Zinc in PDB 5aq6: Structure of E. Coli Zint at 1.79 Angstrom

The structure of Structure of E. Coli Zint at 1.79 Angstrom, PDB code: 5aq6 was solved by P.E.Santo, H.G.Colaco, P.Matias, J.B.Vicente, T.M.Bandeiras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.75 / 1.79
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.010, 62.010, 149.720, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.8

The binding sites of Zinc atom in the Structure of E. Coli Zint at 1.79 Angstrom (pdb code 5aq6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structure of E. Coli Zint at 1.79 Angstrom, PDB code: 5aq6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Structure of E. Coli Zint at 1.79 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of E. Coli Zint at 1.79 Angstrom within 5.0Å range:

Zinc binding site 2 out of 9 in the Structure of E. Coli Zint at 1.79 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of E. Coli Zint at 1.79 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1194 b:26.5 occ:0.75 NE2 A:HIS193 1.9 25.5 1.0 NE2 A:HIS1 1.9 35.6 1.0 OE1 A:GLU189 2.0 26.6 1.0 NE2 A:HIS6 2.0 64.9 1.0 CE1 A:HIS193 2.8 42.6 1.0 CD A:GLU189 2.8 34.2 1.0 CE1 A:HIS1 2.8 50.0 1.0 HE1 A:HIS193 2.9 51.1 1.0 OE2 A:GLU189 2.9 34.9 1.0 CD2 A:HIS1 3.0 38.2 1.0 CD2 A:HIS193 3.0 33.5 1.0 HE1 A:HIS1 3.0 60.0 1.0 CE1 A:HIS6 3.0 65.1 1.0 CD2 A:HIS6 3.1 58.6 1.0 HE1 A:HIS6 3.2 78.2 1.0 HD2 A:HIS1 3.2 45.9 1.0 HD2 A:HIS6 3.3 70.3 1.0 HD2 A:HIS193 3.3 40.2 1.0 HA A:GLU189 3.9 28.8 1.0 ND1 A:HIS193 3.9 40.0 1.0 O A:HOH2148 4.0 38.2 1.0 ND1 A:HIS1 4.0 43.7 1.0 CG A:HIS193 4.0 45.6 1.0 HB2 A:SER192 4.0 47.6 1.0 CG A:HIS1 4.1 44.4 1.0 ND1 A:HIS6 4.1 54.8 1.0 CG A:HIS6 4.2 51.8 1.0 CG A:GLU189 4.3 29.3 1.0 OG A:SER5 4.4 63.1 1.0 HG A:SER5 4.4 75.7 1.0 HB3 A:GLU189 4.6 31.1 1.0 HB3 A:SER192 4.6 47.6 1.0 HG3 A:GLU189 4.7 35.1 1.0 HA A:SER5 4.7 71.3 1.0 CA A:GLU189 4.7 24.0 1.0 CB A:GLU189 4.7 25.9 1.0 CB A:SER192 4.8 39.7 1.0 HG2 A:GLU189 4.8 35.1 1.0

Zinc binding site 3 out of 9 in the Structure of E. Coli Zint at 1.79 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of E. Coli Zint at 1.79 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1195 b:26.6 occ:1.00 NE2 A:HIS155 2.0 19.8 1.0 NE2 A:HIS144 2.0 20.9 1.0 NE2 A:HIS153 2.1 25.1 1.0 O A:HOH2137 2.1 37.6 1.0 CE1 A:HIS155 2.9 25.1 1.0 CD2 A:HIS155 3.0 28.0 1.0 CE1 A:HIS144 3.0 24.8 1.0 CE1 A:HIS153 3.0 25.6 1.0 CD2 A:HIS144 3.0 25.2 1.0 CD2 A:HIS153 3.1 23.3 1.0 HE1 A:HIS155 3.1 30.1 1.0 HD2 A:HIS155 3.2 33.6 1.0 HE1 A:HIS144 3.2 29.8 1.0 HE1 A:HIS153 3.2 30.8 1.0 HD2 A:HIS144 3.2 30.2 1.0 HD2 A:HIS153 3.2 27.9 1.0 ND1 A:HIS155 4.0 20.4 1.0 O A:HOH2161 4.1 23.5 0.6 CG A:HIS155 4.1 20.9 1.0 ND1 A:HIS144 4.1 26.4 1.0 ND1 A:HIS153 4.2 24.7 1.0 CG A:HIS144 4.2 21.8 1.0 CG A:HIS153 4.2 20.7 1.0 O A:HOH2086 4.4 18.3 0.5 HA A:ASP143 4.5 30.9 1.0 O A:HOH2178 4.5 50.0 1.0 HG21 A:THR175 4.9 24.8 1.0

