Iron in PDB 1ji4: Nap Protein From Helicobacter Pylori

The structure of Nap Protein From Helicobacter Pylori, PDB code: 1ji4 was solved by G.Zanotti, E.Papinutto, W.G.Dundon, R.Battistutta, M.Seveso, G.Del Giudice, R.Rappuoli, C.Montecucco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.81 / 2.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.778, 133.225, 95.228, 90.00, 93.99, 90.00
R / Rfree (%)	21.5 / 22.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Nap Protein From Helicobacter Pylori (pdb code 1ji4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Nap Protein From Helicobacter Pylori, PDB code: 1ji4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Nap Protein From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Nap Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe807 b:26.2 occ:1.00 OD2 A:ASP52 2.2 22.6 1.0 OE2 A:GLU56 2.2 31.8 1.0 NE2 D:HIS25 2.2 22.2 1.0 CG A:ASP52 3.0 22.0 1.0 CD A:GLU56 3.0 30.6 1.0 UNK D:UNX808 3.0 18.2 0.5 OD1 A:ASP52 3.1 23.7 1.0 CD2 D:HIS25 3.1 23.3 1.0 CE1 D:HIS25 3.2 21.9 1.0 OE1 A:GLU56 3.4 32.2 1.0 CE1 D:HIS37 3.9 19.8 1.0 OH D:TYR44 3.9 23.0 1.0 NE2 D:HIS37 4.0 19.7 1.0 CG A:GLU56 4.2 27.6 1.0 ND1 D:HIS25 4.3 23.4 1.0 CG D:HIS25 4.3 21.7 1.0 CB A:ASP52 4.4 19.5 1.0 CD1 D:TRP26 4.9 16.5 1.0 NE1 D:TRP26 4.9 17.6 1.0

Iron binding site 2 out of 12 in the Nap Protein From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Nap Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe805 b:26.2 occ:1.00 OD2 B:ASP52 2.2 22.6 1.0 NE2 C:HIS25 2.2 22.2 1.0 OE2 B:GLU56 2.3 31.8 1.0 CG B:ASP52 3.0 22.0 1.0 UNK C:UNX806 3.0 18.2 0.5 CD B:GLU56 3.1 30.6 1.0 OD1 B:ASP52 3.1 23.7 1.0 CD2 C:HIS25 3.1 23.3 1.0 CE1 C:HIS25 3.2 21.9 1.0 OE1 B:GLU56 3.5 32.2 1.0 OH C:TYR44 3.9 23.0 1.0 CE1 C:HIS37 3.9 19.8 1.0 NE2 C:HIS37 4.0 19.7 1.0 ND1 C:HIS25 4.3 23.4 1.0 CG C:HIS25 4.3 21.7 1.0 CG B:GLU56 4.3 27.6 1.0 CB B:ASP52 4.4 19.5 1.0 CD1 C:TRP26 4.9 16.5 1.0 NE1 C:TRP26 4.9 17.6 1.0

Iron binding site 3 out of 12 in the Nap Protein From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Nap Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe803 b:26.2 occ:1.00 OD2 C:ASP52 2.0 22.6 1.0 OE2 C:GLU56 2.2 31.8 1.0 NE2 B:HIS25 2.2 22.2 1.0 CG C:ASP52 2.8 22.0 1.0 CD C:GLU56 3.0 30.6 1.0 OD1 C:ASP52 3.0 23.7 1.0 UNK B:UNX804 3.0 18.2 0.5 CD2 B:HIS25 3.1 23.3 1.0 CE1 B:HIS25 3.2 21.9 1.0 OE1 C:GLU56 3.3 32.2 1.0 CE1 B:HIS37 3.9 19.8 1.0 OH B:TYR44 3.9 23.0 1.0 NE2 B:HIS37 4.0 19.7 1.0 CG C:GLU56 4.2 27.6 1.0 CB C:ASP52 4.3 19.5 1.0 ND1 B:HIS25 4.3 23.4 1.0 CG B:HIS25 4.3 21.7 1.0 CD1 B:TRP26 4.9 16.5 1.0 NE1 B:TRP26 4.9 17.6 1.0 O C:ASP52 5.0 19.6 1.0

