Iron in PDB 23wj: Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II

The structure of Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II also contains other interesting chemical elements:

Zinc

(Zn)

24 atoms

The binding sites of Iron atom in the Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II (pdb code 23wj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II, PDB code: 23wj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:25.6 occ:1.00 CE1 F:HIS169 3.2 5.6 0.8 CE1 G:HIS169 3.2 2.9 0.9 CE1 E:HIS169 3.2 8.6 0.8 CE1 A:HIS169 3.2 1.4 0.9 NE2 F:HIS169 4.0 5.1 0.8 NE2 G:HIS169 4.0 4.7 0.9 NE2 E:HIS169 4.0 5.1 0.8 NE2 A:HIS169 4.0 9.9 0.9 ND1 G:HIS169 4.1 7.6 0.9 ND1 A:HIS169 4.1 5.7 0.9 ND1 F:HIS169 4.1 2.6 0.8 ND1 E:HIS169 4.1 1.9 0.8 CD2 E:LEU165 4.2 2.5 1.0 CD2 A:LEU165 4.2 7.7 1.0 CD2 F:LEU165 4.2 1.9 1.0 CD2 G:LEU165 4.2 7.0 1.0 CD1 G:LEU165 4.4 1.4 1.0 CD1 A:LEU165 4.4 0.4 1.0 CD1 F:LEU165 4.4 4.3 1.0 CD1 E:LEU165 4.4 1.1 1.0 CG E:LEU165 4.9 3.1 1.0 CG A:LEU165 4.9 7.4 1.0 CG F:LEU165 4.9 5.0 1.0 CG G:LEU165 4.9 8.2 1.0

Iron binding site 2 out of 6 in the Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:1.3 occ:0.35 NE2 N:HIS169 3.0 5.2 0.8 CE1 B:HIS169 3.1 3.1 0.9 CE1 H:HIS169 3.1 1.6 0.9 CE1 L:HIS169 3.1 8.0 0.9 CE1 N:HIS169 3.6 3.6 0.8 NE2 B:HIS169 3.9 2.4 0.9 NE2 H:HIS169 3.9 8.7 0.9 NE2 L:HIS169 4.0 3.2 0.9 ND1 L:HIS169 4.1 4.6 0.9 ND1 B:HIS169 4.1 4.8 0.9 ND1 H:HIS169 4.1 7.1 0.9 CD2 N:HIS169 4.2 5.6 0.8 CD2 L:LEU165 4.2 3.1 1.0 CD2 H:LEU165 4.2 1.6 1.0 CD2 B:LEU165 4.2 2.6 1.0 CD2 N:LEU165 4.2 2.1 1.0 CD1 L:LEU165 4.4 5.0 1.0 CD1 B:LEU165 4.4 6.4 1.0 CD1 H:LEU165 4.4 5.9 1.0 CD1 N:LEU165 4.4 4.3 1.0 ND1 N:HIS169 4.9 8.0 0.8 CG L:LEU165 4.9 9.2 1.0 CG H:LEU165 4.9 0.7 1.0 CG B:LEU165 4.9 9.2 1.0 CG N:LEU165 4.9 2.0 1.0

Iron binding site 3 out of 6 in the Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:4.5 occ:0.40 CE1 R:HIS169 3.1 2.8 0.8 CE1 T:HIS169 3.1 10.9 0.8 CE1 S:HIS169 3.1 4.1 0.8 NE2 C:HIS169 3.1 2.3 0.8 NE2 T:HIS169 3.9 5.3 0.8 NE2 R:HIS169 3.9 6.1 0.8 NE2 S:HIS169 3.9 6.9 0.8 CD2 C:HIS169 4.0 1.6 0.8 CE1 C:HIS169 4.1 1.8 0.8 ND1 S:HIS169 4.1 8.4 0.8 ND1 R:HIS169 4.1 1.3 0.8 ND1 T:HIS169 4.1 9.7 0.8 CD2 T:LEU165 4.2 1.7 1.0 CD2 C:LEU165 4.2 1.5 1.0 CD2 S:LEU165 4.2 7.7 1.0 CD2 R:LEU165 4.2 3.7 1.0 CD1 C:LEU165 4.3 3.5 1.0 CD1 T:LEU165 4.3 0.4 1.0 CD1 S:LEU165 4.3 9.0 1.0 CD1 R:LEU165 4.3 5.2 1.0 CG C:LEU165 4.9 0.5 1.0 CG T:LEU165 4.9 5.5 1.0 CG S:LEU165 4.9 3.2 1.0 CG R:LEU165 4.9 5.2 1.0

