Iron in PDB 6lp5: Structure of Sinonovacula Constricta Ferritin

All present enzymatic activity of Structure of Sinonovacula Constricta Ferritin:
1.16.3.1;

The structure of Structure of Sinonovacula Constricta Ferritin, PDB code: 6lp5 was solved by X.R.Su, T.H.Ming, C.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	109.26 / 1.98
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	154.510, 154.510, 129.500, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iron atom in the Structure of Sinonovacula Constricta Ferritin (pdb code 6lp5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 14 binding sites of Iron where determined in the Structure of Sinonovacula Constricta Ferritin, PDB code: 6lp5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 14 in the Structure of Sinonovacula Constricta Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Sinonovacula Constricta Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:0.7 occ:1.00 OD1 A:ASP129 3.0 29.7 1.0 O A:HOH447 4.2 41.5 1.0 CG A:ASP129 4.2 28.8 1.0 OE1 A:GLU132 4.4 29.9 1.0 OD2 A:ASP129 5.0 29.0 1.0

Iron binding site 2 out of 14 in the Structure of Sinonovacula Constricta Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Sinonovacula Constricta Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:26.1 occ:0.79 OE2 A:GLU60 1.9 25.8 1.0 OE1 A:GLU25 2.0 27.2 1.0 FE A:FE203 2.1 68.5 0.7 O A:HOH319 2.1 31.8 1.0 ND1 A:HIS63 2.3 19.8 0.5 CD A:GLU60 2.9 31.1 1.0 CD A:GLU25 3.0 29.0 1.0 ND1 A:HIS63 3.1 34.8 0.5 CE1 A:HIS63 3.2 20.5 0.5 OE1 A:GLU60 3.3 32.1 1.0 CG A:HIS63 3.4 19.9 0.5 OE2 A:GLU25 3.4 27.0 1.0 CB A:HIS63 3.7 25.1 0.5 CB A:HIS63 3.7 18.3 0.5 CG A:HIS63 3.7 31.1 0.5 OE1 A:GLN139 4.1 35.5 1.0 O A:HOH394 4.1 40.4 1.0 CE1 A:HIS63 4.1 34.6 0.5 CG A:GLU60 4.2 23.3 1.0 CA A:GLU60 4.2 21.3 1.0 CG1 A:VAL108 4.2 21.5 1.0 CG A:GLU25 4.3 25.1 1.0 NE2 A:HIS63 4.4 19.2 0.5 CB A:GLU60 4.4 21.7 1.0 CD2 A:HIS63 4.5 18.2 0.5 CB A:GLU25 4.6 22.6 1.0 O A:GLU60 4.8 21.2 1.0 O A:HOH311 4.9 51.8 1.0 CD2 A:HIS63 4.9 31.8 0.5

Iron binding site 3 out of 14 in the Structure of Sinonovacula Constricta Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Sinonovacula Constricta Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:68.5 occ:0.70 FE A:FE202 2.1 26.1 0.8 OE1 A:GLN139 2.5 35.5 1.0 OE1 A:GLU60 2.6 32.1 1.0 O A:HOH319 2.8 31.8 1.0 OE2 A:GLU60 2.8 25.8 1.0 CD A:GLU60 3.0 31.1 1.0 ND1 A:HIS63 3.4 19.8 0.5 CD A:GLN139 3.5 32.6 1.0 CE1 A:HIS63 3.5 20.5 0.5 OE1 A:GLU105 3.7 47.0 1.0 OE1 A:GLU138 3.8 28.7 0.5 O A:HOH394 3.8 40.4 1.0 NE2 A:GLN139 3.8 31.7 1.0 ND1 A:HIS63 3.9 34.8 0.5 OE1 A:GLU25 4.0 27.2 1.0 O A:HOH311 4.0 51.8 1.0 O A:HOH307 4.0 49.8 1.0 CG1 A:VAL108 4.0 21.5 1.0 OE2 A:GLU105 4.2 42.7 1.0 CD A:GLU105 4.3 37.4 1.0 O A:HOH388 4.4 58.2 1.0 CE1 A:HIS63 4.4 34.6 0.5 CG A:GLU60 4.5 23.3 1.0 CD A:GLU138 4.7 31.2 0.5 CG A:HIS63 4.7 19.9 0.5 CG A:GLN139 4.7 30.1 1.0 CD A:GLU25 4.8 29.0 1.0 CB A:VAL108 4.8 19.5 1.0 OE2 A:GLU25 4.8 27.0 1.0 OE2 A:GLU138 4.9 36.3 0.5 NE2 A:HIS63 4.9 19.2 0.5 CG A:HIS63 5.0 31.1 0.5

