Iron in PDB 3egm: Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin

All present enzymatic activity of Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin:
1.16.3.1;

The structure of Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin, PDB code: 3egm was solved by K.H.Kim, K.J.Cho, H.J.Shin, J.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 2.10
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	128.528, 128.528, 165.380, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 20.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iron atom in the Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin (pdb code 3egm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 15 binding sites of Iron where determined in the Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin, PDB code: 3egm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 15 in the Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe168 b:34.4 occ:0.50 OE2 A:GLU17 2.7 13.4 1.0 FE A:FE169 2.7 21.4 0.5 OE1 A:GLN127 2.8 10.3 1.0 ND1 A:HIS53 3.2 10.4 1.0 O A:HOH215 3.3 13.7 1.0 OE1 A:GLU50 3.3 15.1 1.0 CD A:GLU17 3.4 13.6 1.0 OE1 A:GLU17 3.4 14.2 1.0 OE1 A:GLU130 3.6 12.2 1.0 CE1 A:HIS53 3.6 9.8 1.0 CG2 A:ILE97 3.6 11.3 1.0 OE2 A:GLU50 3.8 16.4 1.0 CD A:GLU50 3.8 15.2 1.0 CD A:GLN127 3.8 11.1 1.0 CE1 A:TYR123 4.0 8.7 1.0 CG A:HIS53 4.3 9.9 1.0 OH A:TYR123 4.4 8.6 1.0 CD A:GLU130 4.5 12.7 1.0 CZ A:TYR123 4.6 9.1 1.0 CG A:GLN127 4.6 11.4 1.0 NE2 A:GLN127 4.7 9.0 1.0 OE2 A:GLU94 4.7 11.8 1.0 CB A:GLN127 4.7 11.4 1.0 OE2 A:GLU130 4.8 14.4 1.0 CB A:ILE97 4.8 11.2 1.0 NE2 A:HIS53 4.8 10.9 1.0 CG A:GLU17 4.9 11.7 1.0 CB A:HIS53 4.9 9.2 1.0 CD1 A:TYR123 4.9 9.1 1.0 CD1 A:ILE101 5.0 11.2 1.0 CG A:GLU50 5.0 12.7 1.0

Iron binding site 2 out of 15 in the Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe169 b:21.4 occ:0.50 OE1 A:GLU130 2.2 12.2 1.0 OE2 A:GLU94 2.3 11.8 1.0 OE1 A:GLN127 2.3 10.3 1.0 OE1 A:GLU50 2.4 15.1 1.0 FE A:FE168 2.7 34.4 0.5 CD A:GLU94 3.1 11.5 1.0 CD A:GLN127 3.2 11.1 1.0 OE1 A:GLU94 3.2 11.4 1.0 CD A:GLU50 3.4 15.2 1.0 CD A:GLU130 3.4 12.7 1.0 NE2 A:GLN127 3.5 9.0 1.0 OE2 A:GLU50 3.6 16.4 1.0 O A:HOH215 3.8 13.7 1.0 CB A:GLU130 3.9 11.8 1.0 CE1 A:HIS46 3.9 9.4 1.0 NE2 A:HIS46 4.0 9.5 1.0 CG A:GLU130 4.2 11.8 1.0 OE2 A:GLU130 4.3 14.4 1.0 CG2 A:ILE97 4.4 11.3 1.0 CG A:GLU94 4.6 11.2 1.0 CG A:GLN127 4.7 11.4 1.0 CE1 A:HIS53 4.8 9.8 1.0 CG A:GLU50 4.8 12.7 1.0 CB A:ILE97 4.8 11.2 1.0 ND1 A:HIS53 5.0 10.4 1.0 CA A:GLN127 5.0 11.8 1.0

