Nickel in PDB 8bnw: X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form

The structure of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form, PDB code: 8bnw 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)	70.62 / 2.13
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	35.369, 118.433, 141.046, 90, 90, 90
R / Rfree (%)	22.2 / 26.6

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

Nickel binding site 1 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form


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 - Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:53.5 occ:0.50 O4 A:SO4306 1.9 63.7 0.5 OD2 A:ASP88 2.0 61.9 1.0 O A:HOH403 2.0 53.3 1.0 O2 A:SO4306 2.2 70.6 0.5 S A:SO4306 2.5 61.4 0.5 CG A:ASP88 2.8 52.7 1.0 OD1 A:ASP88 2.9 61.5 1.0 O3 A:SO4306 3.5 76.7 0.5 O1 A:SO4306 3.6 53.2 0.5 HB2 A:LYS91 3.9 52.9 1.0 HB3 A:GLU90 4.2 63.6 1.0 CB A:ASP88 4.2 50.3 1.0 HB3 A:LYS91 4.3 52.9 1.0 H A:LYS91 4.4 57.5 1.0 HB2 A:ASP88 4.4 51.3 1.0 CB A:LYS91 4.6 50.1 1.0 HB3 A:ASP88 4.6 51.3 1.0 N A:LYS91 4.9 55.7 1.0 NI A:NI304 5.0 58.3 0.5

Nickel binding site 2 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form


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 - Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:68.8 occ:0.50 OE1 A:GLU151 1.9 92.7 1.0 OE2 A:GLU151 1.9 99.6 1.0 OE2 A:GLU155 2.0 82.6 1.0 CD A:GLU151 2.1 98.2 1.0 CD A:GLU155 3.2 76.5 1.0 CG A:GLU151 3.6 85.2 1.0 HG2 A:GLU151 4.0 85.1 1.0 OE1 A:GLU155 4.0 74.5 1.0 HG3 A:GLU155 4.0 74.6 1.0 HG3 A:GLU151 4.0 85.2 1.0 CG A:GLU155 4.2 76.0 1.0 HB3 A:GLU151 4.2 74.2 1.0 HG2 A:GLU155 4.4 74.6 1.0 CB A:GLU151 4.5 73.8 1.0

Nickel binding site 3 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form


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 - Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:75.2 occ:1.00 OE1 A:GLU111 1.9 89.4 1.0 CD A:GLU111 3.2 88.9 1.0 HG3 A:GLU111 3.7 88.5 1.0 OE2 A:GLU111 4.0 108.5 1.0 CG A:GLU111 4.0 91.3 1.0 HG2 A:GLU111 4.6 88.4 1.0 HB3 A:GLU111 4.9 81.2 1.0

Nickel binding site 4 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form


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 - Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:58.3 occ:0.50 O1 A:SO4306 1.9 53.2 0.5 OE2 A:GLU94 2.0 74.1 1.0 OE1 A:GLU94 2.1 66.3 1.0 OE2 A:GLU90 2.2 82.2 1.0 O3 A:SO4306 2.2 76.7 0.5 CD A:GLU94 2.3 67.2 1.0 S A:SO4306 2.5 61.4 0.5 HG2 A:GLU90 3.0 74.6 1.0 CD A:GLU90 3.1 84.4 1.0 O2 A:SO4306 3.4 70.6 0.5 CG A:GLU90 3.5 77.5 1.0 O4 A:SO4306 3.6 63.7 0.5 CG A:GLU94 3.8 60.8 1.0 HA A:LYS91 4.0 56.0 1.0 HG3 A:GLU94 4.1 61.6 1.0 HB3 A:GLU90 4.1 63.6 1.0 OE1 A:GLU90 4.1 75.7 1.0 HG3 A:GLU90 4.3 74.7 1.0 HG2 A:GLU94 4.3 61.6 1.0 CB A:GLU90 4.4 60.7 1.0 HE3 A:LYS91 4.6 59.2 1.0 HB2 A:GLU94 4.6 58.1 1.0 C A:GLU90 4.6 60.3 1.0 N A:LYS91 4.7 55.7 1.0 HB2 A:LYS91 4.7 52.9 1.0 O A:GLU90 4.7 61.9 1.0 CA A:LYS91 4.8 59.0 1.0 CB A:GLU94 4.8 58.3 1.0 NI A:NI301 5.0 53.5 0.5

Nickel binding site 5 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni305 b:101.2 occ:0.50 HZ1 A:LYS294 1.6 84.8 0.0 HZ2 A:LYS294 1.6 84.8 0.0 NZ A:LYS294 1.9 82.7 1.0 HZ3 A:LYS294 2.5 84.8 0.0 OE1 A:GLU297 2.6 66.2 1.0 OE2 A:GLU297 3.0 75.6 1.0 HD2 A:LYS294 3.1 84.6 1.0 CE A:LYS294 3.2 84.1 1.0 CD A:GLU297 3.2 88.9 1.0 CD A:LYS294 3.5 87.6 1.0 OE1 A:GLU293 3.5 110.4 1.0 HD3 A:LYS294 3.5 84.5 1.0 HE3 A:LYS294 3.8 84.6 1.0 HE2 A:LYS294 3.8 84.6 1.0 CD A:GLU293 4.4 105.5 1.0 HG2 A:GLU293 4.6 97.0 1.0 CG A:GLU297 4.7 87.3 1.0 CG A:LYS294 5.0 78.6 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