Magnesium in PDB 7plj: Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates.

The structure of Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates., PDB code: 7plj was solved by S.T.N.Silva, C.V.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.04 / 1.64
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.851, 137.144, 85.024, 90, 116.9, 90
R / Rfree (%)	16.9 / 20.2

The binding sites of Magnesium atom in the Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates. (pdb code 7plj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates., PDB code: 7plj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:12.9 occ:1.00 O2B A:ATP301 2.0 14.3 1.0 OD1 A:ASP66 2.1 13.7 1.0 O1G A:ATP302 2.1 11.2 1.0 O2A A:ATP302 2.1 13.5 1.0 O1G A:ATP301 2.1 12.9 1.0 O2B A:ATP302 2.2 10.3 1.0 CG A:ASP66 3.2 15.8 1.0 PB A:ATP302 3.2 11.9 1.0 PB A:ATP301 3.3 14.6 1.0 PG A:ATP301 3.3 14.1 1.0 PA A:ATP302 3.3 13.5 1.0 PG A:ATP302 3.3 11.8 1.0 O3B A:ATP301 3.4 13.6 1.0 O3B A:ATP302 3.5 12.6 1.0 O3A A:ATP302 3.5 13.4 1.0 CA A:ASP66 3.8 14.0 1.0 O A:HOH504 3.9 18.9 1.0 CB A:ASP66 3.9 15.7 1.0 N A:ALA67 4.0 14.9 1.0 NZ A:LYS70 4.1 12.1 1.0 OD2 A:ASP66 4.1 18.2 1.0 NH2 A:ARG182 4.2 17.1 1.0 O3G A:ATP301 4.2 16.0 1.0 O3G A:ATP302 4.2 13.8 1.0 O3A A:ATP301 4.2 16.9 1.0 C5' A:ATP302 4.2 16.8 1.0 O5' A:ATP302 4.3 15.0 1.0 O1B A:ATP301 4.3 17.9 1.0 O2G A:ATP301 4.4 15.9 1.0 O2G A:ATP302 4.4 13.1 1.0 C A:ASP66 4.5 16.3 1.0 O1A A:ATP302 4.5 16.2 1.0 NH2 A:ARG122 4.6 17.0 1.0 NH1 A:ARG182 4.6 20.8 1.0 O1B A:ATP302 4.6 13.4 1.0 CE A:LYS70 4.7 10.8 1.0 CZ A:ARG182 4.9 18.3 1.0 N A:ASP66 4.9 14.8 1.0

Magnesium binding site 2 out of 4 in the Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg307 b:16.6 occ:1.00 O3G B:ATP302 2.0 15.6 1.0 O2A B:ATP302 2.0 15.0 1.0 O1G B:ATP301 2.0 15.5 1.0 O2B B:ATP301 2.1 15.9 1.0 OD1 B:ASP66 2.1 16.9 1.0 O2B B:ATP302 2.2 15.2 1.0 CG B:ASP66 3.2 21.0 1.0 PB B:ATP302 3.2 16.1 1.0 PG B:ATP301 3.3 18.1 1.0 PB B:ATP301 3.3 18.5 1.0 PA B:ATP302 3.3 17.6 1.0 PG B:ATP302 3.3 15.8 1.0 O3B B:ATP301 3.4 14.9 1.0 O3B B:ATP302 3.5 16.6 1.0 O3A B:ATP302 3.5 19.7 1.0 O B:HOH475 3.8 24.0 1.0 CA B:ASP66 3.8 17.8 1.0 CB B:ASP66 4.0 20.2 1.0 NH2 B:ARG182 4.0 24.1 1.0 N B:ALA67 4.0 15.4 1.0 NZ B:LYS70 4.1 15.1 1.0 OD2 B:ASP66 4.1 22.6 1.0 O2G B:ATP302 4.1 14.4 1.0 O3A B:ATP301 4.2 20.9 1.0 O3G B:ATP301 4.2 21.1 1.0 O5' B:ATP302 4.3 18.1 1.0 O1B B:ATP301 4.3 21.4 1.0 C5' B:ATP302 4.3 20.5 1.0 O2G B:ATP301 4.4 19.4 1.0 O1A B:ATP302 4.5 20.2 1.0 O1G B:ATP302 4.5 16.2 1.0 C B:ASP66 4.5 18.1 1.0 NH2 B:ARG122 4.6 18.9 1.0 O1B B:ATP302 4.6 17.9 1.0 O B:HOH410 4.8 28.6 1.0 CE B:LYS70 4.9 14.4 1.0 NH1 B:ARG182 4.9 27.0 1.0 CZ B:ARG182 4.9 25.6 1.0 N B:ASP66 5.0 17.4 1.0

