Zinc in PDB 6hui: The Structure of Dps From Listeria Innocua Soaked with Zinc

The structure of The Structure of Dps From Listeria Innocua Soaked with Zinc, PDB code: 6hui was solved by K.Zeth, M.Okuda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.70 / 3.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	86.330, 86.330, 269.298, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 28.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 62;

Binding sites:

The binding sites of Zinc atom in the The Structure of Dps From Listeria Innocua Soaked with Zinc (pdb code 6hui). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 62 binding sites of Zinc where determined in the The Structure of Dps From Listeria Innocua Soaked with Zinc, PDB code: 6hui:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 62 in the The Structure of Dps From Listeria Innocua Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Dps From Listeria Innocua Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:97.3 occ:1.00 OE2 D:GLU63 2.0 0.2 1.0 NE2 A:HIS44 2.3 0.9 1.0 CD D:GLU63 2.8 0.1 1.0 ZN A:ZN203 2.9 0.6 1.0 OE1 D:GLU63 2.9 0.9 1.0 CE1 A:HIS44 3.2 0.7 1.0 CD2 A:HIS44 3.3 0.1 1.0 NE2 A:HIS32 3.7 0.5 1.0 CE1 A:HIS32 4.0 0.6 1.0 CG D:GLU63 4.1 0.8 1.0 ND1 A:HIS44 4.4 0.9 1.0 CG A:HIS44 4.5 0.1 1.0 OD1 D:ASP59 4.7 0.2 1.0 OD2 A:ASP48 4.7 0.0 1.0 CD2 A:HIS32 4.8 0.1 1.0

Zinc binding site 2 out of 62 in the The Structure of Dps From Listeria Innocua Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Dps From Listeria Innocua Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:0.3 occ:1.00 OD2 D:ASP59 2.0 0.2 1.0 NE2 A:HIS29 2.2 0.1 1.0 CG D:ASP59 3.0 0.3 1.0 CD2 A:HIS29 3.1 0.8 1.0 CE1 A:HIS29 3.3 0.6 1.0 CB D:ASP59 3.6 0.7 1.0 OD1 A:ASP48 3.8 0.8 1.0 OD1 D:ASP59 3.9 0.2 1.0 ZN A:ZN203 4.1 0.6 1.0 CD2 A:TYR51 4.3 0.3 1.0 CG A:HIS29 4.3 0.9 1.0 ND1 A:HIS29 4.3 1.0 1.0 CD2 A:HIS32 4.4 0.1 1.0 CE2 A:TYR51 4.5 0.5 1.0 NE2 A:HIS32 4.5 0.5 1.0 CA D:ASP59 4.7 0.1 1.0 CG A:ASP48 4.9 0.4 1.0 CG A:TYR51 5.0 1.0 1.0

Zinc binding site 3 out of 62 in the The Structure of Dps From Listeria Innocua Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of Dps From Listeria Innocua Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:0.6 occ:1.00 NE2 A:HIS32 2.1 0.5 1.0 OE2 D:GLU63 2.4 0.2 1.0 OD2 D:ASP59 2.8 0.2 1.0 ZN A:ZN201 2.9 97.3 1.0 OD1 D:ASP59 3.0 0.2 1.0 CE1 A:HIS32 3.0 0.6 1.0 CD2 A:HIS32 3.1 0.1 1.0 CG D:ASP59 3.2 0.3 1.0 OD1 A:ASP48 3.4 0.8 1.0 CD D:GLU63 3.5 0.1 1.0 OD2 A:ASP48 3.5 0.0 1.0 NE2 A:HIS44 3.9 0.9 1.0 CG A:ASP48 3.9 0.4 1.0 ND1 A:HIS32 4.1 0.5 1.0 ZN A:ZN202 4.1 0.3 1.0 CG A:HIS32 4.2 0.9 1.0 OE1 D:GLU63 4.3 0.9 1.0 CE1 A:HIS44 4.4 0.7 1.0 CG D:GLU63 4.5 0.8 1.0 CB D:ASP59 4.6 0.7 1.0 CD2 A:HIS44 4.8 0.1 1.0

