Nickel in PDB 8bf6: X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Azotochelin Complex

The structure of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Azotochelin Complex, PDB code: 8bf6 was solved by K.S.Wilson, A.-K.Duhme-Klair, E.V.Blagova, A.Miller, R.Booth, E.J.Dodson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.84 / 1.97
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	36.295, 116.711, 141.471, 90, 90, 90
R / Rfree (%)	20.5 / 25.5

The structure of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Azotochelin 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 - Azotochelin Complex (pdb code 8bf6). 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 - Azotochelin Complex, PDB code: 8bf6:
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 - Azotochelin 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 - Azotochelin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:53.0 occ:0.50 O A:HOH401 1.9 39.9 1.0 OD2 A:ASP88 2.0 48.3 1.0 O4 A:SO4307 2.0 60.1 0.5 O1 A:SO4307 2.0 58.6 0.5 S A:SO4307 2.6 57.0 0.5 CG A:ASP88 2.9 44.1 1.0 OD1 A:ASP88 3.1 46.0 1.0 HB2 A:LYS91 3.5 42.5 1.0 O2 A:SO4307 3.7 57.0 0.5 O3 A:SO4307 3.7 63.3 0.5 CB A:ASP88 4.3 42.5 1.0 H A:LYS91 4.3 41.1 1.0 CB A:LYS91 4.4 44.0 1.0 HB2 A:ASP88 4.5 42.0 1.0 HB3 A:GLU90 4.6 48.0 1.0 HB3 A:LYS91 4.6 41.7 1.0 HB3 A:ASP88 4.7 41.6 1.0 HD3 A:LYS91 4.9 45.7 1.0 N A:LYS91 4.9 42.2 1.0

Nickel binding site 2 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Azotochelin 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 - Azotochelin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:70.2 occ:0.50 OE1 A:GLU155 1.9 78.8 1.0 OE2 A:GLU155 1.9 81.3 1.0 OE1 A:GLU151 2.0 85.7 1.0 CD A:GLU155 2.1 89.2 1.0 CD A:GLU151 2.9 78.8 1.0 O A:HOH416 3.2 63.8 1.0 OE2 A:GLU151 3.5 83.1 1.0 CG A:GLU155 3.6 85.1 1.0 HG3 A:GLU151 3.8 81.5 1.0 HG2 A:GLU155 4.0 84.7 1.0 CG A:GLU151 4.0 81.2 1.0 HG3 A:GLU155 4.1 82.8 1.0 HB2 A:GLU155 4.2 72.7 1.0 O A:HOH403 4.4 65.3 1.0 O A:HOH414 4.5 78.5 1.0 CB A:GLU155 4.5 71.1 1.0 O A:GLU151 4.5 62.7 1.0 HG2 A:GLU151 4.7 79.0 1.0 HB3 A:GLU151 4.8 75.8 1.0 CB A:GLU151 5.0 74.3 1.0

Nickel binding site 3 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Azotochelin 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 - Azotochelin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni305 b:56.0 occ:0.50 OE2 A:GLU94 1.9 47.7 1.0 OE2 A:GLU90 1.9 63.0 1.0 O2 A:SO4307 2.0 57.0 0.5 O3 A:SO4307 2.0 63.3 0.5 S A:SO4307 2.5 57.0 0.5 CD A:GLU94 2.8 47.2 1.0 CD A:GLU90 2.9 63.2 1.0 HG2 A:GLU90 3.0 53.8 1.0 OE1 A:GLU94 3.1 44.9 1.0 CG A:GLU90 3.5 54.9 1.0 O1 A:SO4307 3.6 58.6 0.5 O4 A:SO4307 3.6 60.1 0.5 OE1 A:GLU90 4.0 58.1 1.0 CG A:GLU94 4.1 46.9 1.0 HG3 A:GLU90 4.2 55.5 1.0 HG3 A:GLU94 4.2 47.0 1.0 O A:HOH423 4.3 59.9 1.0 HB3 A:GLU90 4.3 48.0 1.0 HA A:LYS91 4.3 41.9 1.0 CB A:GLU90 4.5 47.1 1.0 HG2 A:GLU94 4.6 48.0 1.0 C A:GLU90 4.9 41.0 1.0 N A:LYS91 4.9 42.2 1.0 O A:GLU90 4.9 39.8 1.0

Nickel binding site 4 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Azotochelin 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 - Azotochelin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni306 b:86.0 occ:0.50 OE1 A:GLU211 1.9 100.1 1.0 CD A:GLU211 3.0 94.7 1.0 OE2 A:GLU211 3.6 106.3 1.0 HG3 A:GLU211 4.2 90.9 1.0 CG A:GLU211 4.2 89.0 1.0 HB3 A:SER213 4.6 63.2 1.0 HG2 A:GLU211 4.8 88.5 1.0

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


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 - Azotochelin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni308 b:63.4 occ:0.50 O A:HOH428 2.2 71.8 1.0 O A:LYS263 3.6 84.0 1.0 HA A:ASN264 4.1 82.5 1.0 C A:LYS263 4.7 83.3 1.0 HB3 A:LYS263 4.9 86.9 1.0 ND2 A:ASN264 4.9 87.6 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