Zinc in PDB 6sev: Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes

The structure of Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes, PDB code: 6sev 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)	2.02 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.831, 84.831, 267.358, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Zinc atom in the Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes (pdb code 6sev). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 21 binding sites of Zinc where determined in the Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes, PDB code: 6sev:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 21 in the Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:65.3 occ:1.00 OD2 A:ASP59 2.0 60.5 1.0 OE2 A:GLU63 2.0 60.6 1.0 NE2 D:HIS32 2.1 55.1 1.0 CG A:ASP59 2.8 54.6 1.0 OD1 A:ASP59 2.9 55.7 1.0 CD2 D:HIS32 3.0 47.6 1.0 ZN A:ZN202 3.1 0.8 1.0 CE1 D:HIS32 3.1 52.8 1.0 CD A:GLU63 3.1 59.2 1.0 ZN A:ZN203 3.7 0.4 1.0 OE1 A:GLU63 3.7 68.1 1.0 OD1 D:ASP48 3.8 86.7 1.0 NE2 D:HIS44 4.0 59.7 1.0 OD2 D:ASP48 4.2 81.8 1.0 ND1 D:HIS32 4.2 56.1 1.0 CG D:HIS32 4.2 51.6 1.0 CB A:ASP59 4.2 49.6 1.0 CG A:GLU63 4.2 47.9 1.0 CE1 D:HIS44 4.3 57.5 1.0 CG D:ASP48 4.4 78.1 1.0 NE1 D:TRP33 4.8 48.1 1.0

Zinc binding site 2 out of 21 in the Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:0.8 occ:1.00 NE2 D:HIS44 2.6 59.7 1.0 OE2 A:GLU63 2.8 60.6 1.0 ZN A:ZN201 3.1 65.3 1.0 OE1 A:GLU63 3.1 68.1 1.0 CD A:GLU63 3.2 59.2 1.0 CD2 D:HIS44 3.4 54.0 1.0 CE1 D:HIS44 3.6 57.5 1.0 NE2 D:HIS32 3.9 55.1 1.0 NZ B:LYS142 3.9 64.0 1.0 CE B:LYS142 4.0 63.2 1.0 CE1 D:HIS32 4.2 52.8 1.0 OD2 A:ASP59 4.5 60.5 1.0 OD2 D:ASP48 4.5 81.8 1.0 CG D:HIS44 4.6 62.5 1.0 CG A:GLU63 4.7 47.9 1.0 ND1 D:HIS44 4.7 57.1 1.0 CZ3 B:TRP145 4.7 60.4 1.0 CH2 B:TRP145 4.7 57.0 1.0 CE B:MET146 4.9 50.8 1.0

Zinc binding site 3 out of 21 in the Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:0.4 occ:1.00 OD1 D:ASP48 2.7 86.7 1.0 CE1 D:HIS29 2.9 50.6 1.0 CG A:ASP59 3.4 54.6 1.0 OD1 A:ASP59 3.5 55.7 1.0 OD2 A:ASP59 3.5 60.5 1.0 ZN A:ZN201 3.7 65.3 1.0 ND1 D:HIS29 3.8 55.7 1.0 NE2 D:HIS29 3.8 52.9 1.0 CG D:ASP48 3.9 78.1 1.0 NE2 D:HIS32 4.0 55.1 1.0 CB A:ASP59 4.1 49.6 1.0 CD2 D:HIS32 4.3 47.6 1.0 CE1 D:HIS32 4.5 52.8 1.0 CD2 D:TYR51 4.6 46.4 1.0 OD2 D:ASP48 4.6 81.8 1.0 CG D:TYR51 4.8 52.8 1.0 CA D:ASP48 4.9 57.9 1.0 CG D:HIS32 4.9 51.6 1.0 CB D:ASP48 4.9 66.6 1.0 CG D:HIS29 5.0 54.4 1.0 CD2 D:HIS29 5.0 55.6 1.0 CE2 D:TYR51 5.0 56.7 1.0

Zinc binding site 4 out of 21 in the Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:0.9 occ:1.00 ND2 A:ASN130 3.8 61.9 1.0 OD2 A:ASP122 3.9 95.1 1.0 OD1 F:ASP127 3.9 88.0 1.0 OD1 F:ASP122 3.9 0.8 1.0 CD1 A:ILE134 4.5 71.2 1.0 OD1 A:ASP122 4.6 0.3 1.0 CG A:ASP122 4.7 96.6 1.0 CG A:ASN130 4.7 63.7 1.0 OD1 A:ASN130 4.7 67.2 1.0 ND2 F:ASN130 4.8 76.8 1.0 CG F:ASP127 4.8 84.2 1.0 CG F:ASP122 4.9 0.4 1.0

Zinc binding site 5 out of 21 in the Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:0.0 occ:1.00 OD2 F:ASP131 2.5 94.2 1.0 OD2 B:ASP131 2.5 95.8 1.0 OD2 A:ASP131 2.8 88.4 1.0 OD1 F:ASP131 2.9 96.7 1.0 OD1 B:ASP131 2.9 95.4 1.0 OD1 A:ASP131 2.9 88.8 1.0 CG F:ASP131 3.0 87.8 1.0 CG B:ASP131 3.1 91.3 1.0 O A:HOH304 3.1 65.7 1.0 CG A:ASP131 3.2 79.7 1.0 ZN A:ZN206 4.0 0.2 1.0 CB F:ASP131 4.5 71.5 1.0 CB B:ASP131 4.6 79.5 1.0 CB A:ASP131 4.7 61.1 1.0

