Iron in PDB 5odh: Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes

All present enzymatic activity of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes:
1.12.1.2; 1.8.98.1;

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes, PDB code: 5odh 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)	48.55 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	366.381, 97.104, 133.974, 90.00, 108.43, 90.00
R / Rfree (%)	21.4 / 24.5

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes also contains other interesting chemical elements:

Nickel

(Ni)

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; Page 12, Binding sites: 111 - 113;

Binding sites:

The binding sites of Iron atom in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes (pdb code 5odh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 113 binding sites of Iron where determined in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes, PDB code: 5odh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes


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 Soaked with Heterodisulfide For 3.5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:20.6 occ:1.00 FE1 A:SF4701 0.0 20.6 1.0 S4 A:SF4701 2.1 14.9 1.0 S2 A:SF4701 2.1 22.4 1.0 S3 A:SF4701 2.1 20.1 1.0 SG A:CYS399 2.5 17.5 1.0 FE3 A:SF4701 3.2 25.3 1.0 FE2 A:SF4701 3.2 22.8 1.0 FE4 A:SF4701 3.2 21.4 1.0 CB A:CYS399 3.5 23.4 1.0 S1 A:SF4701 3.6 19.4 1.0 NH2 A:ARG431 3.7 22.0 1.0 CD A:ARG431 3.8 26.0 1.0 CA A:CYS399 4.0 16.9 1.0 N A:ASN401 4.0 20.3 1.0 N A:SER400 4.1 13.9 1.0 CD A:ARG390 4.2 19.8 1.0 C A:CYS399 4.3 17.4 1.0 NE A:ARG431 4.5 19.9 1.0 CZ A:ARG431 4.5 23.9 1.0 CG A:ARG431 4.5 20.8 1.0 CA A:ASN401 4.7 14.2 1.0 CG A:ARG390 4.8 18.8 1.0 CB A:ARG431 4.9 17.6 1.0 C A:SER400 4.9 17.3 1.0

Iron binding site 2 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes


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 Soaked with Heterodisulfide For 3.5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:22.8 occ:1.00 FE2 A:SF4701 0.0 22.8 1.0 S3 A:SF4701 2.1 20.1 1.0 S1 A:SF4701 2.1 19.4 1.0 S4 A:SF4701 2.1 14.9 1.0 SG A:CYS404 2.5 29.2 1.0 CB A:CYS404 2.9 21.8 1.0 FE4 A:SF4701 3.2 21.4 1.0 FE1 A:SF4701 3.2 20.6 1.0 FE3 A:SF4701 3.2 25.3 1.0 N A:CYS404 3.3 9.4 1.0 CA A:CYS404 3.5 19.1 1.0 S2 A:SF4701 3.6 22.4 1.0 O A:ASP429 4.1 28.6 1.0 O A:HOH852 4.3 16.6 1.0 C A:CYS403 4.3 11.3 1.0 CG A:ARG431 4.4 20.8 1.0 O A:HOH829 4.4 20.4 1.0 CB A:ARG431 4.4 17.6 1.0 NE2 A:GLN385 4.6 21.4 1.0 N A:ARG431 4.6 14.7 1.0 CB A:CYS403 4.7 17.6 1.0 CD A:ARG431 4.7 26.0 1.0 CA A:CYS403 4.9 17.3 1.0 N A:CYS403 4.9 17.4 1.0

Iron binding site 3 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes


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 Soaked with Heterodisulfide For 3.5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:25.3 occ:1.00 FE3 A:SF4701 0.0 25.3 1.0 S2 A:SF4701 2.1 22.4 1.0 S1 A:SF4701 2.1 19.4 1.0 S4 A:SF4701 2.1 14.9 1.0 SG A:CYS386 2.5 21.9 1.0 CB A:CYS386 3.2 15.8 1.0 FE1 A:SF4701 3.2 20.6 1.0 FE4 A:SF4701 3.2 21.4 1.0 FE2 A:SF4701 3.2 22.8 1.0 CA A:CYS386 3.3 18.3 1.0 N A:CYS386 3.5 14.5 1.0 S3 A:SF4701 3.6 20.1 1.0 CD A:ARG390 3.8 19.8 1.0 O A:HOH829 4.1 20.4 1.0 CG A:ARG390 4.5 18.8 1.0 C A:GLN385 4.5 19.4 1.0 NH1 A:ARG390 4.6 15.1 1.0 CB A:GLN385 4.7 16.9 1.0 O A:HOH844 4.7 24.8 1.0 C A:CYS386 4.8 27.2 1.0 CB A:SER389 4.9 24.0 1.0 NE A:ARG390 5.0 19.4 1.0

