Zinc in PDB 3nvo: The Soluble Domain Structure of the Zntb ZN2+ Efflux System

The structure of The Soluble Domain Structure of the Zntb ZN2+ Efflux System, PDB code: 3nvo was solved by Q.Wan, C.Dealwis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.66 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.039, 93.845, 68.231, 90.00, 91.58, 90.00
R / Rfree (%)	20.1 / 25.6

The binding sites of Zinc atom in the The Soluble Domain Structure of the Zntb ZN2+ Efflux System (pdb code 3nvo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the The Soluble Domain Structure of the Zntb ZN2+ Efflux System, PDB code: 3nvo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the The Soluble Domain Structure of the Zntb ZN2+ Efflux System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Soluble Domain Structure of the Zntb ZN2+ Efflux System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn268 b:86.2 occ:1.00 NE2 A:HIS159 2.4 53.3 1.0 OD2 A:ASP131 2.5 56.6 1.0 OD1 A:ASP131 2.9 53.0 1.0 CG A:ASP131 3.0 52.1 1.0 CE1 A:HIS159 3.2 57.7 1.0 CD2 A:HIS159 3.3 54.9 1.0 O A:HOH296 3.7 50.5 1.0 ND1 A:HIS159 4.2 60.0 1.0 CG A:HIS159 4.3 54.7 1.0 CB A:ASP131 4.5 42.3 1.0 O A:LEU127 5.0 42.3 1.0

Zinc binding site 2 out of 8 in the The Soluble Domain Structure of the Zntb ZN2+ Efflux System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Soluble Domain Structure of the Zntb ZN2+ Efflux System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn269 b:71.8 occ:1.00 SG A:CYS246 2.3 53.7 1.0 ND1 A:HIS168 2.6 54.5 1.0 NH2 A:ARG249 2.7 59.1 1.0 CE1 A:HIS168 3.2 55.3 1.0 CB A:CYS246 3.5 31.2 1.0 CA A:CYS246 3.6 27.9 1.0 N A:CYS246 3.7 30.6 1.0 CG A:HIS168 3.7 54.9 1.0 CZ A:ARG249 3.8 70.2 1.0 O A:GLU242 3.9 36.3 1.0 NE A:ARG249 4.1 68.5 1.0 CB A:HIS168 4.2 54.5 1.0 C A:ALA245 4.4 29.3 1.0 CA A:HIS168 4.5 51.4 1.0 NE2 A:HIS168 4.5 59.5 1.0 CB A:ALA245 4.7 24.6 1.0 CD2 A:HIS168 4.7 58.1 1.0 C A:GLU242 4.8 35.5 1.0 O A:ALA245 4.9 34.2 1.0 NH1 A:ARG249 4.9 71.7 1.0

Zinc binding site 3 out of 8 in the The Soluble Domain Structure of the Zntb ZN2+ Efflux System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Soluble Domain Structure of the Zntb ZN2+ Efflux System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn270 b:86.4 occ:1.00 SG A:CYS94 2.6 0.6 1.0 CB A:CYS94 3.1 39.0 1.0 ND1 A:HIS159 3.2 60.0 1.0 CB A:HIS159 3.5 45.2 1.0 CG A:HIS159 3.5 54.7 1.0 CA A:CYS94 4.0 40.3 1.0 N A:ALA128 4.0 38.2 1.0 CB A:ALA128 4.0 38.7 1.0 CE1 A:HIS159 4.1 57.7 1.0 N A:ILE95 4.1 56.0 1.0 CD2 A:LEU156 4.1 31.2 1.0 CB A:LEU127 4.5 36.7 1.0 CA A:ALA128 4.5 39.0 1.0 C A:CYS94 4.5 44.8 1.0 CD2 A:HIS159 4.5 54.9 1.0 N A:LEU127 4.7 34.9 1.0 C A:LEU127 4.8 40.2 1.0 CA A:LEU156 4.8 22.6 1.0 NE2 A:HIS159 4.8 53.3 1.0 CA A:LEU127 4.9 34.6 1.0 O A:LEU156 4.9 26.6 1.0 CG2 A:ILE95 5.0 67.7 1.0 O A:HOH301 5.0 44.9 1.0

Zinc binding site 4 out of 8 in the The Soluble Domain Structure of the Zntb ZN2+ Efflux System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Soluble Domain Structure of the Zntb ZN2+ Efflux System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn271 b:64.0 occ:1.00 OE1 A:GLU115 2.3 52.4 1.0 N A:HIS2 2.3 68.8 1.0 ND1 A:HIS2 2.4 73.1 1.0 N A:GLY1 2.5 68.9 1.0 OE2 A:GLU115 2.8 58.0 1.0 CD A:GLU115 2.9 55.7 1.0 CG A:HIS2 3.1 72.2 1.0 C A:GLY1 3.1 71.6 1.0 CA A:GLY1 3.2 71.4 1.0 CA A:HIS2 3.2 67.6 1.0 CB A:HIS2 3.2 69.5 1.0 CE1 A:HIS2 3.4 71.3 1.0 N A:MET3 3.5 61.5 1.0 C A:HIS2 3.8 65.0 1.0 CD2 A:HIS2 4.1 73.0 1.0 NE2 A:HIS2 4.2 72.0 1.0 O A:GLY1 4.2 71.7 1.0 CG A:GLU115 4.3 52.1 1.0 CG A:MET3 4.4 60.0 1.0 CB A:MET3 4.6 58.6 1.0 CA A:MET3 4.7 59.6 1.0 O A:HIS2 4.9 65.7 1.0 CB A:GLU115 4.9 46.5 1.0

