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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 6xb8

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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 6xb8

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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 6xb8

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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 6xb8

Go back to Zinc Binding Sites List in 6xb8
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

Reference:

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
Page generated: Wed Dec 16 13:09:32 2020

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