Zinc in PDB 4ism: Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc

The structure of Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc, PDB code: 4ism was solved by S.Pfaffen, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.51 / 2.00
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	175.112, 175.112, 175.112, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc (pdb code 4ism). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 32 binding sites of Zinc where determined in the Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc, PDB code: 4ism:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 32 in the Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries 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 Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:29.2 occ:1.00 ND1 A:HIS51 2.1 27.4 1.0 OE1 A:GLU48 2.1 25.0 1.0 O A:HOH383 2.2 35.8 1.0 OE1 A:GLU15 2.2 25.9 1.0 O A:HOH378 2.2 27.8 1.0 CE1 A:HIS51 3.0 29.7 1.0 CD A:GLU15 3.1 26.9 1.0 CD A:GLU48 3.1 24.8 1.0 CG A:HIS51 3.2 28.4 1.0 OE2 A:GLU15 3.3 29.6 1.0 ZN A:ZN203 3.3 37.2 0.8 CB A:HIS51 3.5 21.0 1.0 OE2 A:GLU48 3.5 34.6 1.0 OD1 A:ASN97 3.6 30.6 0.5 O A:HOH375 4.1 33.5 1.0 OD1 A:ASN97 4.1 29.9 0.5 NE2 A:HIS51 4.1 29.7 1.0 CD2 A:HIS51 4.2 24.6 1.0 OE1 A:GLN127 4.2 25.9 1.0 CG A:GLU15 4.4 23.6 1.0 CG A:GLU48 4.5 24.3 1.0 CA A:GLU48 4.5 20.2 1.0 O A:HOH377 4.5 41.3 1.0 CB A:GLU48 4.7 22.1 1.0 CG A:ASN97 4.7 31.7 0.5 CB A:GLU15 4.7 20.8 1.0 CG A:ASN97 4.8 31.2 0.5 O A:GLU48 4.9 22.5 1.0 CA A:GLU15 5.0 21.9 1.0

Zinc binding site 2 out of 32 in the Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries 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 Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:38.0 occ:0.65 OE2 A:GLU130 1.7 56.1 1.0 O A:HOH376 2.0 43.3 1.0 OE2 A:GLU44 2.2 40.7 1.0 OE2 A:GLU47 2.4 45.3 1.0 OE1 A:GLU47 2.5 44.7 1.0 OE1 A:GLU44 2.6 53.4 1.0 CD A:GLU130 2.7 45.8 1.0 CD A:GLU44 2.7 38.8 1.0 CD A:GLU47 2.7 38.8 1.0 OE1 A:GLU130 3.2 49.2 1.0 NE2 A:GLN126 3.8 55.4 1.0 NZ A:LYS133 3.9 58.5 1.0 CG A:GLU130 3.9 38.1 1.0 CG A:GLU44 4.2 30.5 1.0 CG A:GLU47 4.2 33.6 1.0 O A:HOH377 4.4 41.3 1.0 O A:HOH410 4.7 56.9 1.0 CE A:LYS133 4.8 56.1 1.0 CB A:GLU47 4.8 22.5 1.0

Zinc binding site 3 out of 32 in the Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries 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 Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:37.2 occ:0.85 OE2 A:GLU48 1.8 34.6 1.0 O A:HOH383 1.9 35.8 1.0 OE2 A:GLU94 2.4 33.7 1.0 OE1 A:GLU94 2.5 31.8 1.0 O A:HOH377 2.5 41.3 1.0 CD A:GLU94 2.7 29.8 1.0 CD A:GLU48 2.8 24.8 1.0 OE1 A:GLU48 3.1 25.0 1.0 ZN A:ZN201 3.3 29.2 1.0 OD1 A:ASN97 3.5 29.9 0.5 OE1 A:GLN127 3.7 25.9 1.0 CE1 A:HIS51 4.1 29.7 1.0 CG A:GLU48 4.2 24.3 1.0 CG A:GLU94 4.3 28.4 1.0 ND1 A:HIS51 4.3 27.4 1.0 CG A:GLU130 4.4 38.1 1.0 NE2 A:GLN127 4.5 25.9 1.0 CD A:GLN127 4.5 26.6 1.0 CG A:ASN97 4.5 31.2 0.5 OE2 A:GLU130 4.5 56.1 1.0 OH A:TYR22 4.6 21.4 1.0 OE2 A:GLU47 4.6 45.3 1.0 CE1 A:TYR22 4.6 20.6 1.0 CD A:GLU130 4.7 45.8 1.0 O A:HOH378 4.8 27.8 1.0 CB A:GLU130 4.9 26.3 1.0 OE1 A:GLU44 4.9 53.4 1.0 CB A:ASN97 4.9 30.1 0.5 OD1 A:ASN97 5.0 30.6 0.5