Iron binding site 4 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes


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 Soaked with Heterodisulfide For 3.5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:21.4 occ:1.00 FE4 A:SF4701 0.0 21.4 1.0 S3 A:SF4701 2.1 20.1 1.0 S1 A:SF4701 2.1 19.4 1.0 S2 A:SF4701 2.1 22.4 1.0 SG A:CYS403 2.6 25.7 1.0 CB A:CYS403 2.7 17.6 1.0 FE2 A:SF4701 3.2 22.8 1.0 FE3 A:SF4701 3.2 25.3 1.0 FE1 A:SF4701 3.2 20.6 1.0 N A:CYS403 3.5 17.4 1.0 CA A:CYS403 3.5 17.3 1.0 S4 A:SF4701 3.6 14.9 1.0 O A:HOH844 3.7 24.8 1.0 N A:CYS404 3.8 9.4 1.0 C A:CYS403 4.1 11.3 1.0 N A:ASN401 4.1 20.3 1.0 CB A:SER400 4.2 19.3 1.0 N A:SER400 4.3 13.9 1.0 C A:SER400 4.4 17.3 1.0 CA A:SER400 4.5 22.7 1.0 N A:VAL402 4.7 19.2 1.0 C A:VAL402 4.7 24.9 1.0 N A:CYS386 4.8 14.5 1.0 C A:ASN401 5.0 22.5 1.0 CA A:CYS386 5.0 18.3 1.0 CA A:CYS404 5.0 19.1 1.0

Iron binding site 5 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes


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 Soaked with Heterodisulfide For 3.5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:0.8 occ:1.00 FE1 A:SF4702 0.0 0.8 1.0 S2 A:SF4702 2.1 0.9 1.0 S3 A:SF4702 2.1 0.3 1.0 S4 A:SF4702 2.1 1.0 1.0 SG A:CYS303 2.7 0.9 1.0 CB A:CYS303 3.1 98.7 1.0 FE4 A:SF4702 3.2 0.7 1.0 FE3 A:SF4702 3.3 0.1 1.0 FE2 A:SF4702 3.3 0.5 1.0 S1 A:SF4702 3.6 0.6 1.0 CA A:CYS303 3.7 94.2 1.0 CD A:PRO305 4.2 93.8 1.0 N A:GLY304 4.3 91.4 1.0 C A:CYS303 4.4 93.4 1.0 CG1 A:ILE308 4.4 72.4 1.0 CB A:ALA307 4.6 86.6 1.0 CD1 A:ILE308 4.7 80.0 1.0 N A:ALA307 4.7 91.3 1.0 CG A:PRO305 4.8 87.6 1.0 N A:PRO305 4.8 95.7 1.0 N A:CYS303 4.9 87.1 1.0 N A:ASN306 5.0 95.3 1.0

Iron binding site 6 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes


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 Soaked with Heterodisulfide For 3.5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:0.5 occ:1.00 FE2 A:SF4702 0.0 0.5 1.0 S1 A:SF4702 2.1 0.6 1.0 S3 A:SF4702 2.1 0.3 1.0 S4 A:SF4702 2.1 1.0 1.0 SG A:CYS249 2.8 82.2 1.0 FE4 A:SF4702 3.2 0.7 1.0 FE1 A:SF4702 3.3 0.8 1.0 FE3 A:SF4702 3.3 0.1 1.0 S2 A:SF4702 3.7 0.9 1.0 N A:GLN251 4.0 0.7 1.0 N A:GLY250 4.1 0.2 1.0 OG1 A:THR247 4.2 90.2 1.0 CB A:CYS249 4.5 99.1 1.0 CB A:GLN251 4.6 0.2 1.0 CG A:GLN251 4.6 0.0 1.0 N A:CYS249 4.6 90.7 1.0 CG2 A:THR247 4.7 91.9 1.0 CA A:GLN251 4.7 0.9 1.0 CA A:GLY250 4.8 0.6 1.0 C A:GLY250 4.9 0.4 1.0 C A:CYS249 4.9 1.0 1.0 CA A:CYS249 4.9 96.4 1.0

