Zinc in PDB 3e1p: Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity.

The structure of Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity., PDB code: 3e1p was solved by A.Crow, T.Lawson, A.Lewin, G.R.Moore, N.Le Brun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.25 / 2.40
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	207.397, 207.397, 142.451, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 26

The structure of Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity. also contains other interesting chemical elements:

Iron

(Fe)

18 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity. (pdb code 3e1p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity., PDB code: 3e1p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity.


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 E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:13.2 occ:1.00 OE1 A:GLU127 2.0 15.4 1.0 OE2 A:GLU51 2.0 16.3 1.0 OE1 A:GLU18 2.0 18.2 1.0 ND1 A:HIS54 2.1 11.6 1.0 OE2 A:GLU18 2.4 17.5 1.0 CD A:GLU18 2.6 16.3 1.0 CD A:GLU127 3.0 14.6 1.0 CG A:HIS54 3.1 12.0 1.0 CE1 A:HIS54 3.1 12.7 1.0 CD A:GLU51 3.1 15.7 1.0 CB A:HIS54 3.4 11.4 1.0 OE2 A:GLU127 3.4 15.5 1.0 OE1 A:GLU51 3.7 17.8 1.0 CA A:GLU51 3.9 12.7 1.0 CG A:GLU18 4.0 14.7 1.0 ZN A:ZN301 4.0 14.5 1.0 NE2 A:HIS54 4.2 11.5 1.0 CG A:GLU51 4.2 13.4 1.0 CD2 A:HIS54 4.2 11.7 1.0 CB A:GLU51 4.2 12.8 1.0 CG A:GLU127 4.3 14.0 1.0 CG2 A:ILE123 4.3 8.7 1.0 O A:HOH307 4.6 2.0 1.0 N A:GLU51 4.7 12.8 1.0 O A:GLU51 4.7 12.1 1.0 O A:ASP50 4.7 13.2 1.0 CB A:GLU18 4.8 12.3 1.0 C A:GLU51 4.9 12.6 1.0 CA A:HIS54 4.9 11.1 1.0 CE1 A:HIS130 4.9 17.0 1.0 C A:ASP50 5.0 13.0 1.0

Zinc binding site 2 out of 24 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity.


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 E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.5 occ:1.00 OE2 A:GLU127 1.9 15.5 1.0 OE1 A:GLU51 2.0 17.8 1.0 OE2 A:GLU94 2.0 19.1 1.0 ND1 A:HIS130 2.1 16.1 1.0 OE1 A:GLU94 2.7 21.4 1.0 CD A:GLU94 2.7 18.1 1.0 CD A:GLU51 2.9 15.7 1.0 CE1 A:HIS130 3.0 17.0 1.0 CD A:GLU127 3.1 14.6 1.0 CG A:HIS130 3.1 14.6 1.0 OE2 A:GLU51 3.2 16.3 1.0 CB A:HIS130 3.5 12.2 1.0 OE1 A:GLU127 3.6 15.4 1.0 O A:HOH350 4.0 10.2 1.0 ZN A:ZN300 4.0 13.2 1.0 NE2 A:HIS130 4.1 16.9 1.0 OH A:TYR25 4.2 14.2 1.0 CG A:GLU94 4.2 13.1 1.0 CA A:GLU127 4.2 12.3 1.0 CD2 A:HIS130 4.2 15.2 1.0 CE2 A:TYR25 4.2 13.5 1.0 CG A:GLU127 4.3 14.0 1.0 CG A:GLU51 4.3 13.4 1.0 CB A:GLU127 4.5 12.4 1.0 O A:HOH306 4.6 4.5 1.0 CZ A:TYR25 4.7 14.5 1.0 O A:GLU127 4.8 12.0 1.0

Zinc binding site 3 out of 24 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity.


