Zinc in PDB 2vxi: The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin

The structure of The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin, PDB code: 2vxi was solved by S.C.Willies, M.N.Isupov, E.F.Garman, J.A.Littlechild, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	147.44 / 1.91
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	208.100, 208.100, 142.768, 90.00, 90.00, 90.00
R / Rfree (%)	17.851 / 21.561

The structure of The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin also contains other interesting chemical elements:

Iron

(Fe)

12 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 The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin (pdb code 2vxi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin, PDB code: 2vxi:
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 The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:24.6 occ:1.00 OE1 A:GLU127 2.0 25.3 1.0 OE2 A:GLU94 2.0 22.8 1.0 OE2 A:GLU51 2.0 24.4 1.0 ND1 A:HIS130 2.0 16.5 1.0 CD A:GLU94 2.7 33.9 1.0 OE1 A:GLU94 2.7 30.9 1.0 CD A:GLU51 2.9 22.0 1.0 CE1 A:HIS130 2.9 27.2 1.0 OE1 A:GLU51 3.1 19.4 1.0 CG A:HIS130 3.2 20.0 1.0 CD A:GLU127 3.2 22.3 1.0 CB A:HIS130 3.6 13.2 1.0 OE2 A:GLU127 3.7 27.1 1.0 O A:HOH2131 3.8 42.8 1.0 ZN A:ZN202 4.0 21.8 1.0 NE2 A:HIS130 4.1 21.1 1.0 OH A:TYR25 4.1 28.1 1.0 CE2 A:TYR25 4.1 16.8 1.0 CG A:GLU94 4.2 21.0 1.0 CD2 A:HIS130 4.2 17.2 1.0 CG A:GLU51 4.2 19.9 1.0 CA A:GLU127 4.3 16.4 1.0 CG A:GLU127 4.4 14.3 1.0 CB A:GLU127 4.4 16.2 1.0 O A:HOH2132 4.6 25.8 1.0 CZ A:TYR25 4.6 29.9 1.0 O A:GLU127 5.0 14.2 1.0

Zinc binding site 2 out of 24 in the The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:21.8 occ:1.00 OE2 A:GLU127 2.0 27.1 1.0 OE1 A:GLU51 2.0 19.4 1.0 OE1 A:GLU18 2.0 24.1 1.0 ND1 A:HIS54 2.1 13.1 1.0 OE2 A:GLU18 2.4 24.9 1.0 CD A:GLU18 2.6 18.4 1.0 CD A:GLU127 2.9 22.3 1.0 CD A:GLU51 3.0 22.0 1.0 CE1 A:HIS54 3.0 20.2 1.0 CG A:HIS54 3.1 12.4 1.0 OE1 A:GLU127 3.2 25.3 1.0 CB A:HIS54 3.5 7.5 1.0 OE2 A:GLU51 3.5 24.4 1.0 CA A:GLU51 4.0 14.6 1.0 ZN A:ZN201 4.0 24.6 1.0 CG A:GLU18 4.1 18.2 1.0 NE2 A:HIS54 4.1 13.2 1.0 CG A:GLU51 4.2 19.9 1.0 CG2 A:ILE123 4.2 16.9 1.0 CD2 A:HIS54 4.2 18.6 1.0 CB A:GLU51 4.3 16.0 1.0 CG A:GLU127 4.3 14.3 1.0 O A:HOH2158 4.4 34.1 1.0 O A:HOH2083 4.7 21.0 1.0 O A:ASP50 4.8 16.6 1.0 N A:GLU51 4.8 11.3 1.0 O A:GLU51 4.8 11.6 1.0 CE1 A:HIS130 4.8 27.2 1.0 CB A:GLU18 4.9 11.2 1.0 C A:GLU51 5.0 14.7 1.0