Magnesium binding site 3 out of 4 in the Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg308 b:14.9 occ:1.00 O2G C:ATP302 2.1 11.1 1.0 O2B C:ATP301 2.1 14.9 1.0 O3G C:ATP301 2.1 14.6 1.0 OD1 C:ASP66 2.1 15.3 1.0 O2A C:ATP302 2.1 9.5 1.0 O1B C:ATP302 2.2 12.6 1.0 PB C:ATP302 3.2 13.3 1.0 CG C:ASP66 3.3 18.0 1.0 PG C:ATP301 3.3 13.9 1.0 PB C:ATP301 3.4 14.3 1.0 PA C:ATP302 3.4 13.9 1.0 PG C:ATP302 3.4 13.9 1.0 O3B C:ATP301 3.5 14.1 1.0 O3B C:ATP302 3.5 13.5 1.0 O3A C:ATP302 3.5 16.9 1.0 O C:HOH555 3.8 13.7 1.0 CA C:ASP66 3.8 15.5 1.0 NH2 C:ARG182 3.9 19.0 1.0 CB C:ASP66 4.0 18.4 1.0 C5' C:ATP302 4.0 15.7 1.0 N C:ALA67 4.0 15.4 1.0 NZ C:LYS70 4.1 13.6 1.0 O2G C:ATP301 4.1 14.8 1.0 O1G C:ATP302 4.1 14.8 1.0 O5' C:ATP302 4.2 15.1 1.0 OD2 C:ASP66 4.2 18.1 1.0 O3A C:ATP301 4.3 17.2 1.0 O1B C:ATP301 4.4 15.2 1.0 O1A C:ATP302 4.4 16.2 1.0 O1G C:ATP301 4.5 15.5 1.0 C C:ASP66 4.5 18.3 1.0 O3G C:ATP302 4.5 16.2 1.0 O2B C:ATP302 4.6 15.2 1.0 NH2 C:ARG122 4.7 20.8 1.0 CE C:LYS70 4.8 11.9 1.0 CZ C:ARG182 4.9 21.5 1.0 N C:ASP66 4.9 16.6 1.0 O C:HOH598 5.0 27.7 1.0

Magnesium binding site 4 out of 4 in the Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg309 b:13.2 occ:1.00 O2A D:ATP302 2.0 12.8 1.0 O1B D:ATP301 2.0 15.5 1.0 OD1 D:ASP66 2.0 14.5 1.0 O2B D:ATP302 2.1 13.1 1.0 O2G D:ATP302 2.1 12.7 1.0 O1G D:ATP301 2.2 15.8 1.0 CG D:ASP66 3.2 17.0 1.0 PB D:ATP302 3.2 15.2 1.0 PA D:ATP302 3.2 16.6 1.0 PB D:ATP301 3.3 16.0 1.0 PG D:ATP301 3.4 13.9 1.0 PG D:ATP302 3.4 13.6 1.0 O3B D:ATP301 3.4 13.0 1.0 O3A D:ATP302 3.5 16.8 1.0 O3B D:ATP302 3.5 13.4 1.0 O D:HOH500 3.7 18.6 1.0 CA D:ASP66 3.9 16.2 1.0 NH2 D:ARG182 3.9 20.8 1.0 N D:ALA67 4.0 16.5 1.0 CB D:ASP66 4.0 15.8 1.0 C5' D:ATP302 4.0 20.1 1.0 OD2 D:ASP66 4.1 21.0 1.0 NZ D:LYS70 4.1 13.4 1.0 O5' D:ATP302 4.1 18.0 1.0 O3A D:ATP301 4.2 18.4 1.0 O1G D:ATP302 4.2 14.5 1.0 O3G D:ATP301 4.2 16.0 1.0 O2B D:ATP301 4.4 17.1 1.0 O1A D:ATP302 4.4 20.4 1.0 O3G D:ATP302 4.5 13.6 1.0 O2G D:ATP301 4.5 14.3 1.0 C D:ASP66 4.5 15.3 1.0 NH2 D:ARG122 4.5 20.1 1.0 O1B D:ATP302 4.6 15.1 1.0 O D:HOH413 4.7 27.2 1.0 NH1 D:ARG182 4.8 22.4 1.0 CZ D:ARG182 4.8 25.5 1.0 CE D:LYS70 4.9 11.8 1.0

S.T.N.Silva, C.V.Romao. Structure of Polyphosphate Kinase 2 From Deinococcus Radiodurans, in Complex with Atp and Polyphosphates. To Be Published.