Iron in PDB 5odc: Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution

All present enzymatic activity of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution:
1.12.99.6; 1.8.98.1;

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution, PDB code: 5odc was solved by T.Wagner, J.Koch, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.22 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	378.047, 98.446, 137.884, 90.00, 110.70, 90.00
R / Rfree (%)	17.8 / 20

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Magnesium	(Mg)	2 atoms
Calcium	(Ca)	2 atoms
Sodium	(Na)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110;

Binding sites:

The binding sites of Iron atom in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution (pdb code 5odc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 110 binding sites of Iron where determined in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution, PDB code: 5odc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 110 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe705 b:45.6 occ:1.00 FE1 A:SF4705 0.0 45.6 1.0 S3 A:SF4705 2.1 39.1 1.0 S2 A:SF4705 2.2 41.7 1.0 S4 A:SF4705 2.2 43.0 1.0 SG A:CYS11 2.2 31.0 1.0 FE2 A:SF4705 3.0 46.2 1.0 FE4 A:SF4705 3.0 45.9 1.0 FE3 A:SF4705 3.0 45.6 1.0 CB A:CYS11 3.3 28.8 1.0 S1 A:SF4705 3.6 42.1 1.0 CB A:ALA70 4.0 29.2 1.0 N A:MET45 4.0 36.8 1.0 CB A:CYS13 4.0 31.4 1.0 CA A:CYS13 4.1 31.3 1.0 N A:CYS13 4.3 32.0 1.0 SG A:CYS13 4.4 35.2 1.0 CA A:TYR44 4.5 34.9 1.0 CB A:MET45 4.6 37.1 1.0 C A:TYR44 4.7 40.8 1.0 N A:CYS46 4.7 33.5 1.0 CA A:CYS11 4.7 29.2 1.0 CA A:MET45 4.8 35.4 1.0 SG A:CYS46 4.8 34.2 1.0 CD1 A:ILE17 4.9 39.5 1.0 O A:LYS43 5.0 35.6 1.0

Iron binding site 2 out of 110 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe705 b:46.2 occ:1.00 FE2 A:SF4705 0.0 46.2 1.0 SG A:CYS46 2.1 34.2 1.0 S1 A:SF4705 2.2 42.1 1.0 S4 A:SF4705 2.2 43.0 1.0 S3 A:SF4705 2.2 39.1 1.0 FE1 A:SF4705 3.0 45.6 1.0 CB A:CYS46 3.0 31.3 1.0 FE4 A:SF4705 3.0 45.9 1.0 FE3 A:SF4705 3.1 45.6 1.0 N A:CYS46 3.7 33.5 1.0 S2 A:SF4705 3.7 41.7 1.0 CA A:CYS46 3.9 32.0 1.0 CA G:CYS197 4.2 37.8 1.0 CD2 A:HIS76 4.2 44.6 1.0 NE2 A:HIS76 4.4 44.3 1.0 SG G:CYS197 4.4 40.2 1.0 CB G:CYS197 4.6 37.6 1.0 N A:MET45 4.7 36.8 1.0 O G:CYS197 4.8 45.5 1.0 N G:CYS197 4.8 37.9 1.0 C A:CYS46 4.8 38.6 1.0 SG A:CYS11 4.8 31.0 1.0 C A:MET45 4.9 37.4 1.0 C A:TYR44 5.0 40.8 1.0

Iron binding site 3 out of 110 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe705 b:45.6 occ:1.00 FE3 A:SF4705 0.0 45.6 1.0 S4 A:SF4705 2.2 43.0 1.0 S2 A:SF4705 2.2 41.7 1.0 S1 A:SF4705 2.2 42.1 1.0 SG G:CYS197 2.5 40.2 1.0 SG A:CYS13 2.6 35.2 1.0 FE1 A:SF4705 3.0 45.6 1.0 FE2 A:SF4705 3.1 46.2 1.0 FE4 A:SF4705 3.2 45.9 1.0 NH1 A:ARG100 3.5 27.9 1.0 CB A:CYS13 3.6 31.4 1.0 CB G:CYS197 3.8 37.6 1.0 S3 A:SF4705 3.9 39.1 1.0 CA A:CYS13 4.1 31.3 1.0 CZ A:ARG100 4.3 35.9 1.0 CA G:CYS197 4.3 37.8 1.0 N G:CYS197 4.8 37.9 1.0 NE A:ARG100 4.8 23.7 1.0 CD A:ARG100 4.8 32.5 1.0 SG A:CYS11 4.8 31.0 1.0 NH2 A:ARG100 4.9 23.1 1.0 SG A:CYS46 4.9 34.2 1.0 CB G:CYS194 5.0 35.7 1.0

