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

Protein crystallography data

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

Other elements in 7zpf:

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:

Zinc (Zn) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 4 binding sites of Nickel 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 Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 7zpf

Go back to Nickel Binding Sites List in 7zpf
Nickel 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 Nickel with other atoms in the Ni 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:Ni602

b:38.0
occ:1.00
OE1 A:GLU84 2.0 52.6 1.0
ND1 A:HIS88 2.0 31.5 1.0
NE2 C:HIS500 2.1 53.1 1.0
OE2 A:GLU84 2.3 54.3 1.0
CD A:GLU84 2.4 51.8 1.0
CD2 C:HIS500 3.0 52.9 1.0
CG A:HIS88 3.0 30.4 1.0
CE1 A:HIS88 3.0 33.5 1.0
CE1 C:HIS500 3.2 53.1 1.0
CB A:HIS88 3.3 29.0 1.0
O C:HIS504 3.4 80.9 1.0
C C:HIS504 3.6 81.0 1.0
CG A:GLU84 3.9 47.6 1.0
CD2 A:HIS88 4.1 31.5 1.0
CG C:HIS500 4.1 53.8 1.0
NE2 A:HIS88 4.1 33.5 1.0
ND1 C:HIS500 4.3 53.7 1.0
CD A:PRO141 4.3 33.7 1.0
CG A:PRO141 4.5 34.8 1.0
N A:ASN85 4.5 38.2 1.0
CA A:HIS88 4.7 27.8 1.0
CB A:GLU84 4.8 44.9 1.0
CB A:ASN85 4.8 36.1 1.0
CA C:HIS504 4.9 81.3 1.0
CA A:GLU84 4.9 43.8 1.0
N C:HIS504 4.9 81.1 1.0

Nickel binding site 2 out of 4 in 7zpf

Go back to Nickel Binding Sites List in 7zpf
Nickel 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 Nickel with other atoms in the Ni 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
C:Ni602

b:54.1
occ:1.00
ND1 C:HIS88 1.9 45.9 1.0
NE2 A:HIS500 2.0 56.3 1.0
OE1 C:GLU84 2.0 67.6 1.0
OE2 C:GLU84 2.4 66.7 1.0
CD C:GLU84 2.5 63.1 1.0
CE1 A:HIS500 2.9 56.8 1.0
CE1 C:HIS88 2.9 45.8 1.0
CG C:HIS88 2.9 43.8 1.0
O A:HIS504 3.0 79.3 1.0
CD2 A:HIS500 3.0 55.5 1.0
CB C:HIS88 3.3 41.9 1.0
C A:HIS504 3.8 80.0 1.0
ND1 A:HIS500 4.0 56.9 1.0
CG C:GLU84 4.0 51.9 1.0
NE2 C:HIS88 4.0 44.6 1.0
CG A:HIS500 4.1 55.6 1.0
CD2 C:HIS88 4.1 43.8 1.0
N C:ASN85 4.5 43.2 1.0
CD C:PRO141 4.5 45.0 1.0
CG C:PRO141 4.7 46.1 1.0
CB C:ASN85 4.7 44.2 1.0
CA C:HIS88 4.8 41.2 1.0
CB C:GLU84 4.8 46.7 1.0
CA A:HIS504 4.9 81.2 1.0
CA C:GLU84 4.9 45.0 1.0
N A:HIS504 5.0 80.3 1.0
CB A:HIS503 5.0 80.3 1.0

Nickel binding site 3 out of 4 in 7zpf

Go back to Nickel Binding Sites List in 7zpf
Nickel 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 Nickel with other atoms in the Ni 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
D:Ni602

b:48.2
occ:1.00
NE2 D:HIS500 2.0 46.9 1.0
CD2 D:HIS500 2.9 46.6 1.0
O D:HIS504 3.0 72.1 1.0
CE1 D:HIS500 3.1 47.1 1.0
C D:HIS504 3.7 72.7 1.0
CG D:HIS500 4.0 47.2 1.0
ND1 D:HIS500 4.1 47.4 1.0
CA D:HIS504 4.6 73.0 1.0
N D:HIS504 4.7 72.7 1.0
CB D:HIS503 4.9 72.2 1.0
O D:HIS500 5.0 54.5 1.0

Nickel binding site 4 out of 4 in 7zpf

Go back to Nickel Binding Sites List in 7zpf
Nickel 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 Nickel with other atoms in the Ni 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:Ni603

b:50.0
occ:1.00
OE1 D:GLU84 1.9 52.4 1.0
ND1 D:HIS88 2.2 37.4 1.0
OE2 D:GLU84 2.2 53.6 1.0
CD D:GLU84 2.3 51.1 1.0
CE1 D:HIS88 3.2 38.0 1.0
CG D:HIS88 3.2 35.9 1.0
CB D:HIS88 3.5 34.4 1.0
CG D:GLU84 3.9 45.4 1.0
NE2 D:HIS88 4.3 37.6 1.0
CD2 D:HIS88 4.3 36.4 1.0
CD D:PRO141 4.5 44.9 1.0
N D:ASN85 4.5 36.7 1.0
CG D:PRO141 4.6 46.2 1.0
CB D:GLU84 4.7 41.9 1.0
CA D:GLU84 4.8 40.4 1.0
CB D:ASN85 4.9 36.0 1.0
CA D:HIS88 5.0 34.0 1.0

Reference:

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.
Page generated: Fri Jul 28 03:49:44 2023

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