Magnesium in PDB 7d4o: Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp

The structure of Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp, PDB code: 7d4o 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)	29.00 / 1.87
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.773, 107.182, 65.875, 90, 118.29, 90
R / Rfree (%)	13.6 / 16.3

The binding sites of Magnesium atom in the Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp (pdb code 7d4o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp, PDB code: 7d4o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:13.6 occ:1.00 O2B A:ATP401 2.0 12.7 1.0 OD2 A:ASP69 2.0 15.2 1.0 O2A A:ATP401 2.0 13.3 1.0 O2G A:ATP401 2.0 14.8 1.0 OD2 A:ASP71 2.1 13.2 1.0 O A:HOH569 2.1 13.6 1.0 PB A:ATP401 3.1 12.8 1.0 CG A:ASP71 3.1 12.9 1.0 CG A:ASP69 3.2 18.5 1.0 PA A:ATP401 3.3 13.6 1.0 PG A:ATP401 3.3 17.9 1.0 MG A:MG404 3.4 18.8 1.0 O3A A:ATP401 3.5 13.9 1.0 OD1 A:ASP71 3.5 14.2 1.0 O3B A:ATP401 3.6 13.9 1.0 O A:HOH648 3.8 22.9 1.0 O3G A:ATP401 4.0 19.5 1.0 CB A:ASP69 4.0 16.9 1.0 OG A:SER53 4.0 13.9 1.0 C5' A:ATP401 4.1 11.8 1.0 O A:HOH631 4.1 11.5 1.0 O5' A:ATP401 4.2 12.1 1.0 OD1 A:ASP69 4.2 18.6 1.0 O A:ASP69 4.2 17.5 1.0 O1A A:ATP401 4.4 13.8 1.0 N A:SER53 4.4 10.8 1.0 O1B A:ATP401 4.4 13.7 1.0 CB A:ASP71 4.5 12.1 1.0 O A:HOH861 4.5 22.4 1.0 O1G A:ATP401 4.5 17.4 1.0 C A:ASP69 4.6 15.5 1.0 O A:HOH832 4.8 30.8 1.0 CB A:SER53 4.8 12.3 1.0 N A:ASP71 4.9 11.8 1.0 CA A:ASP69 5.0 17.4 1.0 CA A:GLY52 5.0 11.0 1.0

Magnesium binding site 2 out of 6 in the Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:18.8 occ:1.00 OD2 A:ASP121 2.3 26.2 1.0 OD1 A:ASP71 2.3 14.2 1.0 O A:HOH861 2.3 22.4 1.0 OD2 A:ASP69 2.4 15.2 1.0 O2A A:ATP401 2.5 13.3 1.0 O A:HOH785 2.5 26.8 1.0 OD1 A:ASP69 2.8 18.6 1.0 CG A:ASP69 3.0 18.5 1.0 CG A:ASP71 3.3 12.9 1.0 CG A:ASP121 3.4 23.2 1.0 MG A:MG403 3.4 13.6 1.0 OD2 A:ASP71 3.5 13.2 1.0 PA A:ATP401 3.6 13.6 1.0 CB A:ASP121 3.8 16.4 1.0 O A:HOH648 4.0 22.9 1.0 O5' A:ATP401 4.1 12.1 1.0 O A:HOH600 4.1 44.2 1.0 O1A A:ATP401 4.2 13.8 1.0 C5' A:ATP401 4.2 11.8 1.0 O A:HOH836 4.3 30.9 1.0 O A:HOH705 4.4 16.4 1.0 OD1 A:ASP121 4.4 25.1 1.0 CB A:ASP69 4.4 16.9 1.0 O2G A:ATP401 4.5 14.8 1.0 CB A:ASP71 4.7 12.1 1.0 O2B A:ATP401 4.9 12.7 1.0 O A:HOH524 4.9 23.8 1.0 O3A A:ATP401 5.0 13.9 1.0

Magnesium binding site 3 out of 6 in the Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:16.1 occ:1.00 O A:HOH659 2.3 14.0 1.0 O A:ASN258 2.3 12.3 1.0 O A:HOH857 2.4 19.0 1.0 O A:HOH628 2.5 12.3 1.0 O A:LEU260 2.6 13.0 1.0 C A:ASN258 3.4 11.7 1.0 C A:LEU260 3.5 13.1 1.0 NZ A:LYS217 3.7 13.6 1.0 O A:GLY257 3.8 13.7 1.0 CA A:ASN258 4.1 12.9 1.0 C A:ALA259 4.1 12.2 1.0 NH1 A:ARG281 4.2 13.8 1.0 O A:ALA259 4.2 11.4 1.0 N A:LEU260 4.2 12.3 1.0 N A:ASP261 4.3 12.2 1.0 CA A:ASP261 4.3 12.2 1.0 N A:ALA259 4.4 10.9 1.0 NH2 A:ARG281 4.5 15.7 1.0 CA A:LEU260 4.5 10.0 1.0 CA A:ALA259 4.6 11.2 1.0 OD1 A:ASP261 4.6 17.4 1.0 C A:GLY257 4.7 14.6 1.0 CE A:LYS217 4.8 12.0 1.0 CZ A:ARG281 4.8 16.1 1.0 N A:ASN258 4.9 14.1 1.0