Zinc binding site 4 out of 62 in the The Structure of Dps From Listeria Innocua Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of Dps From Listeria Innocua Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:0.2 occ:0.76 NE2 A:HIS143 2.3 0.6 1.0 OE1 A:GLU53 3.1 0.3 1.0 CD2 A:HIS143 3.2 0.2 1.0 CE1 A:HIS143 3.4 0.3 1.0 CD2 A:LEU50 3.4 0.2 1.0 NZ A:LYS46 3.7 0.1 1.0 CE A:LYS46 3.8 0.6 1.0 CD A:GLU53 4.3 0.0 1.0 CG A:HIS143 4.4 0.2 1.0 ND1 A:HIS143 4.5 0.3 1.0 CG A:LEU50 4.5 0.8 1.0 CB A:ASP49 4.5 0.3 1.0 N A:LEU50 4.8 0.3 1.0 C A:ASP49 4.9 1.0 1.0 OE2 A:GLU53 4.9 0.8 1.0 CD A:LYS46 4.9 1.0 1.0 CA A:LEU50 4.9 0.3 1.0 O A:ASP49 5.0 0.4 1.0

Zinc binding site 5 out of 62 in the The Structure of Dps From Listeria Innocua Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of Dps From Listeria Innocua Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:0.2 occ:0.60 OD2 A:ASP49 2.3 0.6 1.0 OE2 A:GLU45 2.5 0.0 1.0 CD A:GLU45 3.1 0.4 1.0 CG A:GLU45 3.3 0.6 1.0 CG A:ASP49 3.3 0.1 1.0 OD1 A:ASP49 3.6 1.0 1.0 OE1 A:GLU45 4.1 0.6 1.0 CB A:GLU45 4.6 1.0 1.0 O A:GLU45 4.6 0.2 1.0 CB A:ASP49 4.7 0.3 1.0 C A:GLU45 4.8 0.0 1.0

Zinc binding site 6 out of 62 in the The Structure of Dps From Listeria Innocua Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of Dps From Listeria Innocua Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:0.6 occ:1.00 CD2 A:HIS16 2.3 0.8 1.0 NE2 A:HIS16 2.4 0.0 1.0 CG A:HIS16 3.7 0.8 1.0 CE1 A:HIS16 3.8 1.0 1.0 ND1 A:HIS16 4.3 0.4 1.0 OD1 A:ASN82 4.4 0.1 1.0 CB A:HIS16 4.7 1.0 1.0 O A:ASN82 4.8 0.5 1.0 O A:GLU12 5.0 0.4 1.0

Zinc binding site 7 out of 62 in the The Structure of Dps From Listeria Innocua Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structure of Dps From Listeria Innocua Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn207 b:0.2 occ:0.64 ZN A:ZN211 2.8 0.8 1.0 ZN A:ZN210 4.4 0.1 1.0 ND1 A:HIS38 4.5 0.6 1.0

Zinc binding site 8 out of 62 in the The Structure of Dps From Listeria Innocua Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Structure of Dps From Listeria Innocua Soaked with Zinc within 5.0Å range:

Zinc binding site 9 out of 62 in the The Structure of Dps From Listeria Innocua Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Structure of Dps From Listeria Innocua Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn209 b:0.5 occ:1.00 NE2 A:HIS38 2.3 0.9 1.0 CD2 A:HIS38 3.1 0.6 1.0 CE1 A:HIS38 3.3 0.2 1.0 CG A:HIS38 4.3 0.3 1.0 ND1 A:HIS38 4.4 0.6 1.0

Zinc binding site 10 out of 62 in the The Structure of Dps From Listeria Innocua Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Structure of Dps From Listeria Innocua Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn210 b:0.1 occ:1.00 CB A:HIS38 3.9 0.5 1.0 ND2 A:ASN39 4.1 0.1 1.0 ND1 A:HIS38 4.2 0.6 1.0 ZN A:ZN207 4.4 0.2 0.6 CG A:HIS38 4.4 0.3 1.0 CG A:ASN39 4.5 0.2 1.0 N A:HIS38 4.5 0.4 1.0 OD1 A:ASN39 4.6 0.3 1.0 CA A:HIS38 4.7 0.2 1.0 N A:ASN39 4.8 0.5 1.0 ZN A:ZN211 4.8 0.8 1.0

K.Zeth, E.Sancho-Vaello, M.Okuda. Metal Positions and Translocation Pathways of the Dodecameric Ferritin-Like Protein Dps. Inorg.Chem. V. 58 11351 2019.
ISSN: ISSN 0020-1669
PubMed: 31433627
DOI: 10.1021/ACS.INORGCHEM.9B00301