Magnesium in PDB 4dzz: Structure of Parf-Adp, Crystal Form 1

The structure of Structure of Parf-Adp, Crystal Form 1, PDB code: 4dzz was solved by M.A.Schumacher, Q.Ye, M.R.Barge, D.Barilla, F.Hayes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.45 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.500, 78.300, 68.500, 90.00, 93.00, 90.00
R / Rfree (%)	20.3 / 24.4

The binding sites of Magnesium atom in the Structure of Parf-Adp, Crystal Form 1 (pdb code 4dzz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Parf-Adp, Crystal Form 1, PDB code: 4dzz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Parf-Adp, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Parf-Adp, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:30.9 occ:1.00 O A:HOH605 2.2 21.4 1.0 OG1 A:THR16 2.3 24.1 1.0 O A:HOH603 2.3 18.3 1.0 O A:HOH601 2.3 20.2 1.0 O A:HOH620 2.3 20.6 1.0 O2B A:ADP501 2.5 24.4 1.0 CB A:THR16 3.3 25.3 1.0 PB A:ADP501 3.4 28.5 1.0 O3B A:ADP501 3.4 27.0 1.0 N A:THR16 3.9 19.6 1.0 OD1 A:ASP82 4.0 25.1 1.0 O A:HOH614 4.0 25.0 1.0 O2A A:ADP501 4.0 36.2 1.0 O A:HOH654 4.1 36.4 1.0 CA A:THR16 4.2 24.8 1.0 O3A A:ADP501 4.2 24.1 1.0 OD2 A:ASP82 4.3 17.8 1.0 CB A:SER43 4.4 32.3 1.0 OD1 A:ASP39 4.4 47.9 1.0 OG A:SER43 4.4 47.0 1.0 CG2 A:THR16 4.4 22.4 1.0 CE A:LYS15 4.5 20.4 1.0 CG A:ASP82 4.5 19.8 1.0 CB A:LYS15 4.5 19.6 1.0 O A:HOH644 4.6 43.9 1.0 O A:GLY83 4.6 22.3 1.0 PA A:ADP501 4.6 27.6 1.0 O1B A:ADP501 4.8 38.3 1.0 O A:HOH608 4.9 22.1 1.0 O1A A:ADP501 4.9 32.7 1.0 CG A:ASP39 5.0 42.4 1.0 C A:LYS15 5.0 22.6 1.0

Magnesium binding site 2 out of 2 in the Structure of Parf-Adp, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Parf-Adp, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:48.3 occ:1.00 OG1 B:THR16 2.3 26.6 1.0 O B:HOH404 2.4 27.4 1.0 O B:HOH426 2.5 40.8 1.0 O B:HOH443 2.5 40.2 1.0 O B:HOH435 2.5 42.8 1.0 O2B B:ADP301 2.6 48.2 1.0 O3B B:ADP301 2.9 46.0 1.0 PB B:ADP301 3.2 40.8 1.0 CB B:THR16 3.4 30.1 1.0 N B:THR16 3.9 34.0 1.0 OD2 B:ASP82 4.0 29.9 1.0 O B:HOH437 4.0 33.4 1.0 O3A B:ADP301 4.1 33.8 1.0 OE1 B:GLN41 4.2 65.3 1.0 O2A B:ADP301 4.2 33.0 1.0 CA B:THR16 4.2 30.2 1.0 OD2 B:ASP39 4.2 49.8 1.0 OD1 B:ASP82 4.2 25.1 1.0 CB B:SER43 4.3 39.5 1.0 CG2 B:THR16 4.5 25.6 1.0 CB B:LYS15 4.5 31.0 1.0 CG B:ASP82 4.5 30.4 1.0 CE B:LYS15 4.6 29.1 1.0 PA B:ADP301 4.6 39.6 1.0 O1B B:ADP301 4.6 51.7 1.0 OG B:SER43 4.6 45.9 1.0 O B:GLY83 4.8 30.8 1.0 O1A B:ADP301 4.8 43.6 1.0 NZ B:LYS15 4.9 36.5 1.0 O B:HOH458 4.9 52.1 1.0 CG B:ASP39 4.9 50.5 1.0 C B:LYS15 4.9 32.9 1.0

M.A.Schumacher, Q.Ye, M.T.Barge, M.Zampini, D.Barilla, F.Hayes. Structural Mechanism of Atp-Induced Polymerization of the Partition Factor Parf: Implications For Dna Segregation. J.Biol.Chem. V. 287 26146 2012.
ISSN: ISSN 0021-9258
PubMed: 22674577
DOI: 10.1074/JBC.M112.373696