Iron in PDB 7y74: Apostichopus Japonicus Ferritin Mutant-D129A/E132A

All present enzymatic activity of Apostichopus Japonicus Ferritin Mutant-D129A/E132A:
1.16.3.1;

The structure of Apostichopus Japonicus Ferritin Mutant-D129A/E132A, PDB code: 7y74 was solved by Y.Wu, T.H.Ming, X.R.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.91 / 1.98
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	192.83, 130.95, 122.62, 90, 119.4, 90
R / Rfree (%)	17.6 / 22

The structure of Apostichopus Japonicus Ferritin Mutant-D129A/E132A also contains other interesting chemical elements:

Cadmium

(Cd)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Iron atom in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A (pdb code 7y74). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 36 binding sites of Iron where determined in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A, PDB code: 7y74:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 36 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:23.8 occ:1.00 OE2 A:GLU60 2.3 31.6 1.0 OE2 A:GLU105 2.3 27.2 1.0 OE1 A:GLU105 2.4 32.9 1.0 O A:HOH392 2.4 22.3 1.0 CD A:GLU105 2.6 33.5 1.0 CD A:GLU60 3.2 27.3 1.0 FE A:FE203 3.5 30.0 1.0 OE1 A:GLU60 3.6 33.8 1.0 NE2 A:GLN139 3.7 53.4 1.0 O A:HOH311 3.8 42.6 1.0 OE1 A:GLU138 4.1 45.0 1.0 CG A:GLU105 4.2 29.2 1.0 CD A:GLN139 4.5 39.1 1.0 OE1 A:GLN139 4.5 47.3 1.0 CG A:GLU60 4.5 25.8 1.0 CE1 A:HIS63 4.5 31.2 1.0 CB A:ALA142 4.6 27.4 1.0 CE2 A:TYR32 4.6 27.8 1.0 ND1 A:HIS63 4.6 26.9 1.0 OH A:TYR32 4.6 29.0 1.0 NE2 A:GLN56 4.9 45.9 1.0 CB A:GLU105 5.0 28.3 1.0

Iron binding site 2 out of 36 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:26.0 occ:1.00 O A:HOH421 2.3 19.6 1.0 NE2 A:HIS50 2.4 24.9 1.0 CD2 A:HIS50 3.2 25.6 1.0 CE1 A:HIS50 3.5 24.9 1.0 CG A:HIS50 4.4 23.1 1.0 OD1 A:ASP40 4.5 30.9 1.0 ND1 A:HIS50 4.6 22.7 1.0 O A:HOH434 4.6 29.5 1.0 CD A:LYS54 4.7 29.2 1.0 CD I:LYS69 4.9 33.1 1.0 CG A:ASP40 4.9 27.8 1.0 NZ I:LYS69 4.9 41.6 1.0 CE1 A:PHE37 4.9 20.3 1.0 CZ A:PHE37 5.0 23.8 1.0

Iron binding site 3 out of 36 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:30.0 occ:1.00 OE1 A:GLU25 2.2 25.5 1.0 OE1 A:GLU60 2.3 33.8 1.0 ND1 A:HIS63 2.3 26.9 1.0 O A:HOH392 2.4 22.3 1.0 CD A:GLU25 3.1 25.5 1.0 CD A:GLU60 3.2 27.3 1.0 CE1 A:HIS63 3.2 31.2 1.0 OE2 A:GLU25 3.3 25.5 1.0 NE2 A:GLN139 3.3 53.4 1.0 OE2 A:GLU60 3.4 31.6 1.0 CG A:HIS63 3.4 26.8 1.0 FE A:FE201 3.5 23.8 1.0 CB A:HIS63 3.8 23.0 1.0 CG1 A:VAL108 4.3 25.4 1.0 NE2 A:HIS63 4.4 32.0 1.0 CG A:GLU25 4.5 23.2 1.0 CD2 A:HIS63 4.5 29.0 1.0 CG A:GLU60 4.6 25.8 1.0 CD A:GLN139 4.6 39.1 1.0 CA A:GLU60 4.8 24.4 1.0 OE1 A:GLU138 5.0 45.0 1.0 CB A:GLU25 5.0 23.8 1.0

