Zinc in PDB 6xb8: Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna

All present enzymatic activity of Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna:
3.6.4.12;

The structure of Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna, PDB code: 6xb8 was solved by C.R.Escalante, F.N.Musayev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.86 / 3.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	170.180, 173.220, 173.450, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 21.8

The binding sites of Zinc atom in the Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna (pdb code 6xb8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna, PDB code: 6xb8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:0.4 occ:1.00 CE1 A:HIS90 2.8 60.2 1.0 OE1 A:GLU83 2.9 63.4 1.0 NE2 A:HIS90 3.2 63.9 1.0 OE2 A:GLU164 3.8 68.9 1.0 NE2 A:HIS92 3.8 56.0 1.0 ND1 A:HIS90 4.1 56.8 1.0 CD A:GLU83 4.1 58.5 1.0 NZ A:LYS160 4.2 66.6 1.0 CD2 A:HIS90 4.5 61.4 1.0 OE1 A:GLU86 4.6 58.1 1.0 CE1 A:HIS92 4.6 56.4 1.0 CA A:GLY85 4.7 61.5 1.0 CB A:GLU83 4.9 55.8 1.0 OE2 A:GLU83 4.9 57.0 1.0 CD A:GLU164 4.9 67.4 1.0 CD2 A:HIS92 4.9 53.6 1.0 CE A:LYS160 4.9 65.5 1.0 CG A:GLU83 5.0 56.4 1.0 CG A:HIS90 5.0 58.0 1.0

Zinc binding site 2 out of 4 in the Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:0.2 occ:0.99 NE2 B:HIS92 2.3 75.0 1.0 OE1 B:GLU83 2.7 78.2 1.0 CE1 B:HIS92 3.1 75.8 1.0 CD2 B:HIS92 3.4 71.9 1.0 CE1 B:HIS90 3.4 73.1 1.0 CD B:GLU83 3.4 77.2 1.0 NZ B:LYS160 3.4 85.1 1.0 OE2 B:GLU83 3.8 76.7 1.0 ND1 B:HIS90 4.2 68.1 1.0 NE2 B:HIS90 4.3 76.1 1.0 ND1 B:HIS92 4.3 72.8 1.0 CG B:GLU83 4.4 74.6 1.0 CG B:HIS92 4.5 70.8 1.0 OE2 B:GLU164 4.6 85.5 1.0 CE B:LYS160 4.7 87.2 1.0 CB B:GLU83 5.0 73.7 1.0

Zinc binding site 3 out of 4 in the Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:0.3 occ:1.00 NE2 C:HIS92 2.3 57.5 1.0 OE2 C:GLU83 2.6 57.8 1.0 CE1 C:HIS92 2.8 60.1 1.0 NZ C:LYS160 3.6 64.0 1.0 CE1 C:HIS90 3.6 60.3 1.0 CD2 C:HIS92 3.6 54.9 1.0 CD C:GLU83 3.7 57.6 1.0 ND1 C:HIS92 4.1 55.9 1.0 NE2 C:HIS90 4.3 65.9 1.0 CG C:GLU83 4.4 59.1 1.0 ND1 C:HIS90 4.5 55.8 1.0 CG C:HIS92 4.5 54.0 1.0 OE1 C:GLU83 4.6 57.1 1.0 CE C:LYS160 4.7 64.6 1.0 OE2 C:GLU164 4.8 64.7 1.0

Zinc binding site 4 out of 4 in the Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:0.9 occ:1.00 NE2 D:HIS92 3.1 74.4 1.0 OE1 D:GLU83 3.2 75.8 1.0 NZ D:LYS160 3.6 86.4 1.0 CE1 D:HIS92 3.6 72.8 1.0 CE D:LYS160 3.7 81.4 1.0 CE1 D:HIS90 3.9 66.3 1.0 CD D:GLU83 4.1 73.9 1.0 CD2 D:HIS92 4.3 70.1 1.0 OE2 D:GLU83 4.4 71.2 1.0 OE2 D:GLU164 4.4 79.6 1.0 NE2 D:HIS90 4.5 68.5 1.0 ND1 D:HIS92 4.8 69.9 1.0 ND1 D:HIS90 4.9 62.7 1.0

V.Santosh, F.N.Musayev, R.Jaiswal, B.Vandewinkel, F.Zarate-Perez, C.Dierckx, M.Endicott, K.Sharifi, K.Dryden, E.Henckaerts, C.R.Escalante. Adeno-Associated Virus Origin Binding Domain in Complex with Ssdna Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAA1133