Zinc binding site 3 out of 24 in the The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:23.8 occ:1.00 OE1 B:GLU127 2.0 31.3 1.0 OE2 B:GLU94 2.0 21.3 1.0 ND1 B:HIS130 2.0 17.2 1.0 OE2 B:GLU51 2.0 23.8 1.0 CD B:GLU94 2.7 34.9 1.0 OE1 B:GLU94 2.7 37.7 1.0 CD B:GLU51 2.9 20.7 1.0 CE1 B:HIS130 2.9 19.0 1.0 OE1 B:GLU51 3.0 17.5 1.0 CD B:GLU127 3.1 24.4 1.0 CG B:HIS130 3.1 20.7 1.0 O B:HOH2074 3.3 54.9 1.0 O B:HOH2125 3.5 50.9 1.0 OE2 B:GLU127 3.5 26.1 1.0 CB B:HIS130 3.6 16.4 1.0 ZN B:ZN202 4.0 21.3 1.0 NE2 B:HIS130 4.1 20.5 1.0 OH B:TYR25 4.1 23.4 1.0 CE2 B:TYR25 4.2 21.3 1.0 CG B:GLU94 4.2 21.5 1.0 CD2 B:HIS130 4.2 19.1 1.0 CG B:GLU51 4.2 17.4 1.0 CA B:GLU127 4.3 17.6 1.0 CG B:GLU127 4.4 23.8 1.0 O B:HOH2126 4.5 27.6 1.0 CB B:GLU127 4.5 15.7 1.0 CZ B:TYR25 4.6 27.9 1.0

Zinc binding site 4 out of 24 in the The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:21.3 occ:1.00 OE2 B:GLU127 2.0 26.1 1.0 OE1 B:GLU51 2.0 17.5 1.0 ND1 B:HIS54 2.1 15.4 1.0 OE1 B:GLU18 2.1 22.9 1.0 OE2 B:GLU18 2.1 25.0 1.0 CD B:GLU18 2.4 17.6 1.0 O B:HOH2074 2.9 54.9 1.0 CD B:GLU51 3.0 20.7 1.0 CE1 B:HIS54 3.0 14.8 1.0 CD B:GLU127 3.0 24.4 1.0 CG B:HIS54 3.1 10.1 1.0 CB B:HIS54 3.4 11.5 1.0 OE1 B:GLU127 3.4 31.3 1.0 OE2 B:GLU51 3.6 23.8 1.0 CG B:GLU18 4.0 16.0 1.0 ZN B:ZN201 4.0 23.8 1.0 CA B:GLU51 4.0 15.4 1.0 NE2 B:HIS54 4.1 15.2 1.0 CG B:GLU51 4.2 17.4 1.0 CD2 B:HIS54 4.2 14.5 1.0 CG2 B:ILE123 4.2 14.5 1.0 CB B:GLU51 4.3 12.3 1.0 CG B:GLU127 4.3 23.8 1.0 O B:HOH2012 4.5 35.9 1.0 O B:HOH2079 4.7 21.6 1.0 O B:ASP50 4.8 15.0 1.0 N B:GLU51 4.8 10.7 1.0 CE1 B:HIS130 4.8 19.0 1.0 CB B:GLU18 4.8 9.2 1.0 O B:GLU51 4.9 12.7 1.0 CA B:HIS54 4.9 11.4 1.0 C B:GLU51 5.0 14.3 1.0

Zinc binding site 5 out of 24 in the The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:24.0 occ:1.00 OE1 C:GLU127 2.0 27.9 1.0 OE2 C:GLU94 2.0 23.9 1.0 OE2 C:GLU51 2.0 30.0 1.0 ND1 C:HIS130 2.0 17.8 1.0 CD C:GLU94 2.7 34.6 1.0 OE1 C:GLU94 2.7 34.7 1.0 CD C:GLU51 2.9 21.4 1.0 CE1 C:HIS130 2.9 21.3 1.0 CD C:GLU127 3.1 24.8 1.0 CG C:HIS130 3.1 17.4 1.0 OE1 C:GLU51 3.1 18.7 1.0 O C:HOH2080 3.4 49.4 1.0 CB C:HIS130 3.6 15.8 1.0 OE2 C:GLU127 3.6 24.3 1.0 O C:HOH2127 3.7 43.3 1.0 ZN C:ZN202 4.0 21.1 1.0 NE2 C:HIS130 4.1 19.5 1.0 CE2 C:TYR25 4.1 23.7 1.0 OH C:TYR25 4.1 24.1 1.0 CG C:GLU94 4.2 13.8 1.0 CD2 C:HIS130 4.2 24.3 1.0 CG C:GLU51 4.2 13.2 1.0 CA C:GLU127 4.3 13.1 1.0 CG C:GLU127 4.4 19.6 1.0 CB C:GLU127 4.5 14.2 1.0 O C:HOH2126 4.6 27.6 1.0 CZ C:TYR25 4.6 28.2 1.0