Iron binding site 7 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes


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 Soaked with Heterodisulfide For 3.5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:0.1 occ:1.00 FE3 A:SF4702 0.0 0.1 1.0 S2 A:SF4702 2.1 0.9 1.0 S1 A:SF4702 2.1 0.6 1.0 S4 A:SF4702 2.1 1.0 1.0 SG A:CYS246 2.8 0.1 1.0 CB A:CYS246 3.1 0.5 1.0 FE4 A:SF4702 3.2 0.7 1.0 FE1 A:SF4702 3.3 0.8 1.0 FE2 A:SF4702 3.3 0.5 1.0 S3 A:SF4702 3.6 0.3 1.0 CA A:CYS246 3.6 0.5 1.0 N A:THR247 3.7 0.2 1.0 C A:CYS246 4.1 0.7 1.0 N A:GLY248 4.3 97.1 1.0 CG2 A:ILE241 4.3 81.2 1.0 CB A:ALA307 4.5 86.6 1.0 OG1 A:THR247 4.6 90.2 1.0 CA A:THR247 4.8 0.7 1.0 CG2 A:THR247 4.9 91.9 1.0 N A:CYS246 4.9 0.9 1.0

Iron binding site 8 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes


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 Soaked with Heterodisulfide For 3.5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:0.7 occ:1.00 FE4 A:SF4702 0.0 0.7 1.0 S2 A:SF4702 2.1 0.9 1.0 S1 A:SF4702 2.1 0.6 1.0 S3 A:SF4702 2.1 0.3 1.0 SG A:CYS252 2.7 0.5 1.0 FE3 A:SF4702 3.2 0.1 1.0 FE1 A:SF4702 3.2 0.8 1.0 FE2 A:SF4702 3.2 0.5 1.0 S4 A:SF4702 3.5 1.0 1.0 CB A:CYS252 3.5 0.5 1.0 CD1 A:ILE274 4.0 86.5 1.0 N A:CYS252 4.4 0.4 1.0 CA A:CYS252 4.6 0.6 1.0 CG1 A:ILE274 4.7 95.7 1.0 N A:GLN251 4.7 0.7 1.0 CA A:GLY250 4.9 0.6 1.0 CB A:TYR286 4.9 71.7 1.0 N A:GLY250 5.0 0.2 1.0

Iron binding site 9 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes


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 Soaked with Heterodisulfide For 3.5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:84.5 occ:1.00 FE1 A:SF4703 0.0 84.5 1.0 S3 A:SF4703 2.1 72.3 1.0 S4 A:SF4703 2.1 78.3 1.0 S2 A:SF4703 2.1 79.9 1.0 SG A:CYS299 2.6 0.6 1.0 CB A:CYS299 3.2 74.8 1.0 FE4 A:SF4703 3.2 0.1 1.0 FE2 A:SF4703 3.2 0.5 1.0 FE3 A:SF4703 3.3 0.1 1.0 S1 A:SF4703 3.5 91.8 1.0 N A:CYS299 4.1 91.1 1.0 CA A:CYS299 4.3 91.9 1.0 CG2 A:ILE288 4.7 64.9 1.0 O A:VAL255 4.8 81.5 1.0

Iron binding site 10 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 3.5 Minutes


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 Soaked with Heterodisulfide For 3.5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:0.5 occ:1.00 FE2 A:SF4703 0.0 0.5 1.0 S3 A:SF4703 2.1 72.3 1.0 S4 A:SF4703 2.1 78.3 1.0 S1 A:SF4703 2.1 91.8 1.0 SG A:CYS293 2.8 76.2 1.0 FE1 A:SF4703 3.2 84.5 1.0 FE4 A:SF4703 3.3 0.1 1.0 FE3 A:SF4703 3.3 0.1 1.0 CB A:CYS293 3.4 71.0 1.0 CA A:CYS293 3.5 71.4 1.0 N A:ILE294 3.6 67.4 1.0 S2 A:SF4703 3.6 79.9 1.0 N A:GLU295 3.6 83.9 1.0 C A:CYS293 3.9 72.9 1.0 CA A:GLU295 4.3 88.6 1.0 CB A:ALA273 4.3 75.8 1.0 CG1 A:ILE294 4.5 78.8 1.0 C A:ILE294 4.5 78.8 1.0 CA A:ILE294 4.6 71.9 1.0 N A:CYS296 4.8 92.2 1.0 N A:CYS293 4.8 64.7 1.0 CG2 A:ILE288 4.8 64.9 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