Iron binding site 3 out of 15 in the Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe170 b:62.1 occ:0.60 NE2 D:HIS149 3.0 26.4 1.0 NE2 A:HIS149 3.1 26.8 1.0 NE2 B:HIS149 3.3 25.4 1.0 CD2 D:HIS149 3.7 25.3 1.0 CD2 B:HIS149 3.7 24.9 1.0 CD2 A:HIS149 3.8 26.0 1.0 CD1 D:LEU153 3.8 15.1 1.0 CE1 D:HIS149 4.1 25.8 1.0 CD1 A:LEU153 4.1 13.9 1.0 CD1 B:LEU153 4.2 13.2 1.0 CE1 A:HIS149 4.2 26.5 1.0 CE1 B:HIS149 4.5 24.6 1.0 CD2 A:LEU153 4.6 13.0 1.0 CD2 B:LEU153 4.6 13.3 1.0 CD2 D:LEU153 4.6 14.0 1.0 CG D:LEU153 4.7 13.7 1.0 CG A:LEU153 4.8 12.3 1.0 CG B:LEU153 4.9 12.4 1.0 CG D:HIS149 4.9 24.3 1.0

Iron binding site 4 out of 15 in the Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe168 b:32.5 occ:0.50 OE2 B:GLU17 2.5 13.8 1.0 FE B:FE169 2.7 22.6 0.5 OE1 B:GLN127 3.0 10.3 1.0 OE1 B:GLU50 3.0 17.8 1.0 ND1 B:HIS53 3.1 15.4 1.0 CD B:GLU17 3.3 13.9 1.0 OE1 B:GLU17 3.3 15.6 1.0 O B:HOH202 3.5 19.7 1.0 OE1 B:GLU130 3.5 14.4 1.0 CD B:GLU50 3.5 16.5 1.0 OE2 B:GLU50 3.6 16.4 1.0 CE1 B:HIS53 3.6 14.4 1.0 CG2 B:ILE97 3.7 14.1 1.0 CD B:GLN127 4.0 12.0 1.0 CE1 B:TYR123 4.1 12.6 1.0 CG B:HIS53 4.3 13.6 1.0 OH B:TYR123 4.4 13.5 1.0 CD B:GLU130 4.5 14.6 1.0 CZ B:TYR123 4.7 12.9 1.0 OE2 B:GLU94 4.7 10.1 1.0 CG B:GLU50 4.8 14.4 1.0 CG B:GLU17 4.8 12.4 1.0 CB B:HIS53 4.8 12.3 1.0 NE2 B:GLN127 4.8 10.8 1.0 CG B:GLN127 4.8 13.0 1.0 OE2 B:GLU130 4.9 15.5 1.0 CB B:GLN127 4.9 14.2 1.0 CB B:ILE97 4.9 14.2 1.0 NE2 B:HIS53 4.9 15.7 1.0

Iron binding site 5 out of 15 in the Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe169 b:22.6 occ:0.50 OE1 B:GLU130 2.2 14.4 1.0 OE1 B:GLN127 2.3 10.3 1.0 OE2 B:GLU94 2.3 10.1 1.0 OE1 B:GLU50 2.4 17.8 1.0 FE B:FE168 2.7 32.5 0.5 CD B:GLU94 3.2 11.7 1.0 CD B:GLN127 3.3 12.0 1.0 CD B:GLU50 3.3 16.5 1.0 OE1 B:GLU94 3.4 12.1 1.0 CD B:GLU130 3.4 14.6 1.0 OE2 B:GLU50 3.5 16.4 1.0 NE2 B:GLN127 3.6 10.8 1.0 O B:HOH202 3.7 19.7 1.0 CB B:GLU130 3.8 13.8 1.0 CE1 B:HIS46 3.9 10.8 1.0 NE2 B:HIS46 4.0 10.5 1.0 CG B:GLU130 4.2 14.2 1.0 OE2 B:GLU130 4.4 15.5 1.0 CG2 B:ILE97 4.4 14.1 1.0 CG B:GLU94 4.6 11.6 1.0 CG B:GLN127 4.7 13.0 1.0 CG B:GLU50 4.7 14.4 1.0 CE1 B:HIS53 4.8 14.4 1.0 CB B:ILE97 4.9 14.2 1.0 ND1 B:HIS53 4.9 15.4 1.0 CA B:GLN127 4.9 14.6 1.0

