Zinc in PDB 7zpf: Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida.

The structure of Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida., PDB code: 7zpf was solved by J.Lisboa, P.J.B.Pereira, N.M.S.Dos Santos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.28 / 2.54
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.129, 193.85, 91.616, 90, 113.24, 90
R / Rfree (%)	24 / 28.2

The structure of Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida. also contains other interesting chemical elements:

Nickel

(Ni)

4 atoms

The binding sites of Zinc atom in the Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida. (pdb code 7zpf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida., PDB code: 7zpf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:52.0 occ:1.00 OD2 A:ASP176 2.0 65.1 1.0 NE2 A:HIS169 2.0 38.8 1.0 NE2 A:HIS165 2.1 39.9 1.0 CD2 A:HIS165 3.0 38.6 1.0 CE1 A:HIS169 3.0 38.8 1.0 CD2 A:HIS169 3.0 38.0 1.0 CE1 A:HIS165 3.1 40.2 1.0 CG A:ASP176 3.2 64.0 1.0 OH A:TYR207 3.3 65.5 1.0 O A:HOH761 3.4 25.0 1.0 OE2 A:GLU166 3.8 49.6 1.0 OD1 A:ASP176 3.9 63.7 1.0 CZ A:TYR207 4.0 64.0 1.0 OE1 A:GLU166 4.0 44.9 1.0 CG A:HIS169 4.1 36.2 1.0 ND1 A:HIS169 4.1 38.2 1.0 CG A:HIS165 4.1 36.8 1.0 ND1 A:HIS165 4.2 39.3 1.0 CD A:GLU166 4.3 44.8 1.0 CB A:ASP176 4.3 62.0 1.0 CG2 A:THR186 4.5 57.8 1.0 CE1 A:TYR207 4.6 63.3 1.0 CE2 A:TYR207 4.6 63.0 1.0 CB A:THR186 4.9 57.9 1.0

Zinc binding site 2 out of 4 in the Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:40.1 occ:1.00 OD2 B:ASP176 1.9 60.3 1.0 NE2 B:HIS165 2.1 41.4 1.0 NE2 B:HIS169 2.2 33.2 1.0 O B:HOH713 2.6 28.0 1.0 CE1 B:HIS169 2.9 32.7 1.0 CG B:ASP176 3.0 59.6 1.0 CD2 B:HIS165 3.0 40.3 1.0 CE1 B:HIS165 3.1 41.2 1.0 OH B:TYR207 3.2 59.7 1.0 CD2 B:HIS169 3.4 32.2 1.0 OD1 B:ASP176 3.7 61.1 1.0 CZ B:TYR207 3.8 58.2 1.0 OE2 B:GLU166 4.0 48.7 1.0 ND1 B:HIS169 4.1 32.2 1.0 CB B:ASP176 4.1 55.0 1.0 CG B:HIS165 4.2 38.7 1.0 OE1 B:GLU166 4.2 49.1 1.0 ND1 B:HIS165 4.2 40.5 1.0 CG B:HIS169 4.3 30.7 1.0 CD B:GLU166 4.4 46.9 1.0 CE1 B:TYR207 4.5 57.1 1.0 CE2 B:TYR207 4.5 57.5 1.0 CG2 B:THR186 4.5 50.7 1.0 CB B:THR186 4.8 51.0 1.0

Zinc binding site 3 out of 4 in the Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:50.3 occ:1.00 OD2 C:ASP176 1.9 65.0 1.0 NE2 C:HIS169 2.1 45.8 1.0 NE2 C:HIS165 2.2 46.2 1.0 CE1 C:HIS169 2.7 46.0 1.0 CG C:ASP176 3.1 62.6 1.0 CD2 C:HIS165 3.1 45.1 1.0 O C:HOH701 3.2 26.5 1.0 CE1 C:HIS165 3.2 46.7 1.0 CD2 C:HIS169 3.3 44.3 1.0 OH C:TYR207 3.4 61.3 1.0 OD1 C:ASP176 3.8 62.0 1.0 OE2 C:GLU166 3.8 50.7 1.0 ND1 C:HIS169 4.0 44.9 1.0 CZ C:TYR207 4.0 59.5 1.0 OE1 C:GLU166 4.0 47.6 1.0 CB C:ASP176 4.1 59.9 1.0 CG C:HIS169 4.2 42.7 1.0 CG C:HIS165 4.2 44.0 1.0 CD C:GLU166 4.3 47.2 1.0 ND1 C:HIS165 4.3 46.4 1.0 CE2 C:TYR207 4.5 58.6 1.0 CG2 C:THR186 4.5 51.0 1.0 CE1 C:TYR207 4.8 58.5 1.0 CB C:THR186 4.8 50.7 1.0

Zinc binding site 4 out of 4 in the Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Three-Dimensional Structure of AIP56, A Short-Trip Single Chain Ab Toxin From Photobacterium Damselae Subsp. Piscicida. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:44.2 occ:1.00 OD2 D:ASP176 1.9 59.0 1.0 NE2 D:HIS165 2.2 42.2 1.0 NE2 D:HIS169 2.3 36.8 1.0 CD2 D:HIS165 3.1 41.6 1.0 CG D:ASP176 3.1 57.0 1.0 CD2 D:HIS169 3.2 35.3 1.0 CE1 D:HIS165 3.2 42.3 1.0 CE1 D:HIS169 3.3 36.6 1.0 OH D:TYR207 3.3 54.0 1.0 OD1 D:ASP176 3.8 59.1 1.0 CZ D:TYR207 4.0 52.2 1.0 OE2 D:GLU166 4.0 48.1 1.0 OE1 D:GLU166 4.0 49.6 1.0 CB D:ASP176 4.2 51.0 1.0 CG D:HIS165 4.3 40.0 1.0 ND1 D:HIS165 4.3 42.1 1.0 CG D:HIS169 4.3 33.2 1.0 CD D:GLU166 4.4 45.9 1.0 ND1 D:HIS169 4.4 35.1 1.0 CE2 D:TYR207 4.6 51.6 1.0 CG2 D:THR186 4.6 45.6 1.0 CE1 D:TYR207 4.6 51.0 1.0 CB D:THR186 4.9 45.6 1.0

J.Lisboa, R.D.Pinto, I.S.Rodrigues, L.M.G.Pereira, C.Pereira, P.Oliveira, P.J.B.Pereira, D.Durand, R.Benz, A.Do Vale, N.M.S.Dos Santos. 3D Structure of the Nf-Kb-Targeting Toxin AIP56 and Characterization of Determinants Required For Low pH-Induced Conformational Changes, Membrane Interaction and Translocation To Be Published.