.0 CB A:SER53 4.9 13.8 1.0 CA A:ASP69 4.9 16.8 1.0

Magnesium binding site 2 out of 4 in the Apo-Form 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 Apo-Form Cyclic Trinucleotide Synthase Cdnd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:17.6 occ:1.00 OD2 A:ASP121 2.2 24.9 1.0 OD1 A:ASP71 2.3 13.2 1.0 O A:HOH768 2.4 27.6 1.0 OD2 A:ASP69 2.4 18.1 1.0 O2A A:APC401 2.4 15.0 1.0 OD1 A:ASP69 2.6 17.8 1.0 CG A:ASP69 2.9 18.8 1.0 CG A:ASP121 3.2 24.5 1.0 CG A:ASP71 3.2 16.2 1.0 MG A:MG403 3.3 13.6 1.0 OD2 A:ASP71 3.5 14.3 1.0 CB A:ASP121 3.5 16.7 1.0 PA A:APC401 3.7 16.4 1.0 O1A A:APC401 3.9 16.2 1.0 O A:HOH543 4.0 23.3 1.0 O A:HOH888 4.2 54.2 1.0 CB A:ASP69 4.3 16.8 1.0 O A:HOH614 4.3 16.6 1.0 OD1 A:ASP121 4.3 26.6 1.0 C5' A:APC401 4.4 11.5 1.0 O5' A:APC401 4.4 15.9 1.0 O A:HOH740 4.4 30.3 1.0 O2G A:APC401 4.5 15.3 1.0 CB A:ASP71 4.6 14.2 1.0 O A:HOH522 4.9 27.4 1.0 O2B A:APC401 4.9 14.6 1.0 CA A:ASP121 5.0 16.4 1.0

Magnesium binding site 3 out of 4 in the Apo-Form Cyclic Trinucleotide Synthase Cdnd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Apo-Form Cyclic Trinucleotide Synthase Cdnd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:16.8 occ:1.00 O A:ASN258 2.4 15.7 1.0 O A:HOH634 2.5 16.8 1.0 O A:HOH821 2.5 18.6 1.0 O A:LEU260 2.5 14.1 1.0 O A:HOH525 2.5 14.2 1.0 C A:ASN258 3.5 13.7 1.0 C A:LEU260 3.5 14.0 1.0 NZ A:LYS217 3.7 16.1 1.0 O A:GLY257 3.9 14.4 1.0 C A:ALA259 4.1 15.4 1.0 NH1 A:ARG281 4.2 13.7 1.0 N A:LEU260 4.2 11.8 1.0 O A:ALA259 4.2 13.6 1.0 CA A:ASN258 4.2 13.2 1.0 N A:ASP261 4.2 12.3 1.0 CA A:ASP261 4.3 12.5 1.0 N A:ALA259 4.4 14.4 1.0 OD1 A:ASP261 4.5 18.3 1.0 CA A:LEU260 4.5 11.4 1.0 NH2 A:ARG281 4.5 15.7 1.0 CA A:ALA259 4.6 14.6 1.0 CE A:LYS217 4.7 12.5 1.0 C A:GLY257 4.8 14.6 1.0 CZ A:ARG281 4.8 17.8 1.0

Magnesium binding site 4 out of 4 in the Apo-Form Cyclic Trinucleotide Synthase Cdnd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Apo-Form Cyclic Trinucleotide Synthase Cdnd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:46.2 occ:1.00 O3G A:APC402 2.1 47.7 1.0 O2B A:APC402 2.2 35.7 1.0 O A:HOH684 2.6 43.2 1.0 PG A:APC402 2.9 48.1 1.0 O2G A:APC402 3.1 48.3 1.0 PB A:APC402 3.1 29.8 1.0 O A:HOH905 3.2 47.5 1.0 O3B A:APC402 3.3 41.1 1.0 O A:HOH647 3.4 47.0 1.0 C3A A:APC402 3.8 21.7 1.0 O1G A:APC402 4.3 55.0 1.0 O1B A:APC402 4.4 25.3 1.0 O A:HOH629 5.0 37.3 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