Iron in PDB 5odi: Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh

All present enzymatic activity of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh:
1.12.1.2; 1.8.98.1;

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh, PDB code: 5odi 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)	48.54 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	370.528, 97.077, 135.149, 90.00, 109.43, 90.00
R / Rfree (%)	20.2 / 24.1

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh 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 - 112;

Binding sites:

The binding sites of Iron atom in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh (pdb code 5odi). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 112 binding sites of Iron where determined in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh, PDB code: 5odi:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 112 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh


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 Cocrystallized with Com-Sh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:15.5 occ:1.00 FE1 A:SF4703 0.0 15.5 1.0 S4 A:SF4703 2.1 20.9 1.0 S3 A:SF4703 2.1 16.9 1.0 S2 A:SF4703 2.1 13.8 1.0 SG A:CYS399 2.3 15.1 1.0 FE2 A:SF4703 2.9 24.6 1.0 FE3 A:SF4703 3.1 19.6 1.0 FE4 A:SF4703 3.1 18.7 1.0 CB A:CYS399 3.4 14.4 1.0 NH2 A:ARG431 3.7 36.1 1.0 S1 A:SF4703 3.7 18.7 1.0 CD A:ARG431 3.8 34.1 1.0 CA A:CYS399 3.8 17.9 1.0 N A:SER400 4.0 21.7 1.0 CD A:ARG390 4.0 23.1 1.0 N A:ASN401 4.2 28.1 1.0 C A:CYS399 4.3 27.6 1.0 CZ A:ARG431 4.6 58.4 1.0 NE A:ARG431 4.6 44.6 1.0 CG A:ARG390 4.7 25.4 1.0 CA A:ASN401 4.9 24.3 1.0 CB A:ARG431 4.9 16.3 1.0 NH1 A:ARG390 4.9 29.5 1.0 SG A:CYS386 5.0 19.2 1.0 SG A:CYS403 5.0 29.4 1.0 CG A:ARG431 5.0 30.7 1.0

Iron binding site 