Iron binding site 4 out of 12 in the Nap Protein From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Nap Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe801 b:26.2 occ:1.00 OE2 D:GLU56 2.2 31.8 1.0 NE2 A:HIS25 2.2 22.2 1.0 OD2 D:ASP52 2.2 22.6 1.0 CG D:ASP52 3.0 22.0 1.0 CD D:GLU56 3.0 30.6 1.0 UNK A:UNX802 3.0 18.2 0.5 OD1 D:ASP52 3.1 23.7 1.0 CD2 A:HIS25 3.1 23.3 1.0 CE1 A:HIS25 3.2 21.9 1.0 OE1 D:GLU56 3.4 32.2 1.0 OH A:TYR44 3.9 23.0 1.0 CE1 A:HIS37 3.9 19.8 1.0 NE2 A:HIS37 4.0 19.7 1.0 CG D:GLU56 4.3 27.6 1.0 ND1 A:HIS25 4.3 23.4 1.0 CG A:HIS25 4.3 21.7 1.0 CB D:ASP52 4.5 19.5 1.0 CD1 A:TRP26 4.9 16.5 1.0 NE1 A:TRP26 4.9 17.6 1.0

Iron binding site 5 out of 12 in the Nap Protein From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Nap Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe815 b:26.2 occ:1.00 OD2 E:ASP52 2.1 22.6 1.0 NE2 H:HIS25 2.2 22.2 1.0 OE2 E:GLU56 2.2 31.8 1.0 CG E:ASP52 3.0 22.0 1.0 CD E:GLU56 3.0 30.6 1.0 UNK H:UNX816 3.0 18.2 0.5 OD1 E:ASP52 3.1 23.7 1.0 CD2 H:HIS25 3.1 23.3 1.0 CE1 H:HIS25 3.2 21.9 1.0 OE1 E:GLU56 3.4 32.2 1.0 OH H:TYR44 3.9 23.0 1.0 CE1 H:HIS37 3.9 19.8 1.0 NE2 H:HIS37 4.0 19.7 1.0 CG E:GLU56 4.3 27.6 1.0 ND1 H:HIS25 4.3 23.4 1.0 CG H:HIS25 4.3 21.7 1.0 CB E:ASP52 4.4 19.5 1.0 CD1 H:TRP26 4.9 16.5 1.0 NE1 H:TRP26 4.9 17.6 1.0

Iron binding site 6 out of 12 in the Nap Protein From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Nap Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe813 b:26.2 occ:1.00 OE2 F:GLU56 2.1 31.8 1.0 OD2 F:ASP52 2.2 22.6 1.0 NE2 G:HIS25 2.2 22.2 1.0 CG F:ASP52 3.0 22.0 1.0 CD F:GLU56 3.0 30.6 1.0 UNK G:UNX814 3.0 18.2 0.5 OD1 F:ASP52 3.1 23.7 1.0 CD2 G:HIS25 3.1 23.3 1.0 CE1 G:HIS25 3.2 21.9 1.0 OE1 F:GLU56 3.3 32.2 1.0 OH G:TYR44 3.9 23.0 1.0 CE1 G:HIS37 4.0 19.8 1.0 NE2 G:HIS37 4.0 19.7 1.0 CG F:GLU56 4.2 27.6 1.0 ND1 G:HIS25 4.3 23.4 1.0 CG G:HIS25 4.3 21.7 1.0 CB F:ASP52 4.4 19.5 1.0 CD1 G:TRP26 4.9 16.5 1.0 NE1 G:TRP26 4.9 17.6 1.0

Iron binding site 7 out of 12 in the Nap Protein From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Nap Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe811 b:26.2 occ:1.00 OE2 G:GLU56 2.2 31.8 1.0 OD2 G:ASP52 2.2 22.6 1.0 NE2 F:HIS25 2.2 22.2 1.0 CD G:GLU56 3.0 30.6 1.0 CG G:ASP52 3.0 22.0 1.0 UNK F:UNX812 3.0 18.2 0.5 CD2 F:HIS25 3.1 23.3 1.0 OD1 G:ASP52 3.2 23.7 1.0 CE1 F:HIS25 3.2 21.9 1.0 OE1 G:GLU56 3.3 32.2 1.0 OH F:TYR44 3.9 23.0 1.0 CE1 F:HIS37 3.9 19.8 1.0 NE2 F:HIS37 4.0 19.7 1.0 CG G:GLU56 4.2 27.6 1.0 ND1 F:HIS25 4.3 23.4 1.0 CG F:HIS25 4.3 21.7 1.0 CB G:ASP52 4.4 19.5 1.0 CD1 F:TRP26 4.9 16.5 1.0 NE1 F:TRP26 4.9 17.6 1.0

