Zinc in PDB 1oek: Yoda From Escherichia Coli Crystallised with Zinc Ions

The structure of Yoda From Escherichia Coli Crystallised with Zinc Ions, PDB code: 1oek was solved by G.David, K.Blondeau, M.Renouard, S.Penel, A.Lewit-Bentley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.05 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.600, 58.600, 152.000, 90.00, 90.00, 90.00
R / Rfree (%)	26.9 / 35.1

The binding sites of Zinc atom in the Yoda From Escherichia Coli Crystallised with Zinc Ions (pdb code 1oek). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Yoda From Escherichia Coli Crystallised with Zinc Ions, PDB code: 1oek:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Yoda From Escherichia Coli Crystallised with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yoda From Escherichia Coli Crystallised with Zinc Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1194 b:63.3 occ:0.70 NE2 A:HIS144 2.0 62.2 1.0 NE2 A:HIS155 2.2 58.9 1.0 O A:HOH2025 2.4 69.5 1.0 CE1 A:HIS144 2.7 65.1 1.0 O A:HOH2023 2.8 57.5 1.0 CE1 A:HIS155 3.0 55.4 1.0 O A:HOH2024 3.1 54.5 1.0 CD2 A:HIS144 3.1 65.8 1.0 O A:HOH2022 3.1 41.0 1.0 CD2 A:HIS155 3.3 53.2 1.0 ND1 A:HIS144 3.9 61.9 1.0 O A:HOH2011 4.0 66.8 1.0 CG A:HIS144 4.2 62.6 1.0 ND1 A:HIS155 4.2 57.1 1.0 CG A:HIS155 4.4 51.1 1.0

Zinc binding site 2 out of 4 in the Yoda From Escherichia Coli Crystallised with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yoda From Escherichia Coli Crystallised with Zinc Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1195 b:75.1 occ:0.70 NE2 A:HIS193 2.0 92.3 1.0 OE2 A:GLU189 2.1 63.6 1.0 OE1 A:GLU189 2.2 67.9 1.0 NE2 A:HIS153 2.2 64.8 1.0 CD A:GLU189 2.4 71.4 1.0 CE1 A:HIS193 2.4 92.8 1.0 CD2 A:HIS193 2.5 93.3 1.0 CD2 A:HIS153 2.9 62.2 1.0 ND1 A:HIS193 3.1 92.7 1.0 CG A:HIS193 3.2 94.1 1.0 CE1 A:HIS153 3.3 64.4 1.0 OH A:TYR177 3.6 58.4 1.0 CG A:GLU189 3.9 74.1 1.0 CG A:HIS153 4.0 61.8 1.0 ND1 A:HIS153 4.2 65.2 1.0 O A:GLU189 4.2 78.7 1.0 CB A:HIS193 4.4 93.8 1.0 CZ A:TYR177 4.4 55.6 1.0 CE1 A:TYR177 4.6 55.2 1.0 CB A:GLU189 4.7 77.3 1.0 C A:GLU189 4.8 78.5 1.0

Zinc binding site 3 out of 4 in the Yoda From Escherichia Coli Crystallised with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yoda From Escherichia Coli Crystallised with Zinc Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1196 b:73.5 occ:1.00 ND1 A:HIS95 2.4 52.4 1.0 O A:HOH2026 2.5 55.1 1.0 CG A:HIS95 3.2 57.9 1.0 CB A:HIS95 3.3 59.6 1.0 CE1 A:HIS95 3.5 56.5 1.0 CD2 A:HIS95 4.4 52.0 1.0 CA A:HIS95 4.4 60.8 1.0 NE2 A:HIS95 4.5 55.3 1.0 ND2 A:ASN98 4.5 85.7 1.0 CA A:ASN98 4.7 84.3 1.0 CG2 A:THR100 4.8 77.0 1.0 N A:ASN98 4.9 84.2 1.0

Zinc binding site 4 out of 4 in the Yoda From Escherichia Coli Crystallised with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yoda From Escherichia Coli Crystallised with Zinc Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1197 b:64.2 occ:1.00 OD1 A:ASP24 2.1 69.3 1.0 O A:HOH2027 2.4 41.2 1.0 O A:HOH2028 2.6 38.2 1.0 CG A:ASP24 3.0 69.8 1.0 OD2 A:ASP24 3.0 65.7 1.0 CB A:ASP24 4.4 69.2 1.0

G.David, K.Blondeau, M.Schiltz, S.Penel, A.Lewit-Bentley. Yoda From Escherichia Coli Is A Metal-Binding, Lipocalin-Like Protein J.Biol.Chem. V. 278 43728 2003.
ISSN: ISSN 0021-9258
PubMed: 12909634
DOI: 10.1074/JBC.M304484200