Zinc binding site 4 out of 32 in the Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries 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 Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:48.1 occ:0.35 O D:HOH352 2.1 44.7 1.0 OD1 A:ASP30 2.3 42.8 1.0 OE2 A:GLU35 3.0 53.2 1.0 CG A:ASP30 3.3 44.8 1.0 O A:HOH391 3.4 48.7 1.0 OD2 D:ASP132 3.8 27.8 1.0 OD2 A:ASP30 4.0 48.1 1.0 OD1 D:ASP132 4.1 27.8 1.0 CD A:GLU35 4.2 47.6 1.0 CG E:LYS61 4.3 25.0 1.0 CG D:ASP132 4.4 25.8 1.0 CB A:ASP30 4.4 32.8 1.0 OD1 E:ASP57 4.4 26.3 1.0 CB E:ASN60 4.6 26.9 1.0 CG A:GLU35 4.9 41.8 1.0

Zinc binding site 5 out of 32 in the Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries 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 Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:26.8 occ:1.00 OE1 D:GLU15 2.0 22.3 1.0 O D:HOH375 2.1 24.9 1.0 ND1 D:HIS51 2.1 19.9 1.0 OE1 D:GLU48 2.1 27.8 1.0 O D:HOH374 2.3 26.0 1.0 CE1 D:HIS51 3.0 27.0 1.0 CD D:GLU15 3.0 26.1 1.0 CD D:GLU48 3.1 26.2 1.0 CG D:HIS51 3.2 22.2 1.0 OE2 D:GLU48 3.3 33.4 1.0 OE2 D:GLU15 3.3 25.0 1.0 ND2 D:ASN97 3.3 28.7 0.5 ZN D:ZN203 3.4 34.3 0.8 CB D:HIS51 3.6 18.0 1.0 ND2 D:ASN97 3.9 20.0 0.5 NE2 D:HIS51 4.1 23.3 1.0 CD2 D:HIS51 4.2 23.9 1.0 OE1 D:GLN127 4.2 27.7 1.0 O D:HOH323 4.3 29.1 1.0 CG D:GLU15 4.4 20.5 1.0 CG D:GLU48 4.4 19.6 1.0 CA D:GLU48 4.5 17.7 1.0 CG D:ASN97 4.6 27.4 0.5 OE2 D:GLU130 4.6 25.2 0.5 CB D:GLU48 4.7 18.0 1.0 CB D:GLU15 4.7 17.3 1.0 CG D:ASN97 4.7 21.2 0.5 O D:GLU48 4.9 19.9 1.0 CA D:GLU15 4.9 17.2 1.0 O D:HOH377 5.0 51.7 1.0

Zinc binding site 6 out of 32 in the Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries 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 Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:37.4 occ:0.70 O D:HOH376 1.9 44.2 1.0 OE2 D:GLU44 2.2 44.8 1.0 OE1 D:GLU130 2.3 36.4 0.5 OE2 D:GLU47 2.3 47.6 1.0 OE1 D:GLU47 2.5 46.4 1.0 OE1 D:GLU44 2.6 45.6 1.0 CD D:GLU47 2.7 41.3 1.0 CD D:GLU44 2.7 38.4 1.0 OE2 D:GLU130 2.9 36.2 0.5 CD D:GLU130 2.9 32.1 0.5 O D:HOH377 3.3 51.7 1.0 NZ D:LYS133 3.4 54.4 1.0 NE2 D:GLN126 3.6 30.6 0.5 OE2 D:GLU130 3.8 25.2 0.5 CD D:GLU130 3.9 25.6 0.5 CG D:GLU130 4.0 22.7 0.5 CG D:GLU47 4.2 31.5 1.0 CG D:GLU44 4.2 34.6 1.0 CG D:GLU130 4.4 29.3 0.5 OE1 D:GLU130 4.4 31.2 0.5 CE D:LYS133 4.6 49.8 1.0 CB D:GLU47 4.8 23.2 1.0 CD D:GLN126 4.9 29.7 0.5