Iron binding site 4 out of 110 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe705 b:45.9 occ:1.00 FE4 A:SF4705 0.0 45.9 1.0 S3 A:SF4705 2.1 39.1 1.0 S2 A:SF4705 2.2 41.7 1.0 S1 A:SF4705 2.2 42.1 1.0 SG A:CYS71 2.3 36.3 1.0 FE1 A:SF4705 3.0 45.6 1.0 CB A:CYS71 3.0 33.0 1.0 FE2 A:SF4705 3.0 46.2 1.0 FE3 A:SF4705 3.2 45.6 1.0 N A:CYS71 3.6 32.0 1.0 S4 A:SF4705 3.8 43.0 1.0 CB A:ALA70 3.8 29.2 1.0 CD2 A:HIS76 3.9 44.6 1.0 CA A:CYS71 3.9 32.6 1.0 C A:ALA70 4.6 33.1 1.0 NE2 A:HIS76 4.8 44.3 1.0 CG A:HIS76 4.8 42.5 1.0 CA A:ALA70 4.8 29.1 1.0 CD2 A:LEU75 4.9 42.8 1.0 SG A:CYS46 4.9 34.2 1.0

Iron binding site 5 out of 110 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe706 b:58.3 occ:1.00 FE1 A:SF4706 0.0 58.3 1.0 S4 A:SF4706 2.1 52.6 1.0 S3 A:SF4706 2.2 56.0 1.0 S2 A:SF4706 2.2 55.1 1.0 SG A:CYS246 2.2 57.5 1.0 FE4 A:SF4706 3.1 62.7 1.0 FE3 A:SF4706 3.1 56.3 1.0 FE2 A:SF4706 3.2 58.0 1.0 CB A:CYS246 3.4 54.2 1.0 N A:GLY248 3.7 52.7 1.0 S1 A:SF4706 3.8 55.8 1.0 N A:THR247 3.8 55.5 1.0 CA A:CYS246 3.8 54.4 1.0 CA A:GLY248 4.2 52.0 1.0 C A:CYS246 4.3 59.5 1.0 CB A:TYR286 4.4 37.8 1.0 CD1 A:TYR286 4.4 35.1 1.0 N A:CYS249 4.6 51.4 1.0 CG A:TYR286 4.6 34.9 1.0 C A:THR247 4.7 57.1 1.0 N A:TYR286 4.7 39.7 1.0 CG2 A:ILE241 4.8 50.9 1.0 CA A:THR247 4.9 55.2 1.0 C A:GLY248 4.9 53.7 1.0

Iron binding site 6 out of 110 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe706 b:58.0 occ:1.00 FE2 A:SF4706 0.0 58.0 1.0 S1 A:SF4706 2.1 55.8 1.0 SG A:CYS249 2.2 55.7 1.0 S3 A:SF4706 2.2 56.0 1.0 S4 A:SF4706 2.2 52.6 1.0 FE4 A:SF4706 2.9 62.7 1.0 FE3 A:SF4706 3.2 56.3 1.0 FE1 A:SF4706 3.2 58.3 1.0 CB A:CYS249 3.5 51.5 1.0 N A:CYS249 3.6 51.4 1.0 S2 A:SF4706 3.8 55.1 1.0 N A:GLY250 3.8 50.9 1.0 CA A:CYS249 3.9 51.0 1.0 C A:CYS249 4.2 55.2 1.0 OG1 A:THR247 4.3 63.0 1.0 N A:GLN251 4.3 52.6 1.0 C A:GLY248 4.7 53.7 1.0 N A:GLY248 4.7 52.7 1.0 CA A:GLY250 4.7 50.4 1.0 SG A:CYS252 4.8 54.8 1.0 CB A:GLN251 4.9 55.4 1.0 C A:GLY250 5.0 55.0 1.0 CA A:GLY248 5.0 52.0 1.0

Iron binding site 7 out of 110 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe706 b:56.3 occ:1.00 FE3 A:SF4706 0.0 56.3 1.0 SG A:CYS252 2.1 54.8 1.0 S4 A:SF4706 2.2 52.6 1.0 S2 A:SF4706 2.2 55.1 1.0 S1 A:SF4706 2.2 55.8 1.0 CB A:CYS252 3.1 52.8 1.0 FE4 A:SF4706 3.1 62.7 1.0 FE1 A:SF4706 3.1 58.3 1.0 FE2 A:SF4706 3.2 58.0 1.0 S3 A:SF4706 3.8 56.0 1.0 N A:CYS252 4.0 54.4 1.0 CA A:CYS252 4.2 53.9 1.0 CG A:TYR286 4.3 34.9 1.0 CD1 A:ILE274 4.3 58.3 1.0 CB A:TYR286 4.4 37.8 1.0 CD2 A:TYR286 4.5 35.2 1.0 N A:GLY250 4.6 50.9 1.0 N A:GLN251 4.7 52.6 1.0 CD1 A:TYR286 4.7 35.1 1.0 CA A:GLY250 4.7 50.4 1.0 CG1 A:ILE274 4.9 47.7 1.0 SG A:CYS249 4.9 55.7 1.0 C A:GLY250 4.9 55.0 1.0

