Iron in PDB 6lpd: Phascolosoma Esculenta

The structure of Phascolosoma Esculenta, PDB code: 6lpd was solved by X.R.Su, T.H.Ming, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	108.65 / 1.65
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	153.005, 153.491, 153.818, 90, 90, 90
R / Rfree (%)	10.8 / 15.3

Pages:

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

Binding sites:

The binding sites of Iron atom in the Phascolosoma Esculenta (pdb code 6lpd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 14 binding sites of Iron where determined in the Phascolosoma Esculenta, PDB code: 6lpd:
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 Phascolosoma Esculenta


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Phascolosoma Esculenta within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:27.9 occ:0.60 O A:HOH383 1.9 42.6 1.0 OE1 A:GLU25 2.0 15.5 0.6 ND1 A:HIS63 2.0 23.3 0.5 OE1 A:GLU25 2.2 24.5 0.4 OE1 A:GLU60 2.4 26.9 0.8 O A:HOH301 2.4 48.2 1.0 OE2 A:GLU60 2.5 40.2 1.0 CD A:GLU60 2.7 21.6 0.8 CE1 A:HIS63 3.0 25.2 0.5 CD A:GLU25 3.0 15.4 0.6 CG A:HIS63 3.1 21.1 0.5 CD A:GLU25 3.2 21.6 0.4 O A:HOH329 3.3 40.1 0.8 OE2 A:GLU25 3.4 13.6 0.6 OE2 A:GLU25 3.4 32.2 0.4 CB A:HIS63 3.5 16.6 0.5 CB A:HIS63 3.8 11.2 0.5 O A:HOH413 4.0 26.2 1.0 CG A:HIS63 4.0 14.4 0.5 CG1 A:VAL108 4.0 17.9 1.0 CG A:GLU60 4.1 16.4 1.0 NE2 A:HIS63 4.1 22.3 0.5 CD2 A:HIS63 4.1 21.3 0.5 OE1 A:GLN139 4.2 20.6 1.0 FE A:FE2202 4.3 60.4 0.6 O A:HOH341 4.3 31.2 1.0 CA A:GLU60 4.4 11.5 1.0 CG A:GLU25 4.4 15.9 0.6 ND1 A:HIS63 4.5 20.4 0.5 CG A:GLU25 4.5 20.3 0.4 CD2 A:HIS63 4.6 17.6 0.5 CB A:GLU60 4.6 12.6 1.0 CB A:GLU25 4.7 13.2 0.6 O A:GLU60 4.9 13.8 1.0 CB A:GLU25 5.0 15.1 0.4 CD A:GLN139 5.0 20.6 1.0

Iron binding site 2 out of 14 in the Phascolosoma Esculenta


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Phascolosoma Esculenta within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:60.4 occ:0.60 O A:HOH301 2.0 48.2 1.0 O A:HOH302 2.1 43.4 1.0 O A:HOH438 2.3 40.9 1.0 O A:HOH329 2.4 40.1 0.8 OE1 A:GLU105 2.8 22.7 1.0 OE2 A:GLU60 3.1 40.2 1.0 OE2 A:GLU105 3.3 24.9 1.0 CD A:GLU105 3.5 18.9 1.0 OE1 A:GLN139 3.5 20.6 1.0 CE1 A:HIS63 3.9 25.2 0.5 O A:HOH341 3.9 31.2 1.0 OG A:SER142 3.9 14.2 0.4 OG A:SER142 4.0 6.2 0.1 CD A:GLU60 4.1 21.6 0.8 OG A:SER142 4.2 8.3 0.1 FE A:FE2201 4.3 27.9 0.6 CD A:GLN139 4.3 20.6 1.0 CB A:SER142 4.3 18.8 0.6 NE2 A:GLN139 4.3 25.1 1.0 ND1 A:HIS63 4.5 23.3 0.5 CB A:SER142 4.5 11.9 0.3 CB A:SER142 4.7 10.2 0.1 CG A:GLU60 4.7 16.4 1.0 O A:HOH413 4.7 26.2 1.0 NE2 A:HIS63 4.8 22.3 0.5 CG A:GLU105 4.9 16.5 1.0 OE1 A:GLU59 4.9 32.8 1.0 O A:HOH383 5.0 42.6 1.0

