Iron in PDB 5xtd: Cryo-Em Structure of Human Respiratory Complex I

All present enzymatic activity of Cryo-Em Structure of Human Respiratory Complex I:
1.6.5.3; 1.6.99.3;

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Human Respiratory Complex I (pdb code 5xtd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Cryo-Em Structure of Human Respiratory Complex I, PDB code: 5xtd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in the Cryo-Em Structure of Human Respiratory Complex I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Human Respiratory Complex I within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:37.0 occ:1.00 FE1 A:SF4501 0.0 37.0 1.0 S2 A:SF4501 2.2 37.0 1.0 S3 A:SF4501 2.2 37.0 1.0 S4 A:SF4501 2.2 37.0 1.0 CG2 A:ILE424 2.5 26.0 1.0 NE2 A:GLN381 2.5 27.9 1.0 CG A:GLN381 2.8 27.9 1.0 FE3 A:SF4501 3.1 37.0 1.0 FE4 A:SF4501 3.1 37.0 1.0 CD A:GLN381 3.1 27.9 1.0 FE2 A:SF4501 3.1 37.0 1.0 SG A:CYS382 3.1 23.4 1.0 S1 A:SF4501 3.8 37.0 1.0 N A:CYS382 3.9 23.4 1.0 CB A:ILE424 3.9 26.0 1.0 CB A:CYS382 4.2 23.4 1.0 CB A:GLN381 4.2 27.9 1.0 OE1 A:GLN381 4.3 27.9 1.0 SG A:CYS425 4.3 33.2 1.0 N A:CYS425 4.5 33.2 1.0 CB A:CYS425 4.5 33.2 1.0 N A:GLN381 4.5 27.9 1.0 N A:ILE424 4.6 26.0 1.0 CA A:CYS382 4.6 23.4 1.0 CA A:ILE424 4.6 26.0 1.0 CA A:GLN381 4.7 27.9 1.0 OG1 A:THR423 4.8 28.0 1.0 C A:ILE424 4.8 26.0 1.0 C A:GLN381 4.8 27.9 1.0 O A:CYS382 4.9 23.4 1.0 CG1 A:ILE424 4.9 26.0 1.0

Iron binding site 2 out of 28 in the Cryo-Em Structure of Human Respiratory Complex I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Human Respiratory Complex I within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:37.0 occ:1.00 FE2 A:SF4501 0.0 37.0 1.0 S4 A:SF4501 2.2 37.0 1.0 S1 A:SF4501 2.2 37.0 1.0 S3 A:SF4501 2.2 37.0 1.0 CB A:CYS425 2.6 33.2 1.0 FE4 A:SF4501 3.1 37.0 1.0 FE3 A:SF4501 3.1 37.0 1.0 FE1 A:SF4501 3.1 37.0 1.0 CA A:CYS425 3.4 33.2 1.0 N A:CYS425 3.5 33.2 1.0 O A:CYS425 3.6 33.2 1.0 SG A:CYS425 3.6 33.2 1.0 C A:CYS425 3.7 33.2 1.0 S2 A:SF4501 3.8 37.0 1.0 OG1 A:THR423 4.0 28.0 1.0 CB A:LEU427 4.1 36.2 1.0 CG2 A:ILE424 4.2 26.0 1.0 N A:LEU427 4.4 36.2 1.0 N A:ALA426 4.5 35.2 1.0 C A:ILE424 4.6 26.0 1.0 NE2 A:GLN381 4.6 27.9 1.0 N A:GLY428 4.8 42.3 1.0 CA A:LEU427 4.8 36.2 1.0 SG A:CYS385 4.8 30.1 1.0

Iron binding site 3 out of 28 in the Cryo-Em Structure of Human Respiratory Complex I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Human Respiratory Complex I within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:37.0 occ:1.00 FE3 A:SF4501 0.0 37.0 1.0 S2 A:SF4501 2.2 37.0 1.0 S1 A:SF4501 2.2 37.0 1.0 S4 A:SF4501 2.2 37.0 1.0 CB A:CYS385 2.9 30.1 1.0 FE4 A:SF4501 3.1 37.0 1.0 FE1 A:SF4501 3.1 37.0 1.0 FE2 A:SF4501 3.1 37.0 1.0 SG A:CYS385 3.2 30.1 1.0 OG A:SER378 3.5 36.3 1.0 S3 A:SF4501 3.8 37.0 1.0 SG A:CYS382 3.8 23.4 1.0 OG1 A:THR423 3.9 28.0 1.0 O A:SER378 3.9 36.3 1.0 CA A:CYS385 4.1 30.1 1.0 N A:ARG386 4.2 26.7 1.0 C A:CYS385 4.3 30.1 1.0 O A:CYS382 4.4 23.4 1.0 N A:CYS385 4.7 30.1 1.0 CB A:SER378 4.8 36.3 1.0 C A:SER378 4.9 36.3 1.0 CA A:GLY380 4.9 27.0 1.0 CG A:GLN381 5.0 27.9 1.0