Iron binding site 4 out of 36 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:12.4 occ:1.00 OE1 B:GLU60 2.2 30.0 1.0 OE1 B:GLU25 2.3 22.4 1.0 ND1 B:HIS63 2.4 28.2 1.0 O B:HOH346 2.4 17.8 1.0 CD B:GLU60 3.1 30.0 1.0 CD B:GLU25 3.1 22.8 1.0 OE2 B:GLU60 3.2 30.0 1.0 CE1 B:HIS63 3.3 31.2 1.0 CG B:HIS63 3.4 27.7 1.0 OE2 B:GLU25 3.4 26.2 1.0 FE B:FE202 3.5 22.4 1.0 CB B:HIS63 3.6 23.4 1.0 NE2 B:GLN139 4.1 31.8 1.0 CG1 B:VAL108 4.4 23.3 1.0 NE2 B:HIS63 4.4 29.5 1.0 CG B:GLU60 4.5 30.0 1.0 CD2 B:HIS63 4.5 27.5 1.0 CG B:GLU25 4.5 22.3 1.0 CA B:GLU60 4.7 22.9 1.0 OE1 B:GLU138 4.7 67.0 1.0 CB B:GLU60 4.8 30.0 1.0 CB B:GLU25 5.0 21.7 1.0

Iron binding site 5 out of 36 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:22.4 occ:1.00 OE2 B:GLU60 2.3 30.0 1.0 OE2 B:GLU105 2.3 31.5 1.0 OE1 B:GLU105 2.3 27.7 1.0 O B:HOH346 2.5 17.8 1.0 CD B:GLU105 2.6 28.8 1.0 CD B:GLU60 3.2 30.0 1.0 FE B:FE201 3.5 12.4 1.0 OE1 B:GLU60 3.5 30.0 1.0 O B:HOH319 3.9 36.9 1.0 OE1 B:GLN139 4.1 37.2 1.0 CG B:GLU105 4.1 26.4 1.0 NE2 B:GLN139 4.3 31.8 1.0 O B:HOH387 4.4 31.9 1.0 OE1 B:GLU138 4.4 67.0 1.0 CG B:GLU60 4.4 30.0 1.0 CE1 B:HIS63 4.6 31.2 1.0 CD B:GLN139 4.6 31.9 1.0 CE2 B:TYR32 4.6 26.8 1.0 ND1 B:HIS63 4.6 28.2 1.0 CB B:ALA142 4.7 21.7 1.0 OH B:TYR32 4.7 27.3 1.0 OE1 B:GLN56 4.8 58.8 1.0 OE2 B:GLU138 4.9 64.3 1.0 CB B:GLU105 5.0 23.9 1.0

Iron binding site 6 out of 36 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe203 b:25.3 occ:1.00 O B:HOH421 2.4 20.8 1.0 NE2 B:HIS50 2.4 29.6 1.0 CD2 B:HIS50 3.3 28.4 1.0 CE1 B:HIS50 3.4 28.7 1.0 NZ B:LYS54 4.2 41.3 1.0 OD1 B:ASP40 4.4 30.3 1.0 CG B:HIS50 4.5 23.4 1.0 ND1 B:HIS50 4.5 24.9 1.0 CD B:LYS54 4.5 33.9 1.0 CE1 B:PHE37 4.8 24.6 1.0 O B:HOH446 4.8 37.1 1.0 CG B:ASP40 4.9 29.5 1.0 CZ B:PHE37 4.9 25.6 1.0 CE B:LYS54 5.0 37.4 1.0

Iron binding site 7 out of 36 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:30.4 occ:1.00 O C:HOH405 2.3 27.4 1.0 CE1 C:HIS50 2.4 27.5 1.0 NZ C:LYS54 2.4 34.4 1.0 ND1 C:HIS50 3.3 30.7 1.0 NE2 C:HIS50 3.4 27.9 1.0 CE C:LYS54 3.6 37.7 1.0 CG C:HIS50 4.5 22.9 1.0 CD C:LYS54 4.6 35.0 1.0 CD2 C:HIS50 4.6 21.9 1.0 OD1 C:ASP40 4.6 31.6 1.0 CD H:LYS69 4.7 30.5 1.0 CE1 C:PHE37 4.9 22.5 1.0 CG C:ASP40 5.0 27.6 1.0 CZ C:PHE37 5.0 25.0 1.0