Iron binding site 3 out of 14 in the Phascolosoma Esculenta


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Phascolosoma Esculenta within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:29.5 occ:0.60 OD1 E:ASP129 2.4 13.8 0.4 OD1 B:ASP129 2.6 19.6 0.5 OE1 C:GLU132 2.8 27.9 1.0 OE2 B:GLU132 2.8 26.4 1.0 OE1 E:GLU132 2.8 27.5 1.0 OD1 C:ASP129 2.9 9.6 0.3 CG E:ASP129 3.6 13.0 0.4 CG B:ASP129 3.9 18.0 0.5 CD C:GLU132 4.0 18.5 1.0 CD B:GLU132 4.0 17.8 1.0 CD E:GLU132 4.0 17.7 1.0 OD1 C:ASP129 4.1 25.7 0.7 CG C:ASP129 4.1 10.6 0.3 O E:HOH396 4.1 40.2 1.0 OD1 E:ASP129 4.2 22.7 0.6 OD1 B:ASP129 4.2 18.1 0.5 OD2 E:ASP129 4.4 14.6 0.4 CB E:ASP129 4.4 12.8 0.4 O C:HOH465 4.6 30.0 1.0 OE1 B:GLU132 4.6 21.8 1.0 OE2 C:GLU132 4.6 20.3 1.0 OE2 E:GLU132 4.6 22.0 1.0 OD2 B:ASP129 4.7 19.2 0.5 CB E:ASP129 4.7 16.2 0.6 CB C:ASP129 4.8 10.0 0.3 CB C:ASP129 4.8 18.0 0.7 CB B:ASP129 4.8 13.9 0.5 CB B:ASP129 4.8 13.4 0.5 CA C:ASP129 4.8 12.2 0.3 CA C:ASP129 4.8 16.2 0.7 CA B:ASP129 4.8 14.6 0.5 CA B:ASP129 4.8 16.2 0.5 CA E:ASP129 4.8 14.4 0.4 CA E:ASP129 4.9 16.1 0.6 CG C:ASP129 4.9 20.6 0.7 CG E:ASP129 4.9 16.5 0.6 CG B:ASP129 4.9 13.5 0.5 CB C:GLU132 5.0 17.8 1.0 CB B:GLU132 5.0 18.3 1.0 OD2 C:ASP129 5.0 11.0 0.3

Iron binding site 4 out of 14 in the Phascolosoma Esculenta


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Phascolosoma Esculenta within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:28.4 occ:0.60 OE1 B:GLU25 1.9 21.6 1.0 O B:HOH471 2.0 43.6 1.0 OE2 B:GLU60 2.0 23.4 0.7 O B:HOH401 2.2 47.1 1.0 ND1 B:HIS63 2.3 28.8 0.5 OE2 B:GLU60 2.3 10.7 0.3 OE1 B:GLU60 2.4 15.0 0.3 CD B:GLU60 2.5 12.9 0.3 CD B:GLU25 3.0 23.9 1.0 CD B:GLU60 3.1 22.8 0.7 CE1 B:HIS63 3.2 30.7 0.5 O B:HOH412 3.2 32.3 0.7 CG B:HIS63 3.3 19.2 0.5 OE2 B:GLU25 3.4 22.9 1.0 OE1 B:GLU60 3.5 37.9 0.7 CB B:HIS63 3.7 15.9 0.5 CG B:GLU60 3.8 10.8 0.3 CB B:HIS63 3.8 11.7 0.5 CG1 B:VAL108 4.0 16.8 1.0 CG B:HIS63 4.1 13.8 0.5 O B:HOH516 4.1 26.0 1.0 O B:HOH409 4.2 30.4 1.0 FE B:FE2303 4.2 59.8 0.6 CG B:GLU25 4.3 25.6 1.0 OE1 B:GLN139 4.3 20.6 1.0 CA B:GLU60 4.3 10.5 0.3 CA B:GLU60 4.3 11.8 0.7 NE2 B:HIS63 4.3 33.9 0.5 CG B:GLU60 4.4 18.8 0.7 ND1 B:HIS63 4.4 14.8 0.5 CD2 B:HIS63 4.4 25.1 0.5 CB B:GLU60 4.5 10.6 0.3 CB B:GLU60 4.6 14.5 0.7 CB B:GLU25 4.6 16.1 1.0 CD2 B:HIS63 4.6 16.7 0.5 O B:GLU60 4.9 14.5 0.7 O B:GLU60 4.9 8.2 0.3