Iron binding site 8 out of 110 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe706 b:62.7 occ:1.00 FE4 A:SF4706 0.0 62.7 1.0 S3 A:SF4706 2.1 56.0 1.0 S1 A:SF4706 2.1 55.8 1.0 S2 A:SF4706 2.2 55.1 1.0 SG A:CYS303 2.3 56.0 1.0 FE2 A:SF4706 2.9 58.0 1.0 FE1 A:SF4706 3.1 58.3 1.0 FE3 A:SF4706 3.1 56.3 1.0 CB A:CYS303 3.3 52.9 1.0 S4 A:SF4706 3.6 52.6 1.0 CA A:CYS303 3.8 52.7 1.0 CD A:PRO305 4.5 60.3 1.0 CB A:ALA307 4.5 59.2 1.0 C A:CYS303 4.7 57.9 1.0 CG1 A:ILE308 4.8 59.8 1.0 SG A:CYS249 4.9 55.7 1.0 N A:CYS303 4.9 52.9 1.0 N A:GLY304 4.9 55.4 1.0 SG A:CYS246 5.0 57.5 1.0

Iron binding site 9 out of 110 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe707 b:66.3 occ:1.00 FE1 A:SF4707 0.0 66.3 1.0 SG A:CYS299 2.1 66.2 1.0 S4 A:SF4707 2.1 61.8 1.0 S2 A:SF4707 2.2 61.1 1.0 S3 A:SF4707 2.2 59.3 1.0 FE2 A:SF4707 2.9 65.3 1.0 FE3 A:SF4707 3.1 64.6 1.0 CB A:CYS299 3.1 63.3 1.0 FE4 A:SF4707 3.2 63.6 1.0 S1 A:SF4707 3.7 62.3 1.0 N A:CYS299 3.8 67.3 1.0 CA A:CYS299 4.1 65.0 1.0 CZ A:PHE310 4.5 73.1 1.0 N A:LEU298 4.8 72.7 1.0 SG A:CYS296 4.8 70.8 1.0 CG2 A:ILE274 4.8 47.1 1.0 N A:GLY297 4.9 70.6 1.0 CB A:ILE274 4.9 47.5 1.0 SG A:CYS293 5.0 59.8 1.0

Iron binding site 10 out of 110 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe707 b:65.3 occ:1.00 FE2 A:SF4707 0.0 65.3 1.0 S4 A:SF4707 2.1 61.8 1.0 S3 A:SF4707 2.1 59.3 1.0 S1 A:SF4707 2.2 62.3 1.0 SG A:CYS296 2.3 70.8 1.0 FE1 A:SF4707 2.9 66.3 1.0 FE4 A:SF4707 3.0 63.6 1.0 FE3 A:SF4707 3.2 64.6 1.0 N A:CYS296 3.4 66.7 1.0 CB A:CYS296 3.4 67.7 1.0 S2 A:SF4707 3.6 61.1 1.0 N A:GLY297 3.8 70.6 1.0 CA A:CYS296 3.9 67.7 1.0 CD A:PRO257 3.9 68.4 1.0 C A:CYS296 4.2 74.0 1.0 N A:LEU298 4.3 72.7 1.0 C A:GLU295 4.5 69.5 1.0 N A:GLU295 4.5 62.8 1.0 CG A:PRO257 4.6 73.5 1.0 CG1 A:ILE294 4.6 63.3 1.0 CA A:GLU295 4.7 63.3 1.0 SG A:CYS299 4.8 66.2 1.0 CA A:GLY297 4.8 70.8 1.0 SG A:CYS256 4.9 64.9 1.0 SG A:CYS293 4.9 59.8 1.0 CB A:LEU298 4.9 73.3 1.0

T.Wagner, J.Koch, U.Ermler, S.Shima. Methanogenic Heterodisulfide Reductase (Hdrabc-Mvhagd) Uses Two Noncubane [4FE-4S] Clusters For Reduction. Science V. 357 699 2017.
ISSN: ESSN 1095-9203
PubMed: 28818947
DOI: 10.1126/SCIENCE.AAN0425