Iron binding site 8 out of 12 in the Nap Protein From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Nap Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe809 b:26.2 occ:1.00 OD2 H:ASP52 2.1 22.6 1.0 NE2 E:HIS25 2.2 22.2 1.0 OE2 H:GLU56 2.2 31.8 1.0 CG H:ASP52 3.0 22.0 1.0 CD H:GLU56 3.0 30.6 1.0 UNK E:UNX810 3.0 18.2 0.5 OD1 H:ASP52 3.1 23.7 1.0 CD2 E:HIS25 3.1 23.3 1.0 CE1 E:HIS25 3.2 21.9 1.0 OE1 H:GLU56 3.3 32.2 1.0 CE1 E:HIS37 3.9 19.8 1.0 OH E:TYR44 4.0 23.0 1.0 NE2 E:HIS37 4.0 19.7 1.0 CG H:GLU56 4.2 27.6 1.0 ND1 E:HIS25 4.3 23.4 1.0 CG E:HIS25 4.3 21.7 1.0 CB H:ASP52 4.4 19.5 1.0 CD1 E:TRP26 4.9 16.5 1.0 NE1 E:TRP26 4.9 17.6 1.0

Iron binding site 9 out of 12 in the Nap Protein From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Nap Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe823 b:26.2 occ:1.00 OD2 I:ASP52 2.1 22.6 1.0 OE2 I:GLU56 2.1 31.8 1.0 NE2 L:HIS25 2.2 22.2 1.0 CG I:ASP52 2.9 22.0 1.0 CD I:GLU56 2.9 30.6 1.0 UNK L:UNX824 3.0 18.2 0.5 OD1 I:ASP52 3.0 23.7 1.0 CD2 L:HIS25 3.1 23.3 1.0 CE1 L:HIS25 3.2 21.9 1.0 OE1 I:GLU56 3.2 32.2 1.0 OH L:TYR44 3.9 23.0 1.0 CE1 L:HIS37 3.9 19.8 1.0 NE2 L:HIS37 4.0 19.7 1.0 CG I:GLU56 4.1 27.6 1.0 ND1 L:HIS25 4.3 23.4 1.0 CG L:HIS25 4.3 21.7 1.0 CB I:ASP52 4.3 19.5 1.0 CD1 L:TRP26 4.9 16.5 1.0 NE1 L:TRP26 4.9 17.6 1.0 O I:ASP52 5.0 19.6 1.0

Iron binding site 10 out of 12 in the Nap Protein From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Nap Protein From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe821 b:26.2 occ:1.00 OD2 J:ASP52 2.1 22.6 1.0 NE2 K:HIS25 2.2 22.2 1.0 OE2 J:GLU56 2.2 31.8 1.0 CG J:ASP52 2.9 22.0 1.0 OD1 J:ASP52 3.0 23.7 1.0 CD J:GLU56 3.0 30.6 1.0 UNK K:UNX822 3.0 18.2 0.5 CD2 K:HIS25 3.1 23.3 1.0 CE1 K:HIS25 3.2 21.9 1.0 OE1 J:GLU56 3.4 32.2 1.0 OH K:TYR44 3.9 23.0 1.0 CE1 K:HIS37 3.9 19.8 1.0 NE2 K:HIS37 4.0 19.7 1.0 CG J:GLU56 4.2 27.6 1.0 ND1 K:HIS25 4.3 23.4 1.0 CG K:HIS25 4.3 21.7 1.0 CB J:ASP52 4.3 19.5 1.0 CD1 K:TRP26 4.9 16.5 1.0 NE1 K:TRP26 4.9 17.6 1.0

G.Zanotti, E.Papinutto, W.G.Dundon, R.Battistutta, M.Seveso, G.Del Giudice, R.Rappuoli, C.Montecucco. Structure of the Neutrophil-Activating Protein From Helicobacter Pylori J.Mol.Biol. V. 323 125 2002.
ISSN: ISSN 0022-2836
PubMed: 12368104
DOI: 10.1016/S0022-2836(02)00879-3