Nickel in PDB 6vd9: Metal-Bound C-Terminal Domain of the Czcd Transporter From Cuprividus Metallidurans

The structure of Metal-Bound C-Terminal Domain of the Czcd Transporter From Cuprividus Metallidurans, PDB code: 6vd9 was solved by M.J.Maher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.57 / 1.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	32.760, 39.029, 63.965, 98.78, 104.76, 90.09
R / Rfree (%)	22.4 / 25.8

The binding sites of Nickel atom in the Metal-Bound C-Terminal Domain of the Czcd Transporter From Cuprividus Metallidurans (pdb code 6vd9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Metal-Bound C-Terminal Domain of the Czcd Transporter From Cuprividus Metallidurans, PDB code: 6vd9:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Metal-Bound C-Terminal Domain of the Czcd Transporter From Cuprividus Metallidurans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Metal-Bound C-Terminal Domain of the Czcd Transporter From Cuprividus Metallidurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:23.0 occ:0.50 O A:HOH401 1.9 32.8 1.0 OE2 A:GLU286 2.0 33.7 1.0 O A:HOH428 2.3 37.9 1.0 NE2 A:HIS234 2.3 21.6 1.0 O A:HOH411 2.5 35.9 1.0 ND1 A:HIS251 2.7 25.5 1.0 CD A:GLU286 2.9 34.6 1.0 OE1 A:GLU286 3.1 39.0 1.0 CE1 A:HIS234 3.2 20.0 1.0 CD2 A:HIS234 3.3 21.8 1.0 CG A:HIS251 3.4 20.2 1.0 CB A:HIS251 3.5 18.4 1.0 CE1 A:HIS251 3.6 24.6 1.0 CG A:GLU286 4.3 30.1 1.0 OD2 A:ASP235 4.4 40.0 1.0 ND1 A:HIS234 4.4 20.7 1.0 CG A:HIS234 4.4 19.3 1.0 CD2 A:HIS251 4.5 23.3 1.0 NE2 A:GLN284 4.5 19.1 1.0 NE2 A:HIS251 4.6 21.4 1.0 O A:HOH419 4.6 57.1 1.0 NZ C:LYS269 4.9 41.7 1.0

Nickel binding site 2 out of 4 in the Metal-Bound C-Terminal Domain of the Czcd Transporter From Cuprividus Metallidurans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Metal-Bound C-Terminal Domain of the Czcd Transporter From Cuprividus Metallidurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:22.7 occ:0.50 O B:HOH402 1.9 30.3 1.0 OE2 B:GLU286 2.1 39.1 1.0 NE2 B:HIS234 2.2 24.5 1.0 O B:HOH416 2.3 36.3 1.0 ND1 B:HIS251 2.6 22.9 1.0 CD B:GLU286 2.9 34.4 1.0 CE1 B:HIS234 3.0 20.4 1.0 OE1 B:GLU286 3.0 41.2 1.0 CD2 B:HIS234 3.3 22.7 1.0 CG B:HIS251 3.4 19.1 1.0 CE1 B:HIS251 3.5 23.5 1.0 CB B:HIS251 3.6 17.1 1.0 ND1 B:HIS234 4.1 21.8 1.0 OD2 B:ASP235 4.3 39.4 1.0 CG B:GLU286 4.3 30.0 1.0 CG B:HIS234 4.4 20.4 1.0 NE2 B:GLN284 4.5 18.3 1.0 NE2 B:HIS251 4.5 20.4 1.0 CD2 B:HIS251 4.5 20.6 1.0 O D:HOH421 4.7 33.4 1.0

Nickel binding site 3 out of 4 in the Metal-Bound C-Terminal Domain of the Czcd Transporter From Cuprividus Metallidurans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Metal-Bound C-Terminal Domain of the Czcd Transporter From Cuprividus Metallidurans within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni301 b:18.5 occ:0.50 O C:HOH417 1.9 34.5 1.0 O C:HOH416 2.0 30.9 1.0 OE1 C:GLU286 2.1 26.1 1.0 O C:HOH420 2.1 35.6 1.0 NE2 C:HIS234 2.1 23.6 1.0 ND1 C:HIS251 2.2 24.4 1.0 CD C:GLU286 2.9 23.5 1.0 CE1 C:HIS234 3.0 23.8 1.0 CE1 C:HIS251 3.1 26.2 1.0 OE2 C:GLU286 3.2 27.8 1.0 CD2 C:HIS234 3.2 24.9 1.0 CG C:HIS251 3.2 21.9 1.0 CB C:HIS251 3.6 18.6 1.0 OD2 C:ASP235 4.1 36.3 1.0 ND1 C:HIS234 4.2 23.8 1.0 NE2 C:HIS251 4.2 22.4 1.0 CG C:HIS234 4.3 22.7 1.0 CD2 C:HIS251 4.3 22.1 1.0 CG C:GLU286 4.3 22.5 1.0 NE2 C:GLN284 4.7 17.4 1.0 O C:HOH444 4.8 35.7 1.0 CG C:ASP235 4.9 32.8 1.0

Nickel binding site 4 out of 4 in the Metal-Bound C-Terminal Domain of the Czcd Transporter From Cuprividus Metallidurans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Metal-Bound C-Terminal Domain of the Czcd Transporter From Cuprividus Metallidurans within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni301 b:18.5 occ:0.50 O D:HOH419 1.8 35.2 1.0 OE1 D:GLU286 2.1 26.3 1.0 O D:HOH415 2.1 35.2 1.0 NE2 D:HIS234 2.1 26.6 1.0 O D:HOH418 2.2 32.6 1.0 ND1 D:HIS251 2.2 22.1 1.0 CD D:GLU286 3.0 26.4 1.0 CE1 D:HIS251 3.1 24.2 1.0 CD2 D:HIS234 3.1 25.0 1.0 CE1 D:HIS234 3.1 24.6 1.0 OE2 D:GLU286 3.2 26.6 1.0 CG D:HIS251 3.3 20.5 1.0 CB D:HIS251 3.6 20.9 1.0 OD2 D:ASP235 4.1 37.9 1.0 ND1 D:HIS234 4.2 23.9 1.0 CG D:HIS234 4.3 25.5 1.0 NE2 D:HIS251 4.3 21.6 1.0 CD2 D:HIS251 4.4 22.1 1.0 CG D:GLU286 4.4 24.4 1.0 NE2 D:GLN284 4.7 18.7 1.0 O D:HOH431 4.8 31.0 1.0 CG D:ASP235 4.8 36.9 1.0

S.R.Udagedara, D.M.La Porta, C.Spehar, G.Purohit, M.J.A.Hein, M.E.Fatmous, G.P.Casas Garcia, K.Ganio, C.A.Mcdevitt, M.J.Maher. Structural and Functional Characterizations of the C-Terminal Domains of Czcd Proteins. J.Inorg.Biochem. V. 208 11087 2020.
ISSN: ISSN 0162-0134
PubMed: 32505855
DOI: 10.1016/J.JINORGBIO.2020.111087