Zinc binding site 5 out of 8 in the The Soluble Domain Structure of the Zntb ZN2+ Efflux System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Soluble Domain Structure of the Zntb ZN2+ Efflux System within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn266 b:32.8 occ:1.00 ND1 B:HIS168 2.3 24.5 1.0 SG B:CYS246 2.3 35.4 1.0 CE1 B:HIS168 3.2 26.9 1.0 CG B:HIS168 3.3 27.6 1.0 CB B:CYS246 3.4 26.8 1.0 CA B:CYS246 3.5 22.7 1.0 CB B:HIS168 3.6 24.9 1.0 N B:CYS246 3.6 20.9 1.0 O B:HOH275 3.7 49.1 1.0 O B:GLU242 4.1 24.7 1.0 CA B:HIS168 4.1 27.0 1.0 C B:ALA245 4.3 27.9 1.0 O B:HOH296 4.3 42.7 1.0 NE2 B:HIS168 4.3 24.1 1.0 CD2 B:HIS168 4.4 26.6 1.0 CB B:ALA245 4.6 26.4 1.0 O B:ALA245 4.6 29.8 1.0 C B:CYS246 5.0 22.7 1.0 C B:HIS168 5.0 32.0 1.0

Zinc binding site 6 out of 8 in the The Soluble Domain Structure of the Zntb ZN2+ Efflux System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Soluble Domain Structure of the Zntb ZN2+ Efflux System within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn267 b:73.6 occ:1.00 OD2 B:ASP131 2.2 59.2 1.0 NE2 B:HIS159 2.4 49.0 1.0 OD1 B:ASP131 2.7 65.7 1.0 CG B:ASP131 2.8 60.0 1.0 O B:HOH297 3.0 55.0 1.0 CD2 B:HIS159 3.3 44.4 1.0 CE1 B:HIS159 3.3 52.0 1.0 O B:HOH308 3.7 60.6 1.0 CB B:ASP131 4.3 56.6 1.0 ND1 B:HIS159 4.4 53.5 1.0 CG B:HIS159 4.4 47.1 1.0 CA B:ALA128 4.6 44.8 1.0 O B:LEU127 4.6 49.0 1.0 O B:ALA128 4.6 55.4 1.0

Zinc binding site 7 out of 8 in the The Soluble Domain Structure of the Zntb ZN2+ Efflux System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Soluble Domain Structure of the Zntb ZN2+ Efflux System within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn268 b:56.4 occ:1.00 ND1 B:HIS41 2.2 63.1 1.0 OD2 B:ASP38 2.4 53.8 1.0 OD1 B:ASP38 2.5 48.5 1.0 CG B:ASP38 2.8 51.1 1.0 CE1 B:HIS41 2.9 63.2 1.0 CG B:HIS41 3.1 57.7 1.0 CB B:HIS41 3.6 48.0 1.0 NE2 B:HIS41 3.8 58.8 1.0 CD2 B:HIS41 4.0 59.7 1.0 N B:HIS41 4.0 38.1 1.0 CB B:ASP38 4.3 48.1 1.0 CB B:GLN40 4.4 44.0 1.0 O B:VAL36 4.4 49.0 1.0 CA B:HIS41 4.4 39.0 1.0 N B:ASP38 4.8 43.0 1.0 C B:GLN40 4.8 44.9 1.0 CG1 B:VAL36 4.9 48.3 1.0

Zinc binding site 8 out of 8 in the The Soluble Domain Structure of the Zntb ZN2+ Efflux System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Soluble Domain Structure of the Zntb ZN2+ Efflux System within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn269 b:65.4 occ:1.00 OE1 B:GLU115 2.1 57.9 1.0 N B:HIS2 2.3 67.4 1.0 N B:GLY1 2.6 70.0 1.0 ND1 B:HIS2 2.6 65.9 1.0 CD B:GLU115 2.8 54.5 1.0 OE2 B:GLU115 2.8 50.2 1.0 CA B:GLY1 3.0 71.3 1.0 C B:GLY1 3.1 70.4 1.0 CG B:HIS2 3.3 65.7 1.0 CA B:HIS2 3.4 65.6 1.0 CB B:HIS2 3.4 64.6 1.0 CE1 B:HIS2 3.6 67.2 1.0 N B:MET3 3.9 59.9 1.0 C B:HIS2 4.1 61.6 1.0 CG B:GLU115 4.3 48.9 1.0 O B:GLY1 4.3 74.1 1.0 CD2 B:HIS2 4.5 65.7 1.0 NE2 B:HIS2 4.6 68.1 1.0 CB B:GLU115 4.8 44.0 1.0 CB B:SER39 4.9 46.3 1.0 OG B:SER39 5.0 48.5 1.0

Q.Wan, B.Gorzelle, M.Fuente, F.Mohammed, C.Dealwis, M.Maguire. The Soluble Domain Structure of the Zntb ZN2+ Efflux System To Be Published.