Iron binding site 4 out of 14 in the Structure of Sinonovacula Constricta Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Sinonovacula Constricta Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:27.2 occ:0.80 OE1 B:GLU60 1.9 28.6 1.0 O B:HOH306 2.0 37.3 1.0 OE1 B:GLU25 2.0 25.0 1.0 FE B:FE202 2.1 48.7 0.6 ND1 B:HIS63 2.1 15.1 0.5 CD B:GLU60 2.9 29.4 1.0 CE1 B:HIS63 3.0 15.3 0.5 CD B:GLU25 3.0 25.5 1.0 CD2 B:HIS63 3.1 36.5 0.5 CG B:HIS63 3.2 16.0 0.5 OE2 B:GLU60 3.3 36.8 1.0 OE2 B:GLU25 3.4 25.3 1.0 CB B:HIS63 3.6 17.2 0.5 CB B:HIS63 3.6 27.9 0.5 CG B:HIS63 3.6 31.7 0.5 O B:HOH332 4.0 33.1 1.0 OE1 B:GLN139 4.0 33.5 1.0 CG B:GLU60 4.1 23.3 1.0 CG1 B:VAL108 4.1 22.6 1.0 CA B:GLU60 4.2 21.5 1.0 NE2 B:HIS63 4.2 14.6 0.5 CD2 B:HIS63 4.3 15.4 0.5 NE2 B:HIS63 4.3 40.2 0.5 CG B:GLU25 4.4 22.8 1.0 CB B:GLU60 4.4 22.0 1.0 O B:GLU60 4.7 20.1 1.0 CB B:GLU25 4.8 21.2 1.0 O B:HOH311 4.9 64.3 1.0 O B:HOH388 4.9 58.9 1.0 CD B:GLN139 4.9 30.0 1.0 ND1 B:HIS63 4.9 36.5 0.5 C B:GLU60 5.0 19.6 1.0 N B:GLU60 5.0 19.4 1.0

Iron binding site 5 out of 14 in the Structure of Sinonovacula Constricta Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Sinonovacula Constricta Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:48.7 occ:0.60 FE B:FE201 2.1 27.2 0.8 O B:HOH306 2.6 37.3 1.0 O B:HOH332 2.6 33.1 1.0 OE2 B:GLU25 2.7 25.3 1.0 OE1 B:GLU25 3.0 25.0 1.0 ND1 B:HIS63 3.1 15.1 0.5 OE1 B:GLN139 3.2 33.5 1.0 CD B:GLU25 3.2 25.5 1.0 CD2 B:HIS63 3.3 36.5 0.5 CD1 B:LEU112 3.5 22.6 1.0 CG1 B:VAL108 3.6 22.6 1.0 CE1 B:HIS63 3.8 15.3 0.5 CD B:GLN139 3.9 30.0 1.0 CG B:HIS63 3.9 16.0 0.5 OE1 B:GLU60 3.9 28.6 1.0 CG B:HIS63 4.0 31.7 0.5 CD1 B:TYR135 4.1 28.8 1.0 CB B:HIS63 4.2 27.9 0.5 CB B:HIS63 4.2 17.2 0.5 NE2 B:HIS63 4.3 40.2 0.5 CG B:GLN139 4.4 31.4 1.0 CG B:LEU112 4.5 19.6 1.0 CD2 B:LEU112 4.6 20.0 1.0 OE1 B:GLU138 4.6 36.7 0.5 NE2 B:GLN139 4.7 31.6 1.0 CG B:GLU25 4.7 22.8 1.0 NE2 B:HIS63 4.8 14.6 0.5 CB B:TYR135 4.8 22.9 1.0 CD B:GLU60 4.8 29.4 1.0 CE1 B:TYR135 4.8 28.5 1.0 CD2 B:HIS63 4.9 15.4 0.5 CG B:TYR135 4.9 22.9 1.0 CB B:VAL108 4.9 22.1 1.0 OE2 B:GLU60 5.0 36.8 1.0