Zinc binding site 6 out of 24 in the The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:21.1 occ:1.00 OE2 C:GLU127 2.0 24.3 1.0 OE1 C:GLU51 2.0 18.7 1.0 ND1 C:HIS54 2.0 14.9 1.0 OE1 C:GLU18 2.1 22.6 1.0 OE2 C:GLU18 2.1 24.0 1.0 CD C:GLU18 2.5 20.4 1.0 CE1 C:HIS54 3.0 17.4 1.0 CD C:GLU127 3.0 24.8 1.0 CD C:GLU51 3.1 21.4 1.0 CG C:HIS54 3.1 16.5 1.0 O C:HOH2080 3.3 49.4 1.0 OE1 C:GLU127 3.4 27.9 1.0 CB C:HIS54 3.4 12.3 1.0 OE2 C:GLU51 3.6 30.0 1.0 CG C:GLU18 4.0 16.9 1.0 ZN C:ZN201 4.0 24.0 1.0 CA C:GLU51 4.1 11.8 1.0 NE2 C:HIS54 4.1 19.1 1.0 CG2 C:ILE123 4.2 17.2 1.0 CD2 C:HIS54 4.2 16.4 1.0 CG C:GLU51 4.2 13.2 1.0 CG C:GLU127 4.3 19.6 1.0 CB C:GLU51 4.3 13.2 1.0 O C:HOH2156 4.4 33.2 1.0 O C:ASP50 4.7 12.6 1.0 O C:HOH2086 4.7 24.1 1.0 N C:GLU51 4.8 13.3 1.0 O C:GLU51 4.8 13.6 1.0 CE1 C:HIS130 4.9 21.3 1.0 CB C:GLU18 4.9 11.8 1.0 CA C:HIS54 5.0 14.3 1.0

Zinc binding site 7 out of 24 in the The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:24.6 occ:1.00 OE1 D:GLU127 2.0 27.9 1.0 OE2 D:GLU94 2.0 20.3 1.0 OE2 D:GLU51 2.0 28.2 1.0 ND1 D:HIS130 2.1 19.4 1.0 CD D:GLU94 2.7 36.4 1.0 OE1 D:GLU94 2.8 28.1 1.0 CD D:GLU51 2.9 22.8 1.0 CE1 D:HIS130 2.9 22.8 1.0 OE1 D:GLU51 3.1 24.2 1.0 CG D:HIS130 3.1 22.2 1.0 CD D:GLU127 3.2 24.3 1.0 CB D:HIS130 3.6 17.8 1.0 O D:HOH2126 3.6 52.3 1.0 OE2 D:GLU127 3.7 26.9 1.0 ZN D:ZN202 4.0 22.2 1.0 OH D:TYR25 4.1 26.4 1.0 NE2 D:HIS130 4.1 23.7 1.0 CE2 D:TYR25 4.2 22.0 1.0 CG D:GLU51 4.2 17.7 1.0 CG D:GLU94 4.2 20.1 1.0 CD2 D:HIS130 4.2 21.2 1.0 CA D:GLU127 4.3 13.9 1.0 CG D:GLU127 4.4 14.0 1.0 CB D:GLU127 4.5 11.5 1.0 O D:HOH2125 4.5 32.1 1.0 CZ D:TYR25 4.6 28.1 1.0 O D:GLU127 5.0 16.0 1.0

Zinc binding site 8 out of 24 in the The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:22.2 occ:1.00 OE2 D:GLU127 2.0 26.9 1.0 OE1 D:GLU18 2.0 24.7 1.0 OE1 D:GLU51 2.0 24.2 1.0 ND1 D:HIS54 2.0 17.0 1.0 OE2 D:GLU18 2.5 26.4 1.0 CD D:GLU18 2.5 21.1 1.0 CE1 D:HIS54 3.0 14.5 1.0 CD D:GLU127 3.0 24.3 1.0 CD D:GLU51 3.0 22.8 1.0 CG D:HIS54 3.1 9.4 1.0 OE1 D:GLU127 3.3 27.9 1.0 CB D:HIS54 3.5 8.9 1.0 OE2 D:GLU51 3.6 28.2 1.0 ZN D:ZN201 4.0 24.6 1.0 CA D:GLU51 4.0 13.9 1.0 CG D:GLU18 4.1 14.5 1.0 NE2 D:HIS54 4.1 13.0 1.0 CG D:GLU51 4.1 17.7 1.0 CD2 D:HIS54 4.2 16.7 1.0 CG2 D:ILE123 4.2 16.1 1.0 CB D:GLU51 4.2 12.7 1.0 CG D:GLU127 4.3 14.0 1.0 O D:HOH2156 4.7 45.0 1.0 O D:HOH2076 4.7 15.5 1.0 O D:ASP50 4.8 14.3 1.0 CE1 D:HIS130 4.8 22.8 1.0 N D:GLU51 4.8 13.2 1.0 CB D:GLU18 4.8 11.7 1.0 O D:GLU51 4.8 12.9 1.0 C D:GLU51 5.0 15.5 1.0 CA D:HIS54 5.0 11.9 1.0

