Magnesium in PDB 5byg: X-Ray Structure of AAV2 Obd-AAVS1 Complex 2:1

The structure of X-Ray Structure of AAV2 Obd-AAVS1 Complex 2:1, PDB code: 5byg was solved by F.N.Musayev, C.R.Escalante, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.40 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.136, 79.595, 139.502, 90.00, 98.12, 90.00
R / Rfree (%)	18.9 / 22.7

The binding sites of Magnesium atom in the X-Ray Structure of AAV2 Obd-AAVS1 Complex 2:1 (pdb code 5byg). 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 AAV2 Obd-AAVS1 Complex 2:1, PDB code: 5byg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the X-Ray Structure of AAV2 Obd-AAVS1 Complex 2:1


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 AAV2 Obd-AAVS1 Complex 2:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:80.7 occ:1.00 CE1 A:HIS92 3.6 79.7 1.0 OE1 A:GLU83 3.7 79.0 1.0 NE2 A:HIS92 3.8 76.4 1.0 OE2 A:GLU83 4.0 63.0 1.0 CE A:LYS160 4.1 75.3 1.0 NZ A:LYS160 4.1 97.2 1.0 ND1 A:HIS92 4.2 77.0 1.0 CD2 A:LEU157 4.3 47.1 1.0 OH A:TYR152 4.3 61.5 1.0 O A:PHE156 4.3 55.8 1.0 CD A:GLU83 4.3 73.2 1.0 CD2 A:HIS92 4.6 68.3 1.0 CG A:HIS92 4.8 66.7 1.0 CE1 A:HIS90 4.9 90.0 1.0

Magnesium binding site 2 out of 3 in the X-Ray Structure of AAV2 Obd-AAVS1 Complex 2:1


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 AAV2 Obd-AAVS1 Complex 2:1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:0.5 occ:1.00 O B:HOH406 2.7 73.2 1.0 NE2 B:HIS92 2.7 78.8 1.0 NE2 B:HIS90 3.0 0.5 1.0 OE1 B:GLU83 3.2 74.1 1.0 O B:HOH431 3.3 75.6 1.0 CE1 B:HIS92 3.6 83.1 1.0 CD2 B:HIS90 3.7 0.1 1.0 CD2 B:HIS92 3.8 74.5 1.0 CD B:GLU83 4.0 68.2 1.0 OE2 B:GLU83 4.1 68.3 1.0 NZ B:LYS160 4.1 88.3 1.0 CE1 B:HIS90 4.1 0.1 1.0 O B:HOH408 4.1 75.7 1.0 CE B:LYS160 4.7 81.2 1.0 ND1 B:HIS92 4.8 79.3 1.0 CG B:HIS92 4.9 76.2 1.0 CG B:HIS90 5.0 88.4 1.0

Magnesium binding site 3 out of 3 in the X-Ray Structure of AAV2 Obd-AAVS1 Complex 2:1


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 AAV2 Obd-AAVS1 Complex 2:1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:97.6 occ:1.00 OE1 C:GLU83 3.4 90.7 1.0 NE2 C:HIS92 3.5 85.6 1.0 CE C:LYS160 3.6 80.8 1.0 CE1 C:HIS92 3.8 76.5 1.0 OE2 C:GLU83 3.9 84.4 1.0 NZ C:LYS160 3.9 98.7 1.0 O C:PHE156 4.0 87.0 1.0 CD C:GLU83 4.0 86.2 1.0 CD2 C:HIS92 4.2 82.3 1.0 CD2 C:LEU157 4.4 69.0 1.0 ND1 C:HIS92 4.5 85.2 1.0 OH C:TYR152 4.6 77.5 1.0 CG C:HIS92 4.7 80.7 1.0 C C:PHE156 5.0 82.0 1.0

F.N.Musayev, F.Zarate-Perez, C.Bishop, J.W.Burgner, C.R.Escalante. Structural Insights Into the Assembly of the Adeno-Associated Virus Type 2 REP68 Protein on the Integration Site AAVS1. J.Biol.Chem. V. 290 27487 2015.
ISSN: ESSN 1083-351X
PubMed: 26370092
DOI: 10.1074/JBC.M115.669960