Iron binding site 6 out of 15 in the Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe168 b:29.8 occ:0.50 FE C:FE169 2.6 20.6 0.5 OE1 C:GLN127 2.8 10.1 1.0 OE2 C:GLU17 2.8 14.2 1.0 ND1 C:HIS53 3.0 13.1 1.0 OE1 C:GLU50 3.3 16.2 1.0 CE1 C:HIS53 3.4 13.3 1.0 OE1 C:GLU130 3.4 13.2 1.0 OE1 C:GLU17 3.5 13.4 1.0 O C:HOH183 3.5 17.2 1.0 OE2 C:GLU50 3.5 15.8 1.0 CD C:GLU17 3.5 13.4 1.0 CD C:GLU50 3.7 15.5 1.0 CG2 C:ILE97 3.8 11.8 1.0 CD C:GLN127 3.9 10.8 1.0 CE1 C:TYR123 4.0 10.7 1.0 CG C:HIS53 4.2 11.6 1.0 CD C:GLU130 4.3 14.0 1.0 OH C:TYR123 4.4 9.8 1.0 NE2 C:HIS53 4.5 13.7 1.0 OE2 C:GLU130 4.6 14.2 1.0 OE2 C:GLU94 4.6 14.1 1.0 CZ C:TYR123 4.6 10.0 1.0 CB C:GLN127 4.7 11.7 1.0 CG C:GLN127 4.7 11.2 1.0 CB C:HIS53 4.8 9.9 1.0 NE2 C:GLN127 4.8 8.9 1.0 CB C:ILE97 4.9 12.1 1.0 CD1 C:TYR123 4.9 10.5 1.0 CD2 C:HIS53 5.0 12.0 1.0

Iron binding site 7 out of 15 in the Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe169 b:20.6 occ:0.50 OE2 C:GLU94 2.2 14.1 1.0 OE1 C:GLU130 2.3 13.2 1.0 OE1 C:GLN127 2.3 10.1 1.0 OE1 C:GLU50 2.5 16.2 1.0 FE C:FE168 2.6 29.8 0.5 CD C:GLU94 3.1 13.5 1.0 CD C:GLN127 3.3 10.8 1.0 OE1 C:GLU94 3.3 12.8 1.0 CD C:GLU50 3.4 15.5 1.0 CD C:GLU130 3.5 14.0 1.0 OE2 C:GLU50 3.6 15.8 1.0 O C:HOH183 3.6 17.2 1.0 NE2 C:GLN127 3.6 8.9 1.0 CB C:GLU130 3.9 13.8 1.0 CE1 C:HIS46 3.9 8.7 1.0 NE2 C:HIS46 4.1 8.2 1.0 CG C:GLU130 4.3 13.9 1.0 OE2 C:GLU130 4.4 14.2 1.0 CG2 C:ILE97 4.4 11.8 1.0 CG C:GLU94 4.5 13.4 1.0 CG C:GLN127 4.7 11.2 1.0 CE1 C:HIS53 4.7 13.3 1.0 CB C:ILE97 4.8 12.1 1.0 CG C:GLU50 4.9 13.3 1.0 ND1 C:HIS53 4.9 13.1 1.0 CG1 C:ILE97 4.9 11.2 1.0

Iron binding site 8 out of 15 in the Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe168 b:38.9 occ:0.50 FE D:FE169 2.7 24.4 0.5 OE2 D:GLU17 2.8 14.1 1.0 OE1 D:GLN127 2.9 12.7 1.0 ND1 D:HIS53 2.9 13.9 1.0 OE1 D:GLU50 3.3 17.9 1.0 CE1 D:HIS53 3.4 14.0 1.0 OE1 D:GLU130 3.4 14.6 1.0 OE1 D:GLU17 3.5 14.4 1.0 O D:HOH182 3.5 16.5 1.0 CD D:GLU17 3.5 13.4 1.0 OE2 D:GLU50 3.6 17.1 1.0 CD D:GLU50 3.8 17.0 1.0 CG2 D:ILE97 3.9 12.7 1.0 CD D:GLN127 3.9 12.1 1.0 CE1 D:TYR123 4.0 13.3 1.0 CG D:HIS53 4.1 12.7 1.0 CD D:GLU130 4.4 14.8 1.0 OH D:TYR123 4.4 14.3 1.0 NE2 D:HIS53 4.6 15.0 1.0 CB D:GLN127 4.6 13.5 1.0 CZ D:TYR123 4.6 13.8 1.0 CG D:GLN127 4.7 13.1 1.0 OE2 D:GLU130 4.7 16.2 1.0 CB D:HIS53 4.7 11.3 1.0 OE2 D:GLU94 4.8 13.2 1.0 NE2 D:GLN127 4.8 11.3 1.0 CD1 D:TYR123 4.9 12.9 1.0 CD2 D:HIS53 4.9 13.8 1.0 CG D:GLU17 5.0 12.2 1.0