Zinc binding site 9 out of 24 in the The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:24.5 occ:1.00 OE1 E:GLU127 2.0 25.3 1.0 OE2 E:GLU94 2.0 22.6 1.0 OE2 E:GLU51 2.0 25.4 1.0 ND1 E:HIS130 2.0 20.9 1.0 CD E:GLU94 2.7 37.6 1.0 OE1 E:GLU94 2.8 33.4 1.0 CE1 E:HIS130 2.9 27.8 1.0 CD E:GLU51 2.9 18.4 1.0 OE1 E:GLU51 3.1 18.6 1.0 CD E:GLU127 3.1 25.6 1.0 CG E:HIS130 3.2 25.6 1.0 O E:HOH2135 3.2 42.5 1.0 OE2 E:GLU127 3.6 26.3 1.0 CB E:HIS130 3.6 19.7 1.0 ZN E:ZN202 4.0 21.5 1.0 NE2 E:HIS130 4.1 25.4 1.0 OH E:TYR25 4.2 25.9 1.0 CD2 E:HIS130 4.2 21.7 1.0 CE2 E:TYR25 4.2 22.3 1.0 CG E:GLU94 4.2 18.3 1.0 CG E:GLU51 4.2 19.3 1.0 CA E:GLU127 4.3 13.0 1.0 CG E:GLU127 4.4 20.3 1.0 CB E:GLU127 4.5 15.2 1.0 CZ E:TYR25 4.7 28.3 1.0 O E:HOH2134 4.7 25.8 1.0

Zinc binding site 10 out of 24 in the The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Binding of Heme and Zinc in Escherichia Coli Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn202 b:21.5 occ:1.00 OE1 E:GLU51 2.0 18.6 1.0 OE2 E:GLU127 2.0 26.3 1.0 OE1 E:GLU18 2.0 26.7 1.0 ND1 E:HIS54 2.0 15.4 1.0 OE2 E:GLU18 2.6 24.6 1.0 CD E:GLU18 2.6 21.5 1.0 CE1 E:HIS54 3.0 18.6 1.0 CD E:GLU51 3.0 18.4 1.0 CD E:GLU127 3.0 25.6 1.0 CG E:HIS54 3.1 12.0 1.0 OE1 E:GLU127 3.4 25.3 1.0 CB E:HIS54 3.5 10.1 1.0 OE2 E:GLU51 3.5 25.4 1.0 ZN E:ZN201 4.0 24.5 1.0 CA E:GLU51 4.0 13.1 1.0 NE2 E:HIS54 4.1 14.4 1.0 CG E:GLU18 4.1 19.0 1.0 CG E:GLU51 4.1 19.3 1.0 CD2 E:HIS54 4.2 13.5 1.0 CB E:GLU51 4.2 13.4 1.0 CG2 E:ILE123 4.3 14.1 1.0 O E:HOH2160 4.3 42.5 1.0 CG E:GLU127 4.3 20.3 1.0 N E:GLU51 4.7 10.3 1.0 O E:HOH2034 4.7 20.8 1.0 CE1 E:HIS130 4.8 27.8 1.0 O E:ASP50 4.8 13.4 1.0 CB E:GLU18 4.8 13.3 1.0 O E:GLU51 4.9 16.1 1.0 O E:HOH2135 5.0 42.5 1.0

S.C.Willies, M.N.Isupov, E.F.Garman, J.A.Littlechild. The Binding of Haem and Zinc in the 1.9 A X-Ray Structure of Escherichia Coli Bacterioferritin. J.Biol.Inorg.Chem. V. 14 201 2009.
ISSN: ISSN 0949-8257
PubMed: 18946693
DOI: 10.1007/S00775-008-0438-8