Iron binding site 4 out of 28 in the Cryo-Em Structure of Human Respiratory Complex I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Human Respiratory Complex I within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:37.0 occ:1.00 FE4 A:SF4501 0.0 37.0 1.0 S3 A:SF4501 2.2 37.0 1.0 S1 A:SF4501 2.2 37.0 1.0 S2 A:SF4501 2.2 37.0 1.0 SG A:CYS379 2.8 32.7 1.0 O A:SER378 3.0 36.3 1.0 FE3 A:SF4501 3.1 37.0 1.0 FE2 A:SF4501 3.1 37.0 1.0 FE1 A:SF4501 3.1 37.0 1.0 CD1 A:ILE205 3.3 40.6 1.0 C A:SER378 3.8 36.3 1.0 S4 A:SF4501 3.8 37.0 1.0 CG A:GLN381 3.9 27.9 1.0 NE2 A:GLN381 4.0 27.9 1.0 OG A:SER378 4.1 36.3 1.0 N A:GLY380 4.1 27.0 1.0 CD A:GLN381 4.3 27.9 1.0 CB A:CYS379 4.4 32.7 1.0 CD A:PRO223 4.5 33.6 1.0 CA A:SER378 4.5 36.3 1.0 N A:CYS379 4.5 32.7 1.0 N A:GLN381 4.6 27.9 1.0 CG1 A:ILE205 4.6 40.6 1.0 CA A:CYS379 4.8 32.7 1.0 CA A:GLY380 4.9 27.0 1.0 CB A:SER378 5.0 36.3 1.0 C A:CYS379 5.0 32.7 1.0

Iron binding site 5 out of 28 in the Cryo-Em Structure of Human Respiratory Complex I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Human Respiratory Complex I within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:30.0 occ:1.00 FE1 B:SF4301 0.0 30.0 1.0 S3 B:SF4301 2.2 30.0 1.0 S4 B:SF4301 2.2 30.0 1.0 S2 B:SF4301 2.2 30.0 1.0 FE2 B:SF4301 3.1 30.0 1.0 CB B:ALA164 3.1 13.0 1.0 FE4 B:SF4301 3.1 30.0 1.0 FE3 B:SF4301 3.1 30.0 1.0 SG B:CYS111 3.1 17.3 1.0 CB B:CYS111 3.6 17.3 1.0 S1 B:SF4301 3.8 30.0 1.0 CA B:CYS111 3.9 17.3 1.0 SG B:CYS160 4.2 11.7 1.0 N B:ILE112 4.4 13.3 1.0 CA B:ALA164 4.5 13.0 1.0 N B:ILE165 4.5 11.1 1.0 N B:ALA113 4.5 12.8 1.0 C B:CYS111 4.7 17.3 1.0 CG2 B:VAL162 4.9 12.4 1.0 N B:CYS111 4.9 17.3 1.0 CA B:ALA113 5.0 12.8 1.0 C B:ALA164 5.0 13.0 1.0

Iron binding site 6 out of 28 in the Cryo-Em Structure of Human Respiratory Complex I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Human Respiratory Complex I within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:30.0 occ:1.00 FE2 B:SF4301 0.0 30.0 1.0 S1 B:SF4301 2.2 30.0 1.0 S4 B:SF4301 2.2 30.0 1.0 S3 B:SF4301 2.2 30.0 1.0 N B:CYS114 2.7 12.1 1.0 CA B:ALA113 3.0 12.8 1.0 FE1 B:SF4301 3.1 30.0 1.0 FE4 B:SF4301 3.1 30.0 1.0 C B:ALA113 3.1 12.8 1.0 N B:LYS115 3.1 13.7 1.0 FE3 B:SF4301 3.1 30.0 1.0 N B:ALA113 3.4 12.8 1.0 SG B:CYS114 3.6 12.1 1.0 CA B:CYS114 3.7 12.1 1.0 S2 B:SF4301 3.8 30.0 1.0 C B:CYS114 3.9 12.1 1.0 CA B:LYS115 4.1 13.7 1.0 O B:ALA113 4.1 12.8 1.0 SG B:CYS111 4.1 17.3 1.0 CB B:CYS114 4.2 12.1 1.0 CD1 B:ILE128 4.2 14.5 1.0 CB B:ALA113 4.4 12.8 1.0 C B:ILE112 4.5 13.3 1.0 N B:ILE112 4.9 13.3 1.0 N B:LEU116 5.0 13.6 1.0 CG B:LYS115 5.0 13.7 1.0

Iron binding site 7 out of 28 in the Cryo-Em Structure of Human Respiratory Complex I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Human Respiratory Complex I within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:30.0 occ:1.00 FE3 B:SF4301 0.0 30.0 1.0 S4 B:SF4301 2.2 30.0 1.0 S1 B:SF4301 2.2 30.0 1.0 S2 B:SF4301 2.2 30.0 1.0 FE4 B:SF4301 3.1 30.0 1.0 FE2 B:SF4301 3.1 30.0 1.0 FE1 B:SF4301 3.1 30.0 1.0 CB B:CYS117 3.2 15.0 1.0 SG B:CYS117 3.5 15.0 1.0 CE1 B:TYR143 3.8 15.1 1.0 S3 B:SF4301 3.8 30.0 1.0 CD1 B:ILE128 3.9 14.5 1.0 OH B:TYR143 4.1 15.1 1.0 CZ B:TYR143 4.3 15.1 1.0 CA B:CYS117 4.4 15.0 1.0 CG2 B:ILE165 4.6 11.1 1.0 N B:CYS117 4.6 15.0 1.0 CD1 B:TYR143 4.6 15.1 1.0 C B:CYS117 4.9 15.0 1.0 N B:GLU118 4.9 15.5 1.0

