Magnesium in PDB 4zo0: X-Ray Structure of Aav-2 Origin Binding Domain

All present enzymatic activity of X-Ray Structure of Aav-2 Origin Binding Domain:
3.6.4.12;

The structure of X-Ray Structure of Aav-2 Origin Binding Domain, PDB code: 4zo0 was solved by F.N.Musayev, F.Zarate-Perez, C.R.Escalante, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.72 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	186.360, 154.400, 38.780, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 24.2

The binding sites of Magnesium atom in the X-Ray Structure of Aav-2 Origin Binding Domain (pdb code 4zo0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the X-Ray Structure of Aav-2 Origin Binding Domain, PDB code: 4zo0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the X-Ray Structure of Aav-2 Origin Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Aav-2 Origin Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:53.8 occ:1.00 OE1 A:GLU83 2.4 39.0 1.0 NE2 A:HIS90 2.7 38.4 1.0 O A:HOH503 2.7 48.8 1.0 NE2 A:HIS92 2.9 39.1 1.0 CD A:GLU83 3.4 42.7 1.0 CE1 A:HIS90 3.5 34.1 1.0 O A:HOH530 3.5 46.5 1.0 CD2 A:HIS90 3.7 37.2 1.0 CD2 A:HIS92 3.7 36.4 1.0 CE1 A:HIS92 3.8 34.0 1.0 OE2 A:GLU83 3.9 44.3 1.0 OE2 A:GLU164 4.4 58.7 1.0 NZ A:LYS160 4.6 61.3 1.0 CG A:GLU83 4.6 35.3 1.0 ND1 A:HIS90 4.7 36.5 1.0 O A:HOH635 4.7 46.1 1.0 CB A:GLU83 4.7 30.5 1.0 CE A:LYS160 4.7 54.1 1.0 CG A:HIS90 4.8 33.6 1.0 CG A:HIS92 4.9 37.0 1.0 ND1 A:HIS92 5.0 36.6 1.0

Magnesium binding site 2 out of 3 in the X-Ray Structure of Aav-2 Origin Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Aav-2 Origin Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:72.8 occ:1.00 OE1 B:GLU83 2.8 53.1 1.0 NE2 B:HIS92 2.9 53.5 1.0 NE2 B:HIS90 3.0 51.1 1.0 O B:HOH406 3.1 57.7 1.0 NZ B:LYS160 3.5 60.4 1.0 CE1 B:HIS92 3.7 51.9 1.0 CE1 B:HIS90 3.8 49.0 1.0 CD B:GLU83 3.9 51.0 1.0 CD2 B:HIS92 4.0 52.2 1.0 CD2 B:HIS90 4.1 49.7 1.0 OE2 B:GLU83 4.3 47.7 1.0 OE2 B:GLU164 4.4 57.2 1.0 CE B:LYS160 4.9 56.4 1.0 ND1 B:HIS92 4.9 53.1 1.0

Magnesium binding site 3 out of 3 in the X-Ray Structure of Aav-2 Origin Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of Aav-2 Origin Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:70.5 occ:1.00 OE2 C:GLU83 2.8 51.8 1.0 NE2 C:HIS92 2.9 48.5 1.0 NZ C:LYS160 3.3 60.4 1.0 NE2 C:HIS90 3.3 50.4 1.0 CE1 C:HIS92 3.7 48.2 1.0 CD C:GLU83 3.8 52.9 1.0 CD2 C:HIS92 4.0 47.2 1.0 OE1 C:GLU83 4.0 57.8 1.0 CE1 C:HIS90 4.1 44.7 1.0 CE C:LYS160 4.4 63.5 1.0 CD2 C:HIS90 4.4 43.9 1.0 OE2 C:GLU164 4.5 60.6 1.0 ND1 C:HIS92 4.9 44.0 1.0

F.N.Musayev, F.Zarate-Perez, M.Bardelli, C.Bishop, E.F.Saniev, R.M.Linden, E.Henckaerts, C.R.Escalante. Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation. Biochemistry V. 54 5907 2015.
ISSN: ISSN 0006-2960
PubMed: 26314310
DOI: 10.1021/ACS.BIOCHEM.5B00610