Nickel in PDB 6tao: The Cytotoxin Make From Vibrio Cholerae

The structure of The Cytotoxin Make From Vibrio Cholerae, PDB code: 6tao was solved by K.Persson, R.Nagampalli, T.Heidler, S.N.Wai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.18 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.929, 94.936, 63.636, 90.00, 110.35, 90.00
R / Rfree (%)	17.7 / 23.5

The binding sites of Nickel atom in the The Cytotoxin Make From Vibrio Cholerae (pdb code 6tao). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the The Cytotoxin Make From Vibrio Cholerae, PDB code: 6tao:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the The Cytotoxin Make From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Cytotoxin Make From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:42.5 occ:0.78 NE2 A:HIS45 2.0 60.8 1.0 O A:HOH582 2.1 48.7 1.0 O3 A:SO4403 2.3 74.5 0.9 O A:HOH709 2.6 48.1 1.0 O4 A:SO4403 2.9 71.9 0.9 CE1 A:HIS45 2.9 57.5 1.0 HE1 A:HIS45 3.0 69.0 1.0 S A:SO4403 3.1 70.6 0.9 CD2 A:HIS45 3.1 54.7 1.0 HD2 A:HIS45 3.4 65.7 1.0 O2 A:SO4403 4.0 69.4 0.9 ND1 A:HIS45 4.1 56.5 1.0 CG A:HIS45 4.2 49.9 1.0 O1 A:SO4403 4.3 61.4 0.9 OE1 A:GLU162 4.3 56.4 1.0 OE2 A:GLU162 4.4 59.6 1.0 O A:HOH698 4.7 47.2 1.0 CD A:GLU162 4.8 57.3 1.0 HD1 A:HIS45 4.8 67.8 1.0 HB3 A:TRP46 4.9 43.8 1.0

Nickel binding site 2 out of 4 in the The Cytotoxin Make From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Cytotoxin Make From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:97.5 occ:1.00 HE1 A:HIS253 1.6 54.5 1.0 CE1 A:HIS253 2.5 45.4 1.0 O2 A:SO4404 2.9 81.7 1.0 NE2 A:HIS253 3.4 45.7 1.0 O4 A:SO4404 3.4 66.9 1.0 HE2 A:HIS253 3.4 54.9 1.0 ND1 A:HIS253 3.5 43.7 1.0 S A:SO4404 3.8 78.0 1.0 O A:HOH569 4.1 46.2 1.0 OD1 A:ASP254 4.5 46.7 1.0 CD2 A:HIS253 4.6 44.3 1.0 CG A:HIS253 4.6 43.2 1.0 O3 A:SO4404 4.8 78.3 1.0 O1 A:SO4404 4.8 83.5 1.0 O A:HOH505 4.9 58.9 1.0

Nickel binding site 3 out of 4 in the The Cytotoxin Make From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Cytotoxin Make From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:0.1 occ:1.00 HE1 B:HIS253 2.5 0.4 1.0 O B:HOH666 2.6 66.2 1.0 O B:HOH675 2.7 60.5 1.0 CE1 B:HIS253 3.0 93.6 1.0 O B:HOH616 3.1 58.2 1.0 HE2 B:HIS253 3.3 0.3 1.0 NE2 B:HIS253 3.3 93.6 1.0 HE21 B:GLN256 3.4 0.1 1.0 HE22 B:GLN256 3.5 0.1 1.0 NE2 B:GLN256 3.8 90.9 1.0 ND1 B:HIS253 3.9 90.5 1.0 CD2 B:HIS253 4.4 91.8 1.0 OD1 B:ASP254 4.6 73.6 1.0 CG B:HIS253 4.7 87.6 1.0 HA B:ASP254 4.8 79.2 1.0 O B:HIS253 4.9 67.4 1.0

Nickel binding site 4 out of 4 in the The Cytotoxin Make From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Cytotoxin Make From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:0.6 occ:1.00 HE2 B:HIS45 2.5 0.5 1.0 NE2 B:HIS45 2.9 96.2 1.0 CD2 B:HIS45 3.5 94.8 1.0 HD2 B:HIS45 3.6 0.8 1.0 CE1 B:HIS45 3.6 95.7 1.0 HE1 B:HIS45 3.9 0.8 1.0 HB3 B:TRP46 4.1 55.6 1.0 OE1 B:GLU162 4.3 76.4 1.0 CG B:HIS45 4.4 90.2 1.0 ND1 B:HIS45 4.4 94.0 1.0 HA B:TRP46 4.6 57.5 1.0 OE2 B:GLU162 4.7 77.7 1.0 CB B:TRP46 4.9 46.3 1.0 CD B:GLU162 5.0 76.1 1.0

K.Persson, R.Nagampalli, T.Heidler, S.N.Wai. The Cytotoxin Make From Vibrio Cholerae To Be Published.