Nickel in PDB 8bj9: X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex.

The structure of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex., PDB code: 8bj9 was solved by E.V.Blagova, M.Bennett, R.Booth, E.J.Dodson, A.-K.Duhme-Klair, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.83 / 2.07
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	36.063, 117.392, 141.712, 90, 90, 90
R / Rfree (%)	21 / 26.6

The structure of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex. also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Nickel atom in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex. (pdb code 8bj9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex., PDB code: 8bj9:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:61.6 occ:0.50 O3 A:SO4307 2.0 61.0 0.5 OD2 A:ASP88 2.0 63.4 1.0 O A:HOH412 2.1 50.7 1.0 CG A:ASP88 2.9 56.3 1.0 OD1 A:ASP88 3.1 57.8 1.0 S A:SO4307 3.4 66.2 0.5 HB2 A:LYS91 3.5 52.1 1.0 O2 A:SO4307 3.9 61.4 0.5 O A:HOH410 4.1 63.7 1.0 O4 A:SO4307 4.2 78.8 0.5 CB A:ASP88 4.3 56.2 1.0 O1 A:SO4307 4.3 78.6 0.5 CB A:LYS91 4.4 51.9 1.0 HB3 A:LYS91 4.4 51.5 1.0 HB2 A:ASP88 4.5 55.3 1.0 H A:LYS91 4.6 54.0 1.0 HB3 A:ASP88 4.6 54.7 1.0 HB3 A:GLU90 4.8 56.6 1.0 HD3 A:LYS91 4.9 54.1 1.0

Nickel binding site 2 out of 4 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:55.9 occ:0.50 O1 A:SO4307 2.0 78.6 0.5 O4 A:SO4307 2.0 78.8 0.5 O2 A:SO4307 2.0 61.4 0.5 OE1 A:GLU94 2.1 59.2 1.0 S A:SO4307 2.2 66.2 0.5 CD A:GLU94 2.9 63.1 1.0 OE2 A:GLU94 3.0 65.6 1.0 HD3 A:LYS91 3.6 54.1 1.0 O3 A:SO4307 3.7 61.0 0.5 HZ2 A:LYS91 3.9 59.8 1.0 HA A:LYS91 4.1 54.7 1.0 CG A:GLU94 4.4 59.1 1.0 HD2 A:LYS91 4.4 54.0 1.0 HB2 A:GLU94 4.4 55.6 1.0 CD A:LYS91 4.5 53.7 1.0 OE2 A:GLU90 4.5 64.7 1.0 HB2 A:LYS91 4.6 52.1 1.0 NZ A:LYS91 4.8 59.9 1.0 HG2 A:GLU90 4.8 60.9 1.0 CB A:GLU94 4.8 55.1 1.0 HB3 A:GLU94 4.8 56.6 1.0 HG3 A:GLU94 4.9 59.6 1.0 HG2 A:GLU94 4.9 60.4 1.0 CA A:LYS91 5.0 53.4 1.0 HZ1 A:LYS91 5.0 59.3 1.0

Nickel binding site 3 out of 4 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni305 b:81.3 occ:0.50 OE1 A:GLU151 2.4 114.7 1.0 OE2 A:GLU155 2.6 89.8 1.0 CD A:GLU151 3.1 112.4 1.0 HB3 A:GLU151 3.6 98.4 1.0 CD A:GLU155 3.7 96.9 1.0 HG3 A:GLU151 3.7 107.0 1.0 CG A:GLU151 3.9 105.9 1.0 OE2 A:GLU151 3.9 120.6 1.0 OE1 A:GLU155 4.0 102.2 1.0 O A:HOH405 4.1 91.3 1.0 CB A:GLU151 4.2 96.2 1.0 HG2 A:GLU151 4.8 103.6 1.0 HB2 A:GLU151 4.9 96.8 1.0 O A:GLU151 5.0 84.3 1.0

Nickel binding site 4 out of 4 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - 5LICAM Complex. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni306 b:73.6 occ:0.50 O A:LEU54 2.4 72.0 1.0 HZ2 A:LYS146 2.6 79.4 1.0 HZ1 A:LYS146 2.7 81.6 1.0 HG2 A:GLU149 2.9 87.5 1.0 NZ A:LYS146 3.0 80.4 1.0 C A:LEU54 3.2 69.5 1.0 HA A:LEU54 3.4 70.4 1.0 HD2 A:LYS146 3.6 79.3 1.0 HZ3 A:LYS146 3.6 81.3 1.0 CA A:LEU54 3.9 69.7 1.0 CG A:GLU149 3.9 89.5 1.0 HA3 A:GLY55 3.9 65.0 1.0 CE A:LYS146 4.1 79.5 1.0 N A:GLY55 4.1 70.0 1.0 HB3 A:LEU54 4.1 69.7 1.0 HG3 A:GLU149 4.2 90.0 1.0 HE3 A:LYS146 4.2 77.7 1.0 CD A:LYS146 4.3 80.1 1.0 HB3 A:GLU149 4.3 82.5 1.0 CA A:GLY55 4.5 59.4 1.0 OE1 A:GLU149 4.6 96.4 1.0 HD3 A:LYS146 4.6 81.3 1.0 CB A:LEU54 4.6 68.9 1.0 HD22 A:LEU54 4.6 69.5 1.0 CD A:GLU149 4.6 90.5 1.0 CB A:GLU149 4.6 85.3 1.0 H A:GLY55 4.8 66.1 1.0 HB2 A:GLU149 4.8 83.0 1.0 HD21 A:LEU54 4.9 68.8 1.0 O A:LYS53 4.9 66.9 1.0 HE2 A:LYS146 4.9 80.0 1.0

E.V.Blagova, A.Miller, M.Bennett, R.Booth, E.J.Dodson, A.-K.Duhme-Klair, K.S.Wilson. Thermostable Homologues of the Periplasmic Siderophore-Binding Protein Ceue From and Acta Crystallogr.,Sect.D 2023.
ISSN: ESSN 1399-0047