Magnesium in PDB 2zgz: Parm with Gmppnp

The structure of Parm with Gmppnp, PDB code: 2zgz was solved by D.Popp, A.Narita, T.Oda, T.Fujisawa, H.Matsuo, Y.Nitanai, M.Iwasa, K.Maeda, H.Onishi, Y.Maeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.41 / 2.25
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	64.214, 64.214, 200.913, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.6

The binding sites of Magnesium atom in the Parm with Gmppnp (pdb code 2zgz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Parm with Gmppnp, PDB code: 2zgz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Parm with Gmppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Parm with Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg321 b:44.6 occ:1.00 O1B A:GNP323 2.3 40.8 1.0 O A:HOH325 2.3 29.6 1.0 O A:HOH326 2.4 35.4 1.0 O A:HOH324 2.4 34.9 1.0 O A:HOH327 2.4 30.1 1.0 O3G A:GNP323 2.5 41.7 1.0 PB A:GNP323 3.5 40.8 1.0 PG A:GNP323 3.6 44.3 1.0 N3B A:GNP323 3.8 43.1 1.0 OE2 A:GLU148 3.9 42.1 1.0 O A:HOH329 4.1 25.2 1.0 O A:HOH331 4.1 29.5 1.0 O2A A:GNP323 4.2 36.2 1.0 O2G A:GNP323 4.2 39.5 1.0 OD2 A:ASP170 4.2 41.9 1.0 OD2 A:ASP6 4.3 40.5 1.0 OD1 A:ASP6 4.3 43.6 1.0 NZ A:LYS13 4.4 36.2 1.0 O3A A:GNP323 4.4 35.6 1.0 O2B A:GNP323 4.5 42.5 1.0 CD A:GLU148 4.5 34.9 1.0 OE1 A:GLU148 4.6 40.8 1.0 PA A:GNP323 4.6 37.5 1.0 OD1 A:ASP170 4.6 46.8 1.0 CG A:ASP6 4.7 38.6 1.0 CA A:GLY8 4.7 38.7 1.0 O1G A:GNP323 4.8 48.0 1.0 O1A A:GNP323 4.8 33.7 1.0 CA A:GLY172 4.9 37.8 1.0 CG A:ASP170 4.9 45.1 1.0

Magnesium binding site 2 out of 4 in the Parm with Gmppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Parm with Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg322 b:43.4 occ:1.00 O A:THR101 2.4 35.3 1.0 OD1 A:ASP7 2.4 37.7 1.0 O A:HOH328 2.5 59.7 1.0 OE1 A:GLN73 2.5 38.8 1.0 O A:ASP7 2.8 38.2 1.0 OG1 A:THR101 2.8 41.3 1.0 CG A:ASP7 2.9 36.9 1.0 OD2 A:ASP7 3.2 40.1 1.0 C A:THR101 3.2 37.8 1.0 CD A:GLN73 3.2 41.6 1.0 NE2 A:GLN73 3.3 34.8 1.0 C A:ASP7 3.6 31.8 1.0 NZ A:LYS122 3.8 36.2 1.0 CA A:THR101 3.8 36.7 1.0 CB A:THR101 3.9 36.5 1.0 N A:THR101 3.9 35.0 1.0 CB A:ASP7 3.9 28.6 1.0 N A:ASP7 4.0 34.2 1.0 CA A:ASP7 4.0 28.1 1.0 CE A:LYS122 4.1 21.6 1.0 N A:LEU102 4.2 36.6 1.0 CA A:LEU102 4.5 30.7 1.0 CG A:GLN73 4.6 34.0 1.0 N A:GLY8 4.7 36.5 1.0 OE2 A:GLU148 4.8 42.1 1.0 CD A:PRO103 4.9 30.5 1.0

Magnesium binding site 3 out of 4 in the Parm with Gmppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Parm with Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg321 b:45.8 occ:1.00 O1B B:GNP323 2.3 41.0 1.0 O B:HOH325 2.3 37.1 1.0 O B:HOH326 2.3 36.2 1.0 O B:HOH324 2.3 33.3 1.0 O B:HOH327 2.4 29.2 1.0 O3G B:GNP323 2.5 37.6 1.0 PB B:GNP323 3.5 39.0 1.0 PG B:GNP323 3.6 43.7 1.0 N3B B:GNP323 3.8 40.4 1.0 OE2 B:GLU148 3.9 48.4 1.0 O B:HOH331 4.1 27.8 1.0 O B:HOH330 4.1 27.4 1.0 O2G B:GNP323 4.1 37.0 1.0 O2A B:GNP323 4.2 34.9 1.0 OD2 B:ASP6 4.2 38.2 1.0 OD1 B:ASP6 4.2 39.6 1.0 OD2 B:ASP170 4.3 42.5 1.0 NZ B:LYS13 4.3 32.6 1.0 O3A B:GNP323 4.5 36.2 1.0 O2B B:GNP323 4.5 38.4 1.0 CD B:GLU148 4.5 40.4 1.0 OE1 B:GLU148 4.5 49.2 1.0 CA B:GLY8 4.6 36.8 1.0 PA B:GNP323 4.7 36.1 1.0 OD1 B:ASP170 4.7 41.6 1.0 CG B:ASP6 4.7 41.8 1.0 O1G B:GNP323 4.8 43.8 1.0 O1A B:GNP323 4.8 30.8 1.0 O B:HOH374 4.9 49.6 1.0 CG B:ASP170 4.9 43.0 1.0 CA B:GLY172 5.0 35.2 1.0

Magnesium binding site 4 out of 4 in the Parm with Gmppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Parm with Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg322 b:45.1 occ:1.00 O B:THR101 2.4 37.4 1.0 OD1 B:ASP7 2.4 33.6 1.0 O B:HOH328 2.4 50.6 1.0 OE1 B:GLN73 2.5 34.8 1.0 OG1 B:THR101 2.8 38.2 1.0 O B:ASP7 2.8 36.5 1.0 CG B:ASP7 2.9 39.7 1.0 C B:THR101 3.2 35.9 1.0 CD B:GLN73 3.2 37.7 1.0 NE2 B:GLN73 3.2 35.5 1.0 OD2 B:ASP7 3.3 35.3 1.0 C B:ASP7 3.6 33.0 1.0 NZ B:LYS122 3.8 32.5 1.0 CA B:THR101 3.8 35.7 1.0 CB B:THR101 3.8 35.5 1.0 N B:THR101 3.9 38.1 1.0 CB B:ASP7 4.0 29.2 1.0 N B:ASP7 4.0 32.7 1.0 CA B:ASP7 4.1 30.2 1.0 N B:LEU102 4.1 36.9 1.0 CE B:LYS122 4.2 27.8 1.0 CA B:LEU102 4.4 32.9 1.0 CG B:GLN73 4.6 32.5 1.0 N B:GLY8 4.7 36.5 1.0 OE2 B:GLU148 4.7 48.4 1.0 CD B:PRO103 4.8 30.9 1.0

D.Popp, A.Narita, T.Oda, T.Fujisawa, H.Matsuo, Y.Nitanai, M.Iwasa, K.Maeda, H.Onishi, Y.Maeda. Molecular Structure of the Parm Polymer and the Mechanism Leading to Its Nucleotide-Driven Dynamic Instability Embo J. V. 27 570 2008.
ISSN: ISSN 0261-4189
PubMed: 18188150
DOI: 10.1038/SJ.EMBOJ.7601978