Iron binding site 8 out of 28 in the Cryo-Em Structure of Human Respiratory Complex I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of Human Respiratory Complex I within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:30.0 occ:1.00 FE4 B:SF4301 0.0 30.0 1.0 S3 B:SF4301 2.2 30.0 1.0 S2 B:SF4301 2.2 30.0 1.0 S1 B:SF4301 2.2 30.0 1.0 SG B:CYS114 3.0 12.1 1.0 SG B:CYS160 3.1 11.7 1.0 FE2 B:SF4301 3.1 30.0 1.0 FE3 B:SF4301 3.1 30.0 1.0 FE1 B:SF4301 3.1 30.0 1.0 SG B:CYS117 3.1 15.0 1.0 CB B:CYS160 3.5 11.7 1.0 S4 B:SF4301 3.8 30.0 1.0 CA B:CYS160 3.9 11.7 1.0 CD B:PRO161 4.1 11.1 1.0 CB B:CYS117 4.1 15.0 1.0 CB B:CYS114 4.5 12.1 1.0 N B:CYS114 4.6 12.1 1.0 CB B:ALA164 4.7 13.0 1.0 N B:CYS117 4.7 15.0 1.0 CG B:PRO161 4.8 11.1 1.0 C B:CYS160 4.8 11.7 1.0 N B:LYS115 4.9 13.7 1.0 N B:PRO161 4.9 11.1 1.0 N B:CYS160 4.9 11.7 1.0 CG2 B:VAL162 5.0 12.4 1.0 CG B:LEU116 5.0 13.6 1.0

Iron binding site 9 out of 28 in the Cryo-Em Structure of Human Respiratory Complex I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of Human Respiratory Complex I within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:30.0 occ:1.00 FE1 B:SF4302 0.0 30.0 1.0 S3 B:SF4302 2.2 30.0 1.0 S4 B:SF4302 2.2 30.0 1.0 S2 B:SF4302 2.2 30.0 1.0 SG B:CYS121 2.9 12.5 1.0 CA B:CYS121 2.9 12.5 1.0 CB B:CYS121 3.0 12.5 1.0 FE2 B:SF4302 3.1 30.0 1.0 FE4 B:SF4302 3.1 30.0 1.0 FE3 B:SF4302 3.1 30.0 1.0 CD B:PRO122 3.2 11.9 1.0 S1 B:SF4302 3.8 30.0 1.0 C B:CYS121 3.8 12.5 1.0 SG B:CYS156 3.8 12.7 1.0 N B:PRO122 3.9 11.9 1.0 N B:CYS121 3.9 12.5 1.0 SG B:CYS153 4.1 12.4 1.0 CG B:PRO122 4.3 11.9 1.0 CB B:PHE155 4.8 12.9 1.0 C B:ILE120 4.8 13.7 1.0 O B:CYS121 4.8 12.5 1.0 CD1 B:ILE126 5.0 12.1 1.0 O B:ILE120 5.0 13.7 1.0 N B:CYS156 5.0 12.7 1.0

Iron binding site 10 out of 28 in the Cryo-Em Structure of Human Respiratory Complex I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of Human Respiratory Complex I within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:30.0 occ:1.00 FE2 B:SF4302 0.0 30.0 1.0 S3 B:SF4302 2.2 30.0 1.0 S4 B:SF4302 2.2 30.0 1.0 S1 B:SF4302 2.2 30.0 1.0 SG B:CYS150 2.7 10.2 1.0 FE4 B:SF4302 3.0 30.0 1.0 FE1 B:SF4302 3.1 30.0 1.0 FE3 B:SF4302 3.1 30.0 1.0 CB B:CYS150 3.4 10.2 1.0 CA B:CYS150 3.7 10.2 1.0 S2 B:SF4302 3.8 30.0 1.0 NE2 B:HIS99 3.8 14.2 1.0 CE1 B:HIS99 3.9 14.2 1.0 CD1 B:ILE145 4.0 13.8 1.0 N B:ILE151 4.0 11.9 1.0 SG B:CYS121 4.0 12.5 1.0 N B:TYR152 4.2 11.9 1.0 C B:CYS150 4.3 10.2 1.0 CA B:TYR152 4.8 11.9 1.0 N B:CYS150 4.9 10.2 1.0 CB B:ALA125 4.9 11.9 1.0 CD2 B:HIS99 5.0 14.2 1.0

R.Guo, S.Zong, M.Wu, J.Gu, M.Yang. Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2. Cell V. 170 1247 2017.
ISSN: ISSN 1097-4172
PubMed: 28844695
DOI: 10.1016/J.CELL.2017.07.050