Iron binding site 5 out of 14 in the Phascolosoma Esculenta


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Phascolosoma Esculenta within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:59.8 occ:0.60 O B:HOH405 2.1 40.9 1.0 O B:HOH493 2.3 40.8 1.0 O B:HOH401 2.4 47.1 1.0 O B:HOH412 2.5 32.3 0.7 OE1 B:GLU60 2.5 37.9 0.7 OE1 B:GLU105 2.8 22.7 1.0 OE2 B:GLU105 3.2 24.4 1.0 OE1 B:GLU60 3.4 15.0 0.3 CD B:GLU105 3.5 18.6 1.0 OE1 B:GLN139 3.6 20.6 1.0 CD B:GLU60 3.6 22.8 0.7 O B:HOH409 3.8 30.4 1.0 OE2 B:GLU60 4.0 23.4 0.7 CE1 B:HIS63 4.0 30.7 0.5 OG B:SER142 4.1 21.1 0.6 FE B:FE2302 4.2 28.4 0.6 CD B:GLU60 4.3 12.9 0.3 CD B:GLN139 4.3 19.8 1.0 NE2 B:GLN139 4.4 25.3 1.0 ND1 B:HIS63 4.5 28.8 0.5 CB B:SER142 4.6 20.5 1.0 CG B:GLU60 4.6 10.8 0.3 O B:HOH516 4.7 26.0 1.0 CG B:GLU60 4.8 18.8 0.7 OE1 B:GLU59 4.9 32.9 1.0 CG B:GLU105 4.9 16.3 1.0

Iron binding site 6 out of 14 in the Phascolosoma Esculenta


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Phascolosoma Esculenta within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:28.9 occ:0.60 OE1 C:GLU25 2.0 21.1 1.0 O C:HOH351 2.0 42.3 1.0 OE1 C:GLU60 2.1 14.1 0.4 ND1 C:HIS63 2.1 26.5 0.5 O C:HOH302 2.2 47.0 1.0 OE1 C:GLU60 2.3 25.4 0.6 OE2 C:GLU60 2.4 21.1 0.6 CD C:GLU60 2.5 18.5 0.6 CE1 C:HIS63 3.0 32.2 0.5 CD C:GLU25 3.0 24.6 1.0 CG C:HIS63 3.2 22.3 0.5 CD C:GLU60 3.2 15.6 0.4 O C:HOH388 3.4 45.5 1.0 OE2 C:GLU25 3.4 22.5 1.0 CB C:HIS63 3.6 15.9 0.5 OE2 C:GLU60 3.6 21.3 0.4 CG C:GLU60 3.8 15.0 0.6 CB C:HIS63 3.9 11.1 0.5 O C:HOH422 4.0 26.9 1.0 CG1 C:VAL108 4.0 16.4 1.0 NE2 C:HIS63 4.1 29.1 0.5 CG C:HIS63 4.1 14.9 0.5 O C:HOH313 4.1 32.0 1.0 FE C:FE2202 4.1 58.7 0.6 CD2 C:HIS63 4.2 25.6 0.5 OE1 C:GLN139 4.2 21.0 1.0 CA C:GLU60 4.3 11.2 0.6 CG C:GLU25 4.3 26.9 1.0 CA C:GLU60 4.3 12.5 0.4 CB C:GLU60 4.4 11.9 0.6 CG C:GLU60 4.5 17.2 0.4 ND1 C:HIS63 4.5 22.3 0.5 CB C:GLU25 4.7 16.1 1.0 CB C:GLU60 4.7 13.2 0.4 CD2 C:HIS63 4.7 18.4 0.5 O C:GLU60 4.9 13.9 0.4 O C:GLU60 4.9 13.6 0.6