Zinc binding site 7 out of 32 in the Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries 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 Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:34.3 occ:0.85 OE2 D:GLU48 1.8 33.4 1.0 O D:HOH375 1.9 24.9 1.0 OE1 D:GLU130 2.1 31.2 0.5 OE2 D:GLU94 2.3 28.0 1.0 OE1 D:GLU94 2.5 29.2 1.0 CD D:GLU94 2.7 26.8 1.0 O D:HOH377 2.7 51.7 1.0 CD D:GLU48 2.8 26.2 1.0 CD D:GLU130 2.9 25.6 0.5 OE2 D:GLU130 3.0 25.2 0.5 OE1 D:GLU48 3.2 27.8 1.0 ND2 D:ASN97 3.3 20.0 0.5 ZN D:ZN201 3.4 26.8 1.0 OE1 D:GLN127 3.7 27.7 1.0 CE1 D:HIS51 4.0 27.0 1.0 CG D:GLU48 4.2 19.6 1.0 CG D:GLU94 4.2 24.5 1.0 ND1 D:HIS51 4.3 19.9 1.0 CG D:GLU130 4.3 29.3 0.5 OE1 D:GLU130 4.3 36.4 0.5 CG D:GLU130 4.4 22.7 0.5 OH D:TYR22 4.5 20.8 1.0 CG D:ASN97 4.6 21.2 0.5 CD D:GLN127 4.6 27.4 1.0 ND2 D:ASN97 4.6 28.7 0.5 NE2 D:GLN127 4.6 23.6 1.0 CD D:GLU130 4.7 32.1 0.5 CE1 D:TYR22 4.7 19.5 1.0 OE2 D:GLU47 4.7 47.6 1.0 CB D:GLU130 4.8 21.5 0.5 CB D:GLU130 4.9 25.3 0.5 O D:HOH374 4.9 26.0 1.0 CB D:ASN97 4.9 23.2 0.5 OE1 D:GLU44 4.9 45.6 1.0

Zinc binding site 8 out of 32 in the Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries 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 Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn204 b:44.9 occ:0.35 O D:HOH412 2.0 51.3 1.0 OD1 D:ASP30 2.2 43.5 1.0 CG D:ASP30 3.2 43.0 1.0 OD2 D:ASP30 3.5 52.6 1.0 OD2 G:ASP132 3.7 27.9 1.0 OD1 G:ASP132 4.0 27.8 1.0 CG G:ASP132 4.2 24.9 1.0 CB D:ASP30 4.5 26.6 1.0 CG D:GLU35 4.8 40.8 1.0 OE2 D:GLU35 4.8 52.0 1.0 O D:ASP30 4.9 23.4 1.0

Zinc binding site 9 out of 32 in the Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries 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 Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:31.8 occ:1.00 O B:HOH375 2.0 32.7 1.0 ND1 B:HIS51 2.0 29.3 1.0 OE1 B:GLU15 2.1 25.8 1.0 OE1 B:GLU48 2.1 30.4 1.0 O B:HOH374 2.2 32.4 1.0 CE1 B:HIS51 2.9 33.3 1.0 CD B:GLU15 3.0 28.1 1.0 CG B:HIS51 3.1 26.6 1.0 CD B:GLU48 3.2 28.6 1.0 OE2 B:GLU15 3.3 31.1 1.0 ZN B:ZN203 3.5 40.9 0.9 OE2 B:GLU48 3.5 40.9 1.0 CB B:HIS51 3.5 23.8 1.0 OD1 B:ASN97 3.8 51.5 1.0 NE2 B:HIS51 4.0 33.8 1.0 OE1 B:GLN127 4.1 30.1 1.0 O B:HOH373 4.1 33.9 1.0 CD2 B:HIS51 4.2 28.7 1.0 CG B:GLU15 4.4 23.3 1.0 CA B:GLU48 4.5 23.6 1.0 CG B:GLU48 4.5 25.3 1.0 CG B:ASN97 4.6 44.5 1.0 CB B:GLU48 4.7 22.9 1.0 O B:HOH301 4.7 34.5 1.0 CB B:GLU15 4.7 21.4 1.0 O B:GLU48 4.9 22.4 1.0 CB B:ASN97 5.0 34.1 1.0

Zinc binding site 10 out of 32 in the Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries 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 Crystal Structure of Ferritin From Pseudo-Nitzschia Multiseries Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:42.1 occ:0.75 O B:HOH376 1.9 47.1 1.0 OE2 B:GLU44 2.2 46.0 1.0 OE2 B:GLU47 2.3 49.6 1.0 OE1 B:GLU130 2.4 57.6 1.0 OE1 B:GLU47 2.5 51.7 1.0 OE1 B:GLU44 2.6 46.3 1.0 CD B:GLU47 2.7 50.2 1.0 CD B:GLU44 2.7 44.4 1.0 CD B:GLU130 3.0 55.6 1.0 OE2 B:GLU130 3.0 66.9 1.0 O B:HOH301 3.7 34.5 1.0 NZ B:LYS133 3.9 69.2 1.0 NE2 B:GLN126 3.9 68.7 1.0 CG B:GLU47 4.2 39.0 1.0 CG B:GLU44 4.2 35.5 1.0 CG B:GLU130 4.3 51.8 1.0 CE B:LYS133 4.6 62.2 1.0 CB B:GLU47 4.7 26.9 1.0

S.Pfaffen, R.Abdulqadir, N.E.Le Brun, M.E.Murphy. Mechanism of Ferrous Iron Binding and Oxidation By Ferritin From A Pennate Diatom. J.Biol.Chem. V. 288 14917 2013.
ISSN: ISSN 0021-9258
PubMed: 23548912
DOI: 10.1074/JBC.M113.454496