Magnesium binding site 4 out of 6 in the Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:13.7 occ:1.00 O2B B:ATP401 2.0 11.4 1.0 O2A B:ATP401 2.0 13.5 1.0 OD2 B:ASP69 2.1 16.1 1.0 O2G B:ATP401 2.1 14.8 1.0 OD2 B:ASP71 2.1 14.9 1.0 O B:HOH625 2.1 14.4 1.0 PB B:ATP401 3.1 13.3 1.0 CG B:ASP71 3.1 12.5 1.0 CG B:ASP69 3.3 16.9 1.0 PA B:ATP401 3.3 13.8 1.0 PG B:ATP401 3.3 18.1 1.0 MG B:MG404 3.4 19.2 1.0 O3A B:ATP401 3.5 14.6 1.0 OD1 B:ASP71 3.5 12.5 1.0 O3B B:ATP401 3.6 14.9 1.0 O B:HOH592 3.8 22.6 1.0 O3G B:ATP401 4.0 18.8 1.0 CB B:ASP69 4.0 15.7 1.0 OG B:SER53 4.0 12.6 1.0 O B:HOH650 4.1 10.6 1.0 C5' B:ATP401 4.1 11.3 1.0 O5' B:ATP401 4.2 13.1 1.0 O B:ASP69 4.2 15.9 1.0 OD1 B:ASP69 4.2 17.7 1.0 N B:SER53 4.4 10.6 1.0 O1A B:ATP401 4.4 13.1 1.0 O1B B:ATP401 4.4 14.6 1.0 CB B:ASP71 4.5 11.2 1.0 O B:HOH851 4.5 22.6 1.0 O1G B:ATP401 4.5 18.3 1.0 C B:ASP69 4.6 14.1 1.0 CB B:SER53 4.8 13.2 1.0 N B:ASP71 4.9 12.4 1.0 CA B:GLY52 4.9 10.9 1.0 O B:HOH840 5.0 33.1 1.0 CA B:ASP69 5.0 16.4 1.0

Magnesium binding site 5 out of 6 in the Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:19.2 occ:1.00 OD2 B:ASP121 2.2 26.9 1.0 OD1 B:ASP71 2.3 12.5 1.0 O B:HOH851 2.3 22.6 1.0 O B:HOH766 2.4 25.6 1.0 O2A B:ATP401 2.5 13.5 1.0 OD2 B:ASP69 2.5 16.1 1.0 OD1 B:ASP69 2.9 17.7 1.0 CG B:ASP69 3.0 16.9 1.0 CG B:ASP71 3.3 12.5 1.0 CG B:ASP121 3.3 23.8 1.0 MG B:MG403 3.4 13.7 1.0 OD2 B:ASP71 3.5 14.9 1.0 PA B:ATP401 3.6 13.8 1.0 CB B:ASP121 3.8 17.6 1.0 O B:HOH592 4.1 22.6 1.0 O5' B:ATP401 4.1 13.1 1.0 O1A B:ATP401 4.2 13.1 1.0 C5' B:ATP401 4.2 11.3 1.0 O B:HOH702 4.2 40.0 1.0 OD1 B:ASP121 4.4 26.0 1.0 O B:HOH818 4.4 27.3 1.0 O B:HOH688 4.4 14.9 1.0 CB B:ASP69 4.5 15.7 1.0 O2G B:ATP401 4.5 14.8 1.0 O B:HOH890 4.6 48.8 1.0 CB B:ASP71 4.6 11.2 1.0 O2B B:ATP401 4.9 11.4 1.0 O3A B:ATP401 5.0 14.6 1.0 O B:HOH531 5.0 27.8 1.0

Magnesium binding site 6 out of 6 in the Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cyclic Trinucleotide Synthase Cdnd in Complex with Atp and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:16.0 occ:1.00 O B:ASN258 2.3 13.2 1.0 O B:HOH646 2.4 12.9 1.0 O B:HOH624 2.4 14.8 1.0 O B:HOH849 2.4 18.0 1.0 O B:LEU260 2.5 11.1 1.0 C B:ASN258 3.4 11.4 1.0 C B:LEU260 3.5 12.0 1.0 NZ B:LYS217 3.8 14.0 1.0 O B:GLY257 3.8 12.5 1.0 C B:ALA259 4.1 12.4 1.0 CA B:ASN258 4.2 13.1 1.0 NH1 B:ARG281 4.2 13.3 1.0 N B:LEU260 4.2 12.2 1.0 O B:ALA259 4.2 11.6 1.0 N B:ASP261 4.2 10.3 1.0 CA B:ASP261 4.3 11.5 1.0 N B:ALA259 4.3 10.6 1.0 CA B:LEU260 4.5 9.7 1.0 NH2 B:ARG281 4.5 13.7 1.0 CA B:ALA259 4.6 10.9 1.0 OD1 B:ASP261 4.6 16.5 1.0 C B:GLY257 4.8 13.3 1.0 CE B:LYS217 4.8 8.9 1.0 CZ B:ARG281 4.8 15.3 1.0 N B:ASN258 5.0 13.5 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