Iron binding site 7 out of 14 in the Phascolosoma Esculenta


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Phascolosoma Esculenta within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:58.7 occ:0.60 O C:HOH303 2.2 38.0 1.0 O C:HOH302 2.3 47.0 1.0 O C:HOH327 2.3 44.5 1.0 O C:HOH388 2.4 45.5 1.0 OE2 C:GLU60 2.5 21.3 0.4 OE1 C:GLU105 2.8 23.3 1.0 OE2 C:GLU60 3.2 21.1 0.6 OE2 C:GLU105 3.3 25.2 1.0 OE1 C:GLN139 3.4 21.0 1.0 CD C:GLU105 3.4 20.9 1.0 CD C:GLU60 3.6 15.6 0.4 O C:HOH313 3.8 32.0 1.0 OE1 C:GLU60 3.9 14.1 0.4 CE1 C:HIS63 3.9 32.2 0.5 OG C:SER142 4.1 26.4 0.7 OG C:SER142 4.1 5.8 0.2 FE C:FE2201 4.1 28.9 0.6 CD C:GLU60 4.2 18.5 0.6 CD C:GLN139 4.3 20.8 1.0 NE2 C:GLN139 4.4 23.4 1.0 CB C:SER142 4.5 24.5 0.7 ND1 C:HIS63 4.5 26.5 0.5 CG C:GLU60 4.6 15.0 0.6 CB C:SER142 4.6 11.1 0.3 O C:HOH422 4.7 26.9 1.0 NE2 C:HIS63 4.9 29.1 0.5 CG C:GLU60 4.9 17.2 0.4 CG C:GLU105 4.9 18.0 1.0 OE1 C:GLU59 4.9 29.7 0.8

Iron binding site 8 out of 14 in the Phascolosoma Esculenta


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Phascolosoma Esculenta within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:28.9 occ:0.60 OE1 D:GLU25 2.0 22.0 1.0 O D:HOH400 2.0 43.0 1.0 OE2 D:GLU60 2.1 11.0 0.3 ND1 D:HIS63 2.2 26.2 0.5 OE2 D:GLU60 2.2 26.6 0.7 OE1 D:GLU60 2.3 27.1 0.7 O D:HOH302 2.3 46.4 1.0 CD D:GLU60 2.5 21.2 0.7 CD D:GLU25 3.0 24.4 1.0 CE1 D:HIS63 3.2 19.6 0.4 CD D:GLU60 3.2 13.1 0.3 CG D:HIS63 3.2 20.8 0.5 OE2 D:GLU25 3.5 22.9 1.0 O D:HOH330 3.5 40.0 0.8 CB D:HIS63 3.6 16.8 0.5 OE1 D:GLU60 3.6 16.5 0.3 CG D:GLU60 3.8 15.3 0.7 CB D:HIS63 3.9 11.4 0.5 CG1 D:VAL108 4.0 18.6 1.0 O D:HOH422 4.1 26.0 1.0 CG D:HIS63 4.1 13.6 0.5 O D:HOH320 4.1 30.9 1.0 FE D:FE2202 4.2 67.9 0.7 OE1 D:GLN139 4.3 21.9 1.0 NE2 D:HIS63 4.3 28.3 0.5 CA D:GLU60 4.3 13.3 0.3 CD2 D:HIS63 4.3 23.7 0.5 CG D:GLU25 4.3 26.8 1.0 CA D:GLU60 4.4 12.6 0.7 ND1 D:HIS63 4.5 16.9 0.5 CB D:GLU60 4.5 12.6 0.7 CG D:GLU60 4.5 13.3 0.3 CB D:GLU60 4.6 12.7 0.3 CB D:GLU25 4.6 16.0 1.0 CD2 D:HIS63 4.7 15.5 0.5 O D:GLU60 4.9 13.6 0.3 O D:GLU60 4.9 13.8 0.7