Zinc binding site 6 out of 21 in the Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:0.2 occ:1.00 OD1 B:ASP131 2.4 95.4 1.0 OD1 A:ASP131 2.5 88.8 1.0 OD1 F:ASP131 2.8 96.7 1.0 CG A:ASP131 3.5 79.7 1.0 CG B:ASP131 3.7 91.3 1.0 ZN A:ZN205 4.0 0.0 1.0 CG F:ASP131 4.1 87.8 1.0 OD2 A:ASP131 4.2 88.4 1.0 CB A:ASP131 4.3 61.1 1.0 CD1 B:ILE134 4.5 48.5 1.0 OD2 B:ASP131 4.5 95.8 1.0 CB B:ASP131 4.6 79.5 1.0 OD2 F:ASP131 4.8 94.2 1.0 CA A:ASP131 4.8 54.3 1.0 O A:HOH304 4.8 65.7 1.0 CA B:ASP131 4.9 68.2 1.0 ND2 A:ASN130 5.0 61.9 1.0 CD1 A:ILE134 5.0 71.2 1.0 ND2 B:ASN130 5.0 62.4 1.0

Zinc binding site 7 out of 21 in the Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:0.3 occ:1.00 NE2 E:HIS44 2.6 56.8 1.0 O E:HOH310 2.8 56.4 1.0 OE2 B:GLU63 3.1 67.8 1.0 OE1 B:GLU63 3.1 65.1 1.0 CD2 E:HIS44 3.3 48.6 1.0 CD B:GLU63 3.4 66.4 1.0 ZN B:ZN202 3.6 61.8 1.0 CE1 E:HIS44 3.7 52.4 1.0 CE F:LYS142 3.7 78.8 1.0 NZ F:LYS142 3.9 81.3 1.0 CH2 F:TRP145 4.3 61.0 1.0 CE F:MET146 4.4 59.7 1.0 NE2 E:HIS32 4.4 59.0 1.0 CZ3 F:TRP145 4.4 57.7 1.0 CG E:HIS44 4.6 52.0 1.0 CE1 E:HIS32 4.6 55.5 1.0 SD F:MET146 4.7 58.7 1.0 ND1 E:HIS44 4.8 54.7 1.0 CG B:GLU63 4.8 65.4 1.0 OD2 B:ASP59 5.0 59.4 1.0 OD2 E:ASP48 5.0 81.0 1.0

Zinc binding site 8 out of 21 in the Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:61.8 occ:1.00 OD2 B:ASP59 2.0 59.4 1.0 OE2 B:GLU63 2.1 67.8 1.0 NE2 E:HIS32 2.1 59.0 1.0 O E:HOH310 2.2 56.4 1.0 CG B:ASP59 2.8 59.2 1.0 OD1 B:ASP59 2.9 52.6 1.0 CE1 E:HIS32 3.1 55.5 1.0 CD2 E:HIS32 3.1 56.5 1.0 CD B:GLU63 3.2 66.4 1.0 ZN B:ZN201 3.6 0.3 1.0 OE1 B:GLU63 3.8 65.1 1.0 OD1 E:ASP48 3.8 81.7 1.0 NE2 E:HIS44 4.0 56.8 1.0 OD2 E:ASP48 4.0 81.0 1.0 ND1 E:HIS32 4.2 58.4 1.0 CB B:ASP59 4.2 52.8 1.0 O E:HOH308 4.2 54.5 1.0 CG E:HIS32 4.3 57.6 1.0 CG E:ASP48 4.3 76.0 1.0 CG B:GLU63 4.3 65.4 1.0 CE1 E:HIS44 4.4 52.4 1.0 NE1 E:TRP33 4.9 51.7 1.0

Zinc binding site 9 out of 21 in the Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:0.7 occ:1.00 ND1 B:HIS38 2.1 0.4 1.0 CG B:HIS38 2.9 92.1 1.0 CB B:HIS38 3.0 71.2 1.0 ZN C:ZN202 3.1 0.2 1.0 CE1 B:HIS38 3.3 0.9 1.0 OD1 C:ASN39 3.7 84.9 1.0 CD2 B:HIS38 4.1 98.3 1.0 ZN D:ZN203 4.2 0.8 1.0 NE2 B:HIS38 4.3 0.8 1.0 CA B:HIS38 4.5 64.9 1.0 CG C:ASN39 4.7 83.1 1.0 ND2 C:ASN39 5.0 75.9 1.0

Zinc binding site 10 out of 21 in the Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Dps From Listeria Innocua Soaked with 10 Mm Zinc For 120 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:0.1 occ:1.00 CE1 B:HIS44 2.6 51.0 1.0 OE2 E:GLU63 2.7 58.6 1.0 ZN E:ZN201 2.7 59.5 1.0 OE1 E:GLU63 3.1 53.2 1.0 CD E:GLU63 3.2 52.9 1.0 NE2 B:HIS44 3.3 52.1 1.0 NE2 B:HIS32 3.3 54.2 1.0 ND1 B:HIS44 3.6 52.4 1.0 CE1 B:HIS32 3.7 48.9 1.0 OD2 E:ASP59 4.2 60.6 1.0 OD2 B:ASP48 4.3 79.3 1.0 NZ C:LYS142 4.4 78.8 1.0 CE C:LYS142 4.4 75.5 1.0 CD2 B:HIS44 4.5 52.2 1.0 CD2 B:HIS32 4.6 51.9 1.0 CG B:HIS44 4.7 54.4 1.0 CG E:GLU63 4.7 49.9 1.0 CH2 C:TRP145 4.8 48.5 1.0 CZ3 C:TRP145 4.9 50.0 1.0 ND1 B:HIS32 4.9 50.5 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