Zinc binding site 4 out of 9 in the Structure of E. Coli Zint at 1.79 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of E. Coli Zint at 1.79 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1196 b:38.6 occ:0.69 ZN A:ZN1196 0.0 38.6 0.7 HE1 A:HIS95 1.6 36.8 0.2 ND1 A:HIS95 1.8 34.2 0.2 CE1 A:HIS95 1.8 30.7 0.2 ND1 A:HIS95 2.2 27.3 0.8 CE1 A:HIS95 2.9 33.2 0.8 HE1 A:HIS95 3.0 39.9 0.8 NE2 A:HIS95 3.2 33.2 0.2 CG A:HIS95 3.2 30.1 0.2 HB3 A:HIS95 3.2 34.6 0.8 CG A:HIS95 3.2 28.1 0.8 HG23 A:THR100 3.4 46.8 1.0 HG22 A:THR100 3.5 46.8 1.0 CB A:HIS95 3.8 28.8 0.8 HE3 A:MET84 3.8 42.3 1.0 CD2 A:HIS95 3.8 33.0 0.2 CG2 A:THR100 3.8 39.0 1.0 HB3 A:HIS95 3.9 34.5 0.2 NE2 A:HIS95 4.0 29.8 0.8 HG21 A:THR100 4.1 46.8 1.0 CB A:HIS95 4.2 28.8 0.2 CD2 A:HIS95 4.2 32.0 0.8 HE2 A:MET84 4.2 42.3 1.0 HB2 A:HIS95 4.3 34.6 0.8 ZN A:ZN1196 4.4 25.6 0.3 CE A:MET84 4.5 35.2 1.0 HA A:ASN98 4.7 84.1 1.0 HD2 A:HIS95 4.7 39.6 0.2 HA A:HIS95 4.7 33.7 0.2 HA A:HIS95 4.7 33.3 0.8 O A:ASN97 4.8 81.5 1.0 HB2 A:HIS95 4.9 34.5 0.2 CA A:HIS95 4.9 27.7 0.8

Zinc binding site 5 out of 9 in the Structure of E. Coli Zint at 1.79 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of E. Coli Zint at 1.79 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1196 b:25.6 occ:0.31 ZN A:ZN1196 0.0 25.6 0.3 NE2 A:HIS95 1.5 29.8 0.8 HE1 A:HIS95 1.6 39.9 0.8 CE1 A:HIS95 1.7 33.2 0.8 NE2 A:HIS95 1.9 33.2 0.2 OE1 A:GLU93 2.0 47.1 1.0 O A:HOH2097 2.1 41.2 1.0 CE1 A:HIS95 2.7 30.7 0.2 HE1 A:HIS95 2.8 36.8 0.2 CD2 A:HIS95 2.9 32.0 0.8 CD A:GLU93 3.0 45.8 1.0 ND1 A:HIS95 3.0 27.3 0.8 CD2 A:HIS95 3.1 33.0 0.2 HG2 A:GLU93 3.1 35.2 1.0 HD2 A:HIS95 3.4 39.6 0.2 HD2 A:HIS95 3.5 38.4 0.8 CG A:GLU93 3.6 29.4 1.0 CG A:HIS95 3.6 28.1 0.8 HE3 A:MET84 3.6 42.3 1.0 HB3 A:GLU93 3.8 27.6 1.0 ND1 A:HIS95 3.9 34.2 0.2 HE1 A:MET84 3.9 42.3 1.0 OE2 A:GLU93 4.0 50.0 1.0 HG22 A:THR100 4.0 46.8 1.0 CG A:HIS95 4.1 30.1 0.2 CE A:MET84 4.1 35.2 1.0 HE2 A:MET84 4.1 42.3 1.0 CB A:GLU93 4.2 23.0 1.0 HG3 A:GLU93 4.4 35.2 1.0 ZN A:ZN1196 4.4 38.6 0.7 HB A:THR100 4.5 53.0 1.0 HA3 A:GLY86 4.6 23.1 1.0 HG23 A:THR100 4.6 46.8 1.0 CG2 A:THR100 4.7 39.0 1.0 HB2 A:GLU93 4.7 27.6 1.0