Iron binding site 9 out of 14 in the Phascolosoma Esculenta


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Phascolosoma Esculenta within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe202 b:67.9 occ:0.70 O D:HOH302 2.2 46.4 1.0 O D:HOH303 2.2 40.7 1.0 O D:HOH341 2.3 39.2 1.0 O D:HOH330 2.4 40.0 0.8 OE1 D:GLU60 2.5 16.5 0.3 OE1 D:GLU105 2.8 24.6 1.0 OE2 D:GLU105 3.2 23.8 1.0 OE2 D:GLU60 3.3 26.6 0.7 CD D:GLU105 3.5 18.5 1.0 OE1 D:GLN139 3.5 21.9 1.0 CD D:GLU60 3.6 13.1 0.3 O D:HOH320 3.8 30.9 1.0 OE2 D:GLU60 3.9 11.0 0.3 OG D:SER142 4.0 15.0 0.4 CE1 D:HIS63 4.0 19.6 0.4 OG D:SER142 4.0 6.9 0.2 CD D:GLU60 4.2 21.2 0.7 FE D:FE2201 4.2 28.9 0.6 CD D:GLN139 4.3 20.1 1.0 OG D:SER142 4.3 22.0 0.4 NE2 D:GLN139 4.4 22.5 1.0 CB D:SER142 4.4 15.8 0.4 ND1 D:HIS63 4.4 26.2 0.5 CG D:GLU60 4.6 15.3 0.7 CB D:SER142 4.6 17.0 0.4 CB D:SER142 4.6 9.9 0.2 O D:HOH422 4.8 26.0 1.0 CG D:GLU60 4.8 13.3 0.3 OE1 D:GLU59 4.9 33.2 1.0 CG D:GLU105 4.9 16.4 1.0

Iron binding site 10 out of 14 in the Phascolosoma Esculenta


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Phascolosoma Esculenta within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe201 b:30.0 occ:0.60 OE1 E:GLU25 2.0 21.9 1.0 ND1 E:HIS63 2.0 24.9 0.5 O E:HOH369 2.0 44.0 1.0 OE2 E:GLU60 2.1 17.4 0.4 OE2 E:GLU60 2.3 23.4 0.6 OE1 E:GLU60 2.3 16.4 0.4 CD E:GLU60 2.4 16.9 0.6 O E:HOH304 2.6 51.4 1.0 CE1 E:HIS63 3.0 26.9 0.5 CD E:GLU25 3.0 21.5 1.0 CG E:HIS63 3.1 18.7 0.5 O E:HOH306 3.1 32.0 0.6 CD E:GLU60 3.2 16.4 0.4 OE2 E:GLU25 3.5 21.7 1.0 CB E:HIS63 3.5 15.0 0.5 OE1 E:GLU60 3.5 21.3 0.4 CG E:GLU60 3.8 14.2 0.6 CG1 E:VAL108 4.0 19.3 1.0 CB E:HIS63 4.0 11.7 0.5 NE2 E:HIS63 4.1 21.9 0.5 O E:HOH402 4.1 27.6 1.0 CD2 E:HIS63 4.1 23.6 0.5 O E:HOH313 4.2 31.2 1.0 CG E:HIS63 4.2 14.3 0.5 OE1 E:GLN139 4.2 21.3 1.0 FE E:FE2202 4.3 66.0 0.6 CA E:GLU60 4.3 12.0 0.4 CA E:GLU60 4.3 10.4 0.6 CG E:GLU25 4.3 25.5 1.0 CG E:GLU60 4.5 15.1 0.4 CB E:GLU60 4.5 13.1 0.6 ND1 E:HIS63 4.5 21.4 0.5 CB E:GLU60 4.6 14.5 0.4 CB E:GLU25 4.6 17.0 1.0 CD2 E:HIS63 4.7 17.6 0.5 O E:GLU60 4.9 12.6 0.4 O E:GLU60 4.9 12.4 0.6

X.R.Su, T.H.Ming. Crystallographic Analysis of One Novel Ferritins From Phascolosoma Esculenta (FER147) at A Resolution of 1.65 Angstroms. To Be Published.