Iron binding site 8 out of 36 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:30.0 occ:1.00 O C:HOH307 2.2 25.4 1.0 OE1 C:GLU25 2.4 25.8 1.0 OE1 C:GLU60 2.4 30.0 1.0 ND1 C:HIS63 2.5 30.0 1.0 CD C:GLU25 3.2 23.7 1.0 CD C:GLU60 3.3 30.0 1.0 OE2 C:GLU25 3.3 24.6 1.0 CE1 C:HIS63 3.4 30.0 1.0 OE2 C:GLU60 3.4 30.0 1.0 NE2 C:GLN139 3.4 33.5 1.0 FE C:FE203 3.5 30.0 1.0 CG C:HIS63 3.5 30.0 1.0 CB C:HIS63 3.8 30.0 1.0 O C:HOH420 3.9 37.7 1.0 CG1 C:VAL108 4.1 27.3 1.0 NE2 C:HIS63 4.5 30.0 1.0 CG C:GLU25 4.6 24.9 1.0 CD2 C:HIS63 4.6 30.0 1.0 CD C:GLN139 4.6 33.3 1.0 CG C:GLU60 4.7 30.0 1.0 CA C:GLU60 4.9 24.6 1.0 OE1 C:GLU138 5.0 51.6 1.0 OE1 C:GLU105 5.0 33.4 1.0

Iron binding site 9 out of 36 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe203 b:30.0 occ:1.00 OE2 C:GLU60 2.2 30.0 1.0 OE1 C:GLU105 2.3 33.4 1.0 O C:HOH307 2.7 25.4 1.0 OE2 C:GLU105 2.7 29.1 1.0 CD C:GLU105 2.8 31.0 1.0 CD C:GLU60 3.1 30.0 1.0 FE C:FE202 3.5 30.0 1.0 OE1 C:GLU60 3.5 30.0 1.0 NE2 C:GLN139 3.7 33.5 1.0 OE1 C:GLU138 3.9 51.6 1.0 CG C:GLU105 4.3 27.9 1.0 CE1 C:HIS63 4.4 30.0 1.0 CG C:GLU60 4.4 30.0 1.0 OE1 C:GLN139 4.4 40.9 1.0 CD C:GLN139 4.5 33.3 1.0 ND1 C:HIS63 4.5 30.0 1.0 O C:HOH406 4.5 40.8 1.0 CB C:ALA142 4.5 27.3 1.0 OE1 C:GLN56 4.8 56.5 1.0 CD C:GLU138 4.9 45.0 1.0 OE2 C:GLU59 4.9 57.3 1.0 CE2 C:TYR32 4.9 24.5 1.0 OH C:TYR32 4.9 27.7 1.0

Iron binding site 10 out of 36 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:12.6 occ:1.00 O D:HOH322 2.2 23.4 1.0 OE1 D:GLU25 2.3 25.8 1.0 ND1 D:HIS63 2.3 26.9 1.0 OE1 D:GLU60 2.3 30.0 1.0 CD D:GLU60 3.1 30.0 1.0 CD D:GLU25 3.2 24.1 1.0 CE1 D:HIS63 3.2 29.1 1.0 OE2 D:GLU60 3.2 30.0 1.0 CG D:HIS63 3.3 27.4 1.0 OE2 D:GLU25 3.5 25.4 1.0 FE D:FE202 3.5 23.2 1.0 CB D:HIS63 3.6 24.5 1.0 NE2 D:GLN139 4.2 28.7 1.0 NE2 D:HIS63 4.4 25.6 1.0 CD2 D:HIS63 4.4 29.4 1.0 CG1 D:VAL108 4.5 25.1 1.0 CG D:GLU60 4.5 30.0 1.0 CG D:GLU25 4.6 23.1 1.0 CA D:GLU60 4.7 22.5 1.0 CB D:GLU60 4.9 30.0 1.0 CB D:GLU25 5.0 22.6 1.0 OE1 D:GLU138 5.0 44.1 1.0

Y.Wu, Y.Wu, T.H.Ming, X.R.Su. N/A N/A.