Magnesium in PDB 2zgy: Parm with Gdp

The structure of Parm with Gdp, PDB code: 2zgy 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)	44.44 / 1.90
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	64.437, 64.437, 201.021, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.7

The binding sites of Magnesium atom in the Parm with Gdp (pdb code 2zgy). 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 Gdp, PDB code: 2zgy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Parm with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg321 b:34.1 occ:1.00 O A:HOH325 2.1 26.7 1.0 O1B A:GDP323 2.1 28.6 1.0 O A:HOH327 2.2 28.2 1.0 O A:HOH328 2.2 27.8 1.0 O A:HOH324 2.2 25.4 1.0 O A:HOH326 2.2 29.9 1.0 PB A:GDP323 3.4 31.2 1.0 O3A A:GDP323 3.6 37.3 1.0 O3B A:GDP323 3.7 28.9 1.0 O A:HOH331 3.9 26.6 1.0 NZ A:LYS13 4.0 32.1 1.0 O A:HOH335 4.0 29.3 1.0 O A:HOH365 4.1 42.5 1.0 OE2 A:GLU148 4.2 37.4 1.0 OD2 A:ASP170 4.2 30.8 1.0 OD2 A:ASP6 4.3 30.7 1.0 O2A A:GDP323 4.3 31.7 1.0 OD1 A:ASP6 4.3 29.4 1.0 OE1 A:GLU148 4.4 34.3 1.0 O2B A:GDP323 4.4 25.2 1.0 CD A:GLU148 4.5 33.4 1.0 PA A:GDP323 4.6 30.9 1.0 OD1 A:ASP170 4.6 31.7 1.0 CA A:GLY8 4.7 31.7 1.0 CG A:ASP6 4.7 26.6 1.0 O1A A:GDP323 4.9 29.4 1.0 CG A:ASP170 4.9 32.6 1.0 CA A:GLY172 4.9 29.5 1.0 CE A:LYS13 5.0 27.1 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Parm with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg322 b:32.9 occ:1.00 O A:HOH329 2.3 32.2 1.0 O A:THR101 2.4 32.0 1.0 OE1 A:GLN73 2.4 34.9 1.0 OD1 A:ASP7 2.4 32.4 1.0 OG1 A:THR101 2.7 32.9 1.0 O A:ASP7 2.7 28.4 1.0 CG A:ASP7 3.0 34.4 1.0 C A:THR101 3.1 31.4 1.0 CD A:GLN73 3.2 37.9 1.0 NE2 A:GLN73 3.4 39.4 1.0 C A:ASP7 3.5 30.7 1.0 OD2 A:ASP7 3.6 32.7 1.0 CA A:THR101 3.7 30.8 1.0 CB A:THR101 3.7 30.9 1.0 N A:THR101 3.8 31.9 1.0 N A:ASP7 3.9 30.2 1.0 CA A:ASP7 3.9 28.2 1.0 CB A:ASP7 4.0 27.8 1.0 NZ A:LYS122 4.0 36.0 1.0 N A:LEU102 4.1 31.6 1.0 CE A:LYS122 4.2 31.1 1.0 OE2 A:GLU148 4.4 37.4 1.0 CA A:LEU102 4.4 27.5 1.0 CG A:GLN73 4.5 36.7 1.0 N A:GLY8 4.5 30.5 1.0 CD A:PRO103 4.8 29.4 1.0 CG2 A:THR101 4.9 30.3 1.0 C A:ASP6 4.9 29.1 1.0 CA A:GLY8 4.9 31.7 1.0 OD1 A:ASP6 5.0 29.4 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Parm with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg321 b:33.6 occ:1.00 O1B B:GDP323 2.1 28.2 1.0 O B:HOH325 2.1 26.6 1.0 O B:HOH324 2.2 26.0 1.0 O B:HOH327 2.2 28.2 1.0 O B:HOH328 2.2 28.5 1.0 O B:HOH326 2.2 28.7 1.0 PB B:GDP323 3.4 31.8 1.0 O3A B:GDP323 3.7 37.8 1.0 O3B B:GDP323 3.7 31.0 1.0 O B:HOH331 3.9 26.0 1.0 NZ B:LYS13 4.0 31.9 1.0 O B:HOH368 4.0 42.0 1.0 O B:HOH335 4.1 29.1 1.0 OE2 B:GLU148 4.1 38.9 1.0 OD2 B:ASP6 4.2 31.2 1.0 OD2 B:ASP170 4.3 31.6 1.0 OD1 B:ASP6 4.3 31.3 1.0 O2A B:GDP323 4.3 31.1 1.0 OE1 B:GLU148 4.3 34.0 1.0 O2B B:GDP323 4.4 25.5 1.0 CD B:GLU148 4.4 33.2 1.0 O B:HOH454 4.4 53.6 1.0 PA B:GDP323 4.6 31.8 1.0 OD1 B:ASP170 4.6 31.0 1.0 CG B:ASP6 4.7 28.1 1.0 CA B:GLY8 4.7 29.2 1.0 O1A B:GDP323 4.9 31.4 1.0 CG B:ASP170 4.9 30.6 1.0 CE B:LYS13 4.9 25.6 1.0 CA B:GLY172 4.9 28.1 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Parm with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg322 b:34.0 occ:1.00 O B:THR101 2.4 30.7 1.0 O B:HOH329 2.4 33.0 1.0 OD1 B:ASP7 2.4 31.6 1.0 OE1 B:GLN73 2.4 35.8 1.0 O B:ASP7 2.7 27.9 1.0 OG1 B:THR101 2.7 31.2 1.0 CG B:ASP7 3.0 31.5 1.0 C B:THR101 3.2 31.9 1.0 CD B:GLN73 3.2 37.8 1.0 C B:ASP7 3.5 28.3 1.0 NE2 B:GLN73 3.5 39.0 1.0 OD2 B:ASP7 3.5 34.7 1.0 CA B:THR101 3.7 31.4 1.0 CB B:THR101 3.7 29.9 1.0 N B:THR101 3.8 32.7 1.0 N B:ASP7 3.9 30.7 1.0 CA B:ASP7 3.9 26.9 1.0 NZ B:LYS122 3.9 34.2 1.0 CB B:ASP7 4.0 27.8 1.0 N B:LEU102 4.1 31.4 1.0 CE B:LYS122 4.2 31.4 1.0 OE2 B:GLU148 4.4 38.9 1.0 CA B:LEU102 4.5 27.5 1.0 N B:GLY8 4.5 28.4 1.0 CG B:GLN73 4.6 36.2 1.0 C B:ASP6 4.9 29.8 1.0 CA B:GLY8 4.9 29.2 1.0 CD B:PRO103 4.9 30.1 1.0 CG2 B:THR101 5.0 28.8 1.0 OD1 B:ASP6 5.0 31.3 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