Iron binding site 9 out of 15 in the Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe169 b:24.4 occ:0.50 OE1 D:GLU130 2.2 14.6 1.0 OE1 D:GLN127 2.3 12.7 1.0 OE2 D:GLU94 2.3 13.2 1.0 OE1 D:GLU50 2.6 17.9 1.0 FE D:FE168 2.7 38.9 0.5 CD D:GLU94 3.2 13.2 1.0 CD D:GLN127 3.3 12.1 1.0 OE1 D:GLU94 3.3 13.1 1.0 CD D:GLU50 3.4 17.0 1.0 CD D:GLU130 3.4 14.8 1.0 OE2 D:GLU50 3.6 17.1 1.0 NE2 D:GLN127 3.6 11.3 1.0 O D:HOH182 3.8 16.5 1.0 CE1 D:HIS46 3.8 9.4 1.0 CB D:GLU130 3.8 14.0 1.0 NE2 D:HIS46 4.0 9.0 1.0 CG D:GLU130 4.2 14.1 1.0 OE2 D:GLU130 4.4 16.2 1.0 CG2 D:ILE97 4.5 12.7 1.0 CG D:GLU94 4.6 12.5 1.0 CG D:GLN127 4.7 13.1 1.0 CE1 D:HIS53 4.7 14.0 1.0 CG D:GLU50 4.9 14.0 1.0 ND1 D:HIS53 4.9 13.9 1.0 CB D:ILE97 4.9 13.2 1.0 CA D:GLN127 5.0 13.8 1.0

Iron binding site 10 out of 15 in the Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structural Basis of Iron Transport Gating in Helicobacter Pylori Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe168 b:33.4 occ:0.50 FE E:FE169 2.6 16.8 0.5 OE2 E:GLU17 2.7 10.8 1.0 OE1 E:GLN127 2.8 10.6 1.0 ND1 E:HIS53 3.0 13.8 1.0 OE1 E:GLU50 3.2 13.1 1.0 OE1 E:GLU130 3.3 11.8 1.0 CE1 E:HIS53 3.4 14.4 1.0 O E:HOH198 3.4 18.0 1.0 OE1 E:GLU17 3.4 10.5 1.0 CD E:GLU17 3.5 10.4 1.0 OE2 E:GLU50 3.6 12.7 1.0 CD E:GLU50 3.7 12.6 1.0 CG2 E:ILE97 3.8 11.0 1.0 CD E:GLN127 3.9 10.2 1.0 CE1 E:TYR123 4.1 12.6 1.0 CD E:GLU130 4.2 12.8 1.0 CG E:HIS53 4.3 12.0 1.0 OH E:TYR123 4.6 12.0 1.0 OE2 E:GLU130 4.6 13.5 1.0 CB E:GLN127 4.6 12.0 1.0 OE2 E:GLU94 4.6 11.1 1.0 CG E:GLN127 4.6 10.8 1.0 NE2 E:HIS53 4.6 14.9 1.0 CZ E:TYR123 4.8 12.4 1.0 NE2 E:GLN127 4.8 9.3 1.0 CB E:ILE97 4.9 11.1 1.0 CB E:HIS53 4.9 9.8 1.0 CG E:GLU50 4.9 10.6 1.0 CG E:GLU17 5.0 8.8 1.0 CA E:GLN127 5.0 12.2 1.0 CD1 E:TYR123 5.0 12.5 1.0

K.J.Cho, H.J.Shin, J.H.Lee, K.J.Kim, S.S.Park, Y.Lee, C.Lee, S.S.Park, K.H.Kim. The Crystal Structure of Ferritin From Helicobacter Pylori Reveals Unusual Conformational Changes For Iron Uptake. J.Mol.Biol. V. 390 83 2009.
ISSN: ISSN 0022-2836
PubMed: 19427319
DOI: 10.1016/J.JMB.2009.04.078