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 E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:13.3 occ:1.00 OE1 B:GLU127 2.0 15.4 1.0 OE1 B:GLU18 2.0 18.2 1.0 OE2 B:GLU51 2.0 16.2 1.0 ND1 B:HIS54 2.1 11.5 1.0 OE2 B:GLU18 2.4 17.6 1.0 CD B:GLU18 2.5 16.3 1.0 CD B:GLU127 3.0 14.6 1.0 CD B:GLU51 3.1 15.7 1.0 CG B:HIS54 3.1 12.1 1.0 CE1 B:HIS54 3.1 12.7 1.0 CB B:HIS54 3.4 11.4 1.0 OE2 B:GLU127 3.4 15.5 1.0 OE1 B:GLU51 3.7 17.8 1.0 CA B:GLU51 4.0 12.7 1.0 CG B:GLU18 4.0 14.7 1.0 ZN B:ZN301 4.0 14.4 1.0 CG B:GLU51 4.2 13.4 1.0 NE2 B:HIS54 4.2 11.4 1.0 CB B:GLU51 4.2 12.8 1.0 CD2 B:HIS54 4.2 11.7 1.0 CG B:GLU127 4.3 14.0 1.0 CG2 B:ILE123 4.3 8.7 1.0 O B:HOH319 4.5 19.3 1.0 O B:HOH315 4.7 2.5 1.0 N B:GLU51 4.7 12.8 1.0 O B:GLU51 4.7 12.0 1.0 CB B:GLU18 4.8 12.3 1.0 O B:ASP50 4.8 13.2 1.0 C B:GLU51 4.9 12.6 1.0 CA B:HIS54 4.9 11.2 1.0 CE1 B:HIS130 4.9 17.0 1.0

Zinc binding site 4 out of 24 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity.


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 E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:14.4 occ:1.00 OE2 B:GLU127 2.0 15.5 1.0 OE1 B:GLU51 2.0 17.8 1.0 OE2 B:GLU94 2.0 19.1 1.0 ND1 B:HIS130 2.1 16.1 1.0 OE1 B:GLU94 2.7 21.4 1.0 CD B:GLU94 2.7 18.1 1.0 CD B:GLU51 2.9 15.7 1.0 CE1 B:HIS130 3.0 17.0 1.0 CD B:GLU127 3.1 14.6 1.0 CG B:HIS130 3.1 14.6 1.0 OE2 B:GLU51 3.2 16.2 1.0 CB B:HIS130 3.5 12.2 1.0 OE1 B:GLU127 3.6 15.4 1.0 ZN B:ZN300 4.0 13.3 1.0 NE2 B:HIS130 4.1 16.9 1.0 O B:HOH320 4.1 13.2 1.0 OH B:TYR25 4.1 14.2 1.0 CG B:GLU94 4.2 13.2 1.0 CD2 B:HIS130 4.2 15.2 1.0 CA B:GLU127 4.2 12.4 1.0 CE2 B:TYR25 4.2 13.5 1.0 CG B:GLU51 4.3 13.4 1.0 CG B:GLU127 4.3 14.0 1.0 CB B:GLU127 4.5 12.3 1.0 O B:HOH313 4.5 4.0 1.0 CZ B:TYR25 4.7 14.5 1.0 O B:GLU127 4.8 12.0 1.0

Zinc binding site 5 out of 24 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity.


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 E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn300 b:13.3 occ:1.00 OE1 C:GLU127 2.0 15.4 1.0 OE1 C:GLU18 2.0 18.2 1.0 OE2 C:GLU51 2.0 16.3 1.0 ND1 C:HIS54 2.1 11.5 1.0 OE2 C:GLU18 2.4 17.6 1.0 CD C:GLU18 2.5 16.3 1.0 CD C:GLU127 3.0 14.6 1.0 CD C:GLU51 3.1 15.7 1.0 CE1 C:HIS54 3.1 12.7 1.0 CG C:HIS54 3.1 12.0 1.0 OE2 C:GLU127 3.4 15.5 1.0 CB C:HIS54 3.4 11.4 1.0 OE1 C:GLU51 3.6 17.8 1.0 CA C:GLU51 4.0 12.7 1.0 ZN C:ZN301 4.0 14.4 1.0 CG C:GLU18 4.0 14.7 1.0 CG C:GLU51 4.2 13.4 1.0 NE2 C:HIS54 4.2 11.4 1.0 CB C:GLU51 4.2 12.8 1.0 CD2 C:HIS54 4.2 11.7 1.0 CG C:GLU127 4.3 14.0 1.0 CG2 C:ILE123 4.3 8.6 1.0 O C:HOH306 4.7 3.9 1.0 N C:GLU51 4.7 12.7 1.0 O C:GLU51 4.7 12.0 1.0 O C:ASP50 4.8 13.2 1.0 CB C:GLU18 4.8 12.2 1.0 C C:GLU51 4.9 12.6 1.0 CA C:HIS54 4.9 11.1 1.0 CE1 C:HIS130 4.9 17.0 1.0

Zinc binding site 6 out of 24 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity.