Iron binding site 4 out of 6 in the Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:3.6 occ:0.40 NE2 D:HIS169 3.0 5.4 0.9 CE1 M:HIS169 3.1 6.1 0.9 CE1 Q:HIS169 3.1 7.9 0.8 CE1 K:HIS169 3.1 10.6 0.8 CE1 D:HIS169 3.6 4.1 0.9 NE2 M:HIS169 4.0 3.9 0.9 NE2 Q:HIS169 4.0 5.5 0.8 NE2 K:HIS169 4.0 10.5 0.8 ND1 M:HIS169 4.1 10.5 0.9 ND1 Q:HIS169 4.1 0.8 0.8 ND1 K:HIS169 4.1 5.9 0.8 CD2 K:LEU165 4.2 0.2 1.0 CD2 M:LEU165 4.2 2.3 1.0 CD2 D:HIS169 4.2 6.5 0.9 CD2 D:LEU165 4.2 5.5 1.0 CD2 Q:LEU165 4.2 7.5 1.0 CD1 K:LEU165 4.3 2.6 1.0 CD1 D:LEU165 4.4 2.0 1.0 CD1 Q:LEU165 4.4 4.6 1.0 CD1 M:LEU165 4.4 2.3 1.0 ND1 D:HIS169 4.9 4.0 0.9 CG K:LEU165 4.9 4.7 1.0 CG D:LEU165 4.9 2.6 1.0 CG Q:LEU165 4.9 2.7 1.0 CG M:LEU165 4.9 3.6 1.0

Iron binding site 5 out of 6 in the Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe202 b:0.2 occ:0.35 NE2 I:HIS169 3.0 5.8 0.8 NE2 V:HIS169 3.0 1.8 0.9 CE1 J:HIS169 3.1 7.8 0.9 CE1 U:HIS169 3.1 6.8 0.8 CE1 I:HIS169 3.5 2.3 0.8 CE1 V:HIS169 3.8 8.7 0.9 NE2 J:HIS169 3.9 2.4 0.9 NE2 U:HIS169 3.9 3.6 0.8 CD2 V:HIS169 4.1 1.1 0.9 ND1 J:HIS169 4.1 6.8 0.9 ND1 U:HIS169 4.1 4.6 0.8 CD2 I:LEU165 4.2 5.8 1.0 CD2 U:LEU165 4.2 1.5 1.0 CD2 J:LEU165 4.2 4.1 1.0 CD2 V:LEU165 4.2 1.4 1.0 CD2 I:HIS169 4.2 4.4 0.8 CD1 I:LEU165 4.3 3.5 1.0 CD1 U:LEU165 4.3 5.4 1.0 CD1 V:LEU165 4.4 2.3 1.0 CD1 J:LEU165 4.4 0.9 1.0 ND1 I:HIS169 4.8 10.2 0.8 CG I:LEU165 4.9 0.2 1.0 CG U:LEU165 4.9 5.6 1.0 CG V:LEU165 4.9 4.0 1.0 CG J:LEU165 4.9 0.6 1.0

Iron binding site 6 out of 6 in the Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Subtomogram Average of Apoferrtin (11X11) Using Cryo Arm 300II within 5.0Å range: probe atom residue distance (Å) B Occ O:Fe202 b:1.9 occ:0.36 NE2 X:HIS169 3.0 3.1 0.8 CE1 W:HIS169 3.1 7.4 0.8 CE1 P:HIS169 3.1 3.9 0.8 CE1 O:HIS169 3.2 8.6 0.9 CE1 X:HIS169 3.7 8.7 0.8 NE2 W:HIS169 4.0 10.7 0.8 NE2 P:HIS169 4.0 1.9 0.8 NE2 O:HIS169 4.0 11.1 0.9 ND1 O:HIS169 4.1 9.5 0.9 ND1 W:HIS169 4.1 2.5 0.8 ND1 P:HIS169 4.1 1.4 0.8 CD2 X:HIS169 4.1 8.3 0.8 CD2 P:LEU165 4.2 8.2 1.0 CD2 W:LEU165 4.2 3.1 1.0 CD2 O:LEU165 4.2 4.1 1.0 CD2 X:LEU165 4.2 3.4 1.0 CD1 O:LEU165 4.4 2.0 1.0 CD1 P:LEU165 4.4 1.4 1.0 CD1 W:LEU165 4.4 10.0 1.0 CD1 X:LEU165 4.4 0.1 1.0 CG P:LEU165 4.9 1.5 1.0 CG W:LEU165 4.9 6.3 1.0 CG O:LEU165 4.9 2.2 1.0 CG X:LEU165 4.9 2.6 1.0 ND1 X:HIS169 5.0 9.7 0.8

F.Makino, H.Yanagisawa, F.Eisenstein, T.Miyata, M.Kinoshita, M.Kikkawa, K.Namba. Subtomogram Averaging By Cryo Electron Tomography Using Cryo Armtm 300 II For Purified and Cellular Samples Aims Biophysics V. 13 131 2026.
DOI: 10.3934/BIOPHY.2026008