Iron binding site 6 out of 14 in the Structure of Sinonovacula Constricta Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Sinonovacula Constricta Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:25.7 occ:0.80 OE1 C:GLU60 1.9 28.1 1.0 OE1 C:GLU25 1.9 28.2 1.0 ND1 C:HIS63 2.1 22.7 0.8 O C:HOH339 2.1 32.2 1.0 FE C:FE202 2.2 71.4 0.7 CE1 C:HIS63 2.9 24.2 0.8 CD C:GLU60 2.9 27.3 1.0 CD C:GLU25 3.0 27.3 1.0 CG C:HIS63 3.2 23.7 0.8 ND1 C:HIS63 3.2 28.1 0.2 OE2 C:GLU60 3.3 33.8 1.0 OE2 C:GLU25 3.4 29.1 1.0 CB C:HIS63 3.6 23.8 0.2 CB C:HIS63 3.6 22.2 0.8 CG C:HIS63 3.7 26.4 0.2 OE1 C:GLN139 4.0 28.1 0.7 NE2 C:HIS63 4.1 27.8 0.8 O C:HOH375 4.1 35.9 1.0 CG1 C:VAL108 4.1 20.9 1.0 CA C:GLU60 4.2 20.6 1.0 CG C:GLU60 4.2 21.8 1.0 CD2 C:HIS63 4.2 24.4 0.8 CE1 C:HIS63 4.3 28.1 0.2 CG C:GLU25 4.3 24.9 1.0 CB C:GLU60 4.5 20.0 1.0 CB C:GLU25 4.6 19.3 1.0 O C:HOH362 4.7 60.8 1.0 O C:GLU60 4.7 22.0 1.0 O C:HOH352 4.8 53.3 1.0 CD C:GLN139 4.9 30.4 1.0 CD2 C:HIS63 4.9 27.5 0.2 C C:GLU60 5.0 19.4 1.0

Iron binding site 7 out of 14 in the Structure of Sinonovacula Constricta Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Sinonovacula Constricta Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:71.4 occ:0.70 FE C:FE201 2.2 25.7 0.8 OE1 C:GLN139 2.5 28.1 0.7 OE2 C:GLU60 2.6 33.8 1.0 O C:HOH362 2.7 60.8 1.0 O C:HOH339 2.9 32.2 1.0 OE1 C:GLU60 2.9 28.1 1.0 OE1 C:GLU105 3.0 39.1 1.0 CD C:GLU60 3.1 27.3 1.0 CD C:GLN139 3.3 30.4 1.0 CE1 C:HIS63 3.4 24.2 0.8 ND1 C:HIS63 3.4 22.7 0.8 NE2 C:GLN139 3.6 31.6 1.0 O C:HOH352 3.8 53.3 1.0 CD C:GLU105 3.9 37.2 1.0 OE1 C:GLU138 3.9 33.9 0.5 O C:HOH375 4.0 35.9 1.0 CG1 C:VAL108 4.0 20.9 1.0 OE2 C:GLU105 4.0 41.0 1.0 OE1 C:GLU25 4.0 28.2 1.0 ND1 C:HIS63 4.2 28.1 0.2 O C:HOH301 4.6 36.6 1.0 CB C:VAL108 4.6 21.2 1.0 CG C:GLU60 4.6 21.8 1.0 NE2 C:HIS63 4.7 27.8 0.8 CG C:GLN139 4.7 28.9 1.0 CE1 C:HIS63 4.7 28.1 0.2 CG C:HIS63 4.8 23.7 0.8 CD C:GLU138 4.8 35.3 0.5 OE2 C:GLU138 4.8 38.9 0.5 CD C:GLU25 4.9 27.3 1.0 CG2 C:VAL108 4.9 21.8 1.0 OE2 C:GLU25 5.0 29.1 1.0

Iron binding site 8 out of 14 in the Structure of Sinonovacula Constricta Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Sinonovacula Constricta Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:28.7 occ:0.90 OE1 D:GLU60 1.9 27.1 1.0 OE1 D:GLU25 2.0 26.7 1.0 ND1 D:HIS63 2.1 18.0 0.5 O D:HOH316 2.1 30.1 1.0 FE D:FE202 2.2 62.5 0.6 CD D:GLU60 2.9 27.3 1.0 CE1 D:HIS63 3.0 20.0 0.5 CD D:GLU25 3.0 27.1 1.0 CG D:HIS63 3.1 18.2 0.5 OE2 D:GLU60 3.3 28.3 1.0 OE2 D:GLU25 3.4 24.3 1.0 CB D:HIS63 3.5 16.7 0.5 CB D:HIS63 3.8 26.6 0.5 OE1 D:GLN139 4.0 36.4 1.0 O D:HOH340 4.0 31.9 1.0 CG1 D:VAL108 4.1 21.6 1.0 NE2 D:HIS63 4.1 19.4 0.5 CA D:GLU60 4.2 21.8 1.0 CG D:GLU60 4.2 23.5 1.0 CD2 D:HIS63 4.2 18.2 0.5 CG D:HIS63 4.2 28.6 0.5 CG D:GLU25 4.3 24.9 1.0 O D:HOH318 4.4 58.3 1.0 CB D:GLU60 4.5 22.3 1.0 CB D:GLU25 4.6 22.0 1.0 ND1 D:HIS63 4.7 30.3 0.5 O D:GLU60 4.7 21.8 1.0 CD2 D:HIS63 4.8 31.9 0.5 C D:GLU60 5.0 18.6 1.0 CD D:GLN139 5.0 32.6 1.0 CA D:GLU25 5.0 19.8 1.0