Zinc binding site 6 out of 9 in the Structure of E. Coli Zint at 1.79 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of E. Coli Zint at 1.79 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1197 b:30.8 occ:0.74 OXT A:ACY1201 1.7 24.5 1.0 NE2 A:HIS75 2.1 35.2 1.0 O A:HOH2085 2.2 18.4 1.0 C A:ACY1201 2.5 40.8 1.0 O A:ACY1201 2.8 39.7 1.0 CD2 A:HIS75 3.0 34.9 1.0 CE1 A:HIS75 3.1 45.0 1.0 HD2 A:HIS75 3.2 41.9 1.0 HE1 A:HIS75 3.3 54.0 1.0 HG2 A:GLN47 3.7 38.4 1.0 HE21 A:GLN47 3.7 46.1 1.0 CH3 A:ACY1201 3.9 35.6 1.0 OH A:TYR43 4.0 35.9 1.0 H1 A:ACY1201 4.1 42.7 1.0 ND1 A:HIS75 4.2 43.1 1.0 CG A:HIS75 4.2 33.2 1.0 HH A:TYR43 4.3 43.1 1.0 H2 A:ACY1201 4.5 42.7 1.0 H3 A:ACY1201 4.5 42.7 1.0 NE2 A:GLN47 4.5 38.4 1.0 CG A:GLN47 4.7 32.0 1.0 HA A:GLN47 4.8 31.6 1.0 HE1 A:TYR43 4.9 33.6 1.0 CZ A:TYR43 4.9 27.4 1.0 HD23 A:LEU46 4.9 33.5 1.0

Zinc binding site 7 out of 9 in the Structure of E. Coli Zint at 1.79 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of E. Coli Zint at 1.79 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1198 b:50.3 occ:0.49 O A:HOH2095 2.3 51.1 1.0 OE2 A:GLU88 2.4 44.0 0.5 O A:HOH2179 2.5 40.5 1.0 OE2 A:GLU88 2.7 45.2 0.5 CD A:GLU88 3.3 48.5 0.5 OE1 A:GLU88 3.5 62.4 0.5 CD A:GLU88 3.5 43.2 0.5 O A:HOH2094 3.9 55.7 1.0 OE1 A:GLU88 4.1 59.2 0.5 HG2 A:GLU88 4.3 38.3 0.5 CG A:GLU88 4.5 31.9 0.5 HG2 A:GLU88 4.5 41.0 0.5 CG A:GLU88 4.6 34.2 0.5 HG3 A:GLU88 4.9 41.0 0.5 HG3 A:GLU88 4.9 38.3 0.5

Zinc binding site 8 out of 9 in the Structure of E. Coli Zint at 1.79 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of E. Coli Zint at 1.79 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1199 b:35.6 occ:0.45 OE2 A:GLU188 1.8 71.5 1.0 CD A:GLU188 2.7 63.8 1.0 HB2 A:HIS1 2.8 54.3 1.0 OE1 A:GLU188 3.0 69.5 1.0 O A:HOH2176 3.1 38.1 1.0 CB A:HIS1 3.8 45.2 1.0 HB3 A:HIS1 4.0 54.3 1.0 CG A:GLU188 4.1 46.8 1.0 N A:HIS1 4.1 61.6 1.0 HG2 A:GLU188 4.2 56.1 1.0 HD2 A:HIS1 4.5 45.9 1.0 HG3 A:GLU188 4.5 56.1 1.0 CG A:HIS1 4.6 44.4 1.0 CA A:HIS1 4.6 55.9 1.0 O A:HOH2175 4.6 36.9 1.0 O A:HOH2174 4.7 39.6 1.0 CD2 A:HIS1 4.8 38.2 1.0 HB3 A:GLU188 5.0 42.2 1.0

Zinc binding site 9 out of 9 in the Structure of E. Coli Zint at 1.79 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of E. Coli Zint at 1.79 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1200 b:63.0 occ:0.34 OD1 A:ASP89 2.2 39.9 1.0 O A:HOH2180 2.4 33.3 1.0 CG A:ASP89 3.4 36.6 1.0 OD2 A:ASP89 4.0 43.8 1.0 HA A:ASP89 4.1 37.6 1.0 O A:HOH2050 4.1 41.4 1.0 H A:ASP89 4.3 39.2 0.5 H A:ASP89 4.3 39.2 0.5 CB A:ASP89 4.5 32.1 1.0 CA A:ASP89 4.6 31.3 1.0 N A:ASP89 4.7 32.7 1.0 HB3 A:ASP89 4.7 38.6 1.0

H.G.Colaco, P.E.Santo, P.Matias, T.M.Bandeiras, J.B.Vicente. Roles of Escherichia Coli Zint in Cobalt, Mercury and Cadmium Resistance and Structural Insights Into the Metal Binding Mechanism Metallomics V. 8 327 2016.
ISSN: ISSN 1756-5901
PubMed: 26758285
DOI: 10.1039/C5MT00291E