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 E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:14.4 occ:1.00 OE2 C:GLU127 1.9 15.5 1.0 OE1 C:GLU51 2.0 17.8 1.0 OE2 C:GLU94 2.1 19.1 1.0 ND1 C:HIS130 2.1 16.1 1.0 OE1 C:GLU94 2.7 21.5 1.0 CD C:GLU94 2.7 18.1 1.0 CD C:GLU51 2.9 15.7 1.0 CE1 C:HIS130 3.0 17.0 1.0 CD C:GLU127 3.1 14.6 1.0 CG C:HIS130 3.1 14.6 1.0 OE2 C:GLU51 3.2 16.3 1.0 CB C:HIS130 3.5 12.2 1.0 OE1 C:GLU127 3.6 15.4 1.0 ZN C:ZN300 4.0 13.3 1.0 NE2 C:HIS130 4.1 16.9 1.0 OH C:TYR25 4.2 14.2 1.0 CG C:GLU94 4.2 13.1 1.0 CA C:GLU127 4.2 12.4 1.0 CD2 C:HIS130 4.2 15.3 1.0 CE2 C:TYR25 4.3 13.5 1.0 CG C:GLU127 4.3 14.0 1.0 CG C:GLU51 4.3 13.4 1.0 CB C:GLU127 4.4 12.4 1.0 O C:HOH316 4.5 12.9 1.0 CZ C:TYR25 4.7 14.5 1.0 O C:GLU127 4.8 12.0 1.0

Zinc binding site 7 out of 24 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity.


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 E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn300 b:13.2 occ:1.00 OE1 D:GLU127 2.0 15.4 1.0 OE2 D:GLU51 2.0 16.2 1.0 OE1 D:GLU18 2.1 18.2 1.0 ND1 D:HIS54 2.1 11.6 1.0 OE2 D:GLU18 2.5 17.5 1.0 CD D:GLU18 2.6 16.3 1.0 CD D:GLU127 3.0 14.6 1.0 CD D:GLU51 3.0 15.7 1.0 CE1 D:HIS54 3.1 12.7 1.0 CG D:HIS54 3.1 12.0 1.0 OE2 D:GLU127 3.4 15.5 1.0 CB D:HIS54 3.4 11.4 1.0 OE1 D:GLU51 3.6 17.8 1.0 CA D:GLU51 3.9 12.7 1.0 ZN D:ZN301 4.0 14.5 1.0 CG D:GLU18 4.1 14.7 1.0 CG D:GLU51 4.2 13.4 1.0 NE2 D:HIS54 4.2 11.4 1.0 CB D:GLU51 4.2 12.8 1.0 CD2 D:HIS54 4.2 11.7 1.0 CG D:GLU127 4.3 14.0 1.0 CG2 D:ILE123 4.3 8.7 1.0 O D:HOH345 4.4 9.1 1.0 O D:HOH304 4.6 2.0 1.0 N D:GLU51 4.7 12.8 1.0 O D:GLU51 4.7 12.0 1.0 O D:ASP50 4.8 13.2 1.0 CB D:GLU18 4.8 12.3 1.0 CE1 D:HIS130 4.9 17.0 1.0 C D:GLU51 4.9 12.6 1.0 CA D:HIS54 4.9 11.1 1.0 C D:ASP50 5.0 13.0 1.0

Zinc binding site 8 out of 24 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity.


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 E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:14.5 occ:1.00 OE2 D:GLU127 2.0 15.5 1.0 OE1 D:GLU51 2.0 17.8 1.0 OE2 D:GLU94 2.0 19.2 1.0 ND1 D:HIS130 2.1 16.1 1.0 OE1 D:GLU94 2.7 21.4 1.0 CD D:GLU94 2.7 18.1 1.0 CD D:GLU51 2.9 15.7 1.0 CE1 D:HIS130 3.0 17.0 1.0 CD D:GLU127 3.1 14.6 1.0 CG D:HIS130 3.1 14.6 1.0 OE2 D:GLU51 3.2 16.2 1.0 CB D:HIS130 3.5 12.2 1.0 OE1 D:GLU127 3.6 15.4 1.0 ZN D:ZN300 4.0 13.2 1.0 NE2 D:HIS130 4.1 16.9 1.0 OH D:TYR25 4.1 14.2 1.0 CG D:GLU94 4.2 13.1 1.0 CD2 D:HIS130 4.2 15.2 1.0 CE2 D:TYR25 4.2 13.5 1.0 CA D:GLU127 4.2 12.4 1.0 CG D:GLU51 4.3 13.4 1.0 CG D:GLU127 4.3 14.0 1.0 CB D:GLU127 4.5 12.3 1.0 O D:HOH314 4.6 6.4 1.0 CZ D:TYR25 4.7 14.5 1.0 O D:GLU127 4.8 12.0 1.0 O D:HOH345 4.9 9.1 1.0

Zinc binding site 9 out of 24 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity.


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 E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity. within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn300 b:13.2 occ:1.00 OE1 E:GLU127 2.0 15.4 1.0 OE2 E:GLU51 2.0 16.2 1.0 OE1 E:GLU18 2.0 18.2 1.0 ND1 E:HIS54 2.1 11.6 1.0 OE2 E:GLU18 2.4 17.6 1.0 CD E:GLU18 2.5 16.3 1.0 CD E:GLU127 3.0 14.6 1.0 CD E:GLU51 3.1 15.7 1.0 CG E:HIS54 3.1 12.0 1.0 CE1 E:HIS54 3.1 12.7 1.0 CB E:HIS54 3.4 11.3 1.0 OE2 E:GLU127 3.4 15.5 1.0 OE1 E:GLU51 3.6 17.8 1.0 CA E:GLU51 4.0 12.7 1.0 ZN E:ZN301 4.0 14.5 1.0 CG E:GLU18 4.0 14.7 1.0 CG E:GLU51 4.2 13.4 1.0 NE2 E:HIS54 4.2 11.4 1.0 CB E:GLU51 4.2 12.8 1.0 CD2 E:HIS54 4.2 11.7 1.0 CG E:GLU127 4.3 14.0 1.0 CG2 E:ILE123 4.3 8.7 1.0 O E:HOH315 4.5 14.4 1.0 N E:GLU51 4.7 12.8 1.0 O E:GLU51 4.7 12.0 1.0 O E:HOH316 4.7 4.3 1.0 O E:ASP50 4.8 13.2 1.0 CB E:GLU18 4.8 12.2 1.0 C E:GLU51 4.9 12.6 1.0 CA E:HIS54 4.9 11.1 1.0 CE1 E:HIS130 4.9 17.0 1.0

Zinc binding site 10 out of 24 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity.


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 E. Coli Bacterioferritin (Bfr) in Which the Ferroxidase Centre Is Inhibited with Zn(II) and High Occupancy Iron Is Bound Within the Cavity. within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:14.5 occ:1.00 OE2 E:GLU127 1.9 15.5 1.0 OE1 E:GLU51 2.0 17.8 1.0 OE2 E:GLU94 2.0 19.1 1.0 ND1 E:HIS130 2.1 16.0 1.0 OE1 E:GLU94 2.7 21.4 1.0 CD E:GLU94 2.7 18.1 1.0 CD E:GLU51 2.9 15.7 1.0 CE1 E:HIS130 3.0 17.0 1.0 CD E:GLU127 3.1 14.6 1.0 CG E:HIS130 3.2 14.6 1.0 OE2 E:GLU51 3.2 16.2 1.0 CB E:HIS130 3.6 12.2 1.0 OE1 E:GLU127 3.6 15.4 1.0 ZN E:ZN300 4.0 13.2 1.0 NE2 E:HIS130 4.2 16.9 1.0 OH E:TYR25 4.2 14.2 1.0 CG E:GLU94 4.2 13.1 1.0 CE2 E:TYR25 4.2 13.5 1.0 CA E:GLU127 4.2 12.4 1.0 CD2 E:HIS130 4.3 15.3 1.0 CG E:GLU51 4.3 13.4 1.0 CG E:GLU127 4.3 14.0 1.0 CB E:GLU127 4.5 12.4 1.0 O E:HOH314 4.6 10.0 1.0 CZ E:TYR25 4.7 14.5 1.0 O E:GLU127 4.9 12.0 1.0

A.Crow, T.L.Lawson, A.Lewin, G.R.Moore, N.E.Le Brun. Structural Basis For Iron Mineralization By Bacterioferritin J.Am.Chem.Soc. V. 131 6808 2009.
ISSN: ISSN 0002-7863
PubMed: 19391621
DOI: 10.1021/JA8093444