Iron binding site 9 out of 14 in the Structure of Sinonovacula Constricta Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Sinonovacula Constricta Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe202 b:62.5 occ:0.62 FE D:FE201 2.2 28.7 0.9 OE1 D:GLN139 2.3 36.4 1.0 OE2 D:GLU60 2.7 28.3 1.0 O D:HOH316 2.8 30.1 1.0 OE1 D:GLU60 2.9 27.1 1.0 O D:HOH318 2.9 58.3 1.0 CD D:GLU60 3.2 27.3 1.0 CD D:GLN139 3.3 32.6 1.0 OE1 D:GLU105 3.3 38.9 1.0 ND1 D:HIS63 3.3 18.0 0.5 CE1 D:HIS63 3.4 20.0 0.5 NE2 D:GLN139 3.6 33.2 1.0 O D:HOH340 3.6 31.9 1.0 CG1 D:VAL108 3.8 21.6 1.0 OE1 D:GLU25 4.0 26.7 1.0 OE2 D:GLU105 4.1 39.5 1.0 CD D:GLU105 4.1 36.7 1.0 OE2 D:GLU138 4.2 39.2 0.5 CB D:VAL108 4.6 20.5 1.0 CG D:GLN139 4.6 28.8 1.0 O D:HOH319 4.6 48.1 1.0 CG D:GLU60 4.6 23.5 1.0 CG D:HIS63 4.7 18.2 0.5 NE2 D:HIS63 4.7 19.4 0.5 OE2 D:GLU25 4.8 24.3 1.0 CD D:GLU25 4.8 27.1 1.0

Iron binding site 10 out of 14 in the Structure of Sinonovacula Constricta Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Sinonovacula Constricta Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe201 b:28.3 occ:0.83 OE2 E:GLU60 2.0 28.5 1.0 OE1 E:GLU25 2.0 26.4 1.0 ND1 E:HIS63 2.1 20.1 0.5 O E:HOH392 2.2 34.7 1.0 FE E:FE202 2.3 61.1 0.7 CD E:GLU60 2.9 30.0 1.0 CE1 E:HIS63 3.0 21.1 0.5 CD E:GLU25 3.0 28.2 1.0 CD2 E:HIS63 3.1 40.1 0.5 CG E:HIS63 3.2 20.6 0.5 OE1 E:GLU60 3.3 33.6 1.0 OE2 E:GLU25 3.5 28.3 1.0 CB E:HIS63 3.6 20.4 0.5 CB E:HIS63 3.6 29.3 0.5 CG E:HIS63 3.6 35.0 0.5 CG1 E:VAL108 4.0 21.2 1.0 OE1 E:GLN139 4.0 31.5 1.0 O E:HOH385 4.1 33.5 1.0 NE2 E:HIS63 4.1 22.1 0.5 CA E:GLU60 4.2 21.8 1.0 CG E:GLU60 4.2 25.1 1.0 CD2 E:HIS63 4.3 21.9 0.5 NE2 E:HIS63 4.3 42.3 0.5 CG E:GLU25 4.3 27.1 1.0 CB E:GLU60 4.5 21.6 1.0 CB E:GLU25 4.6 22.6 1.0 O E:GLU60 4.7 21.0 1.0 ND1 E:HIS63 5.0 38.7 0.5 CD E:GLN139 5.0 28.0 1.0

C.Su, T.Ming, Y.Wu, Q.Jiang, H.Huan, C.Lu, J.Zhou, Y.Li, H.Song, X.Su. Crystallographic Characterization of Ferritin From Sinonovacula Constricta. Biochem.Biophys.Res.Commun. V. 524 217 2020.
ISSN: ESSN 1090-2104
PubMed: 31983429
DOI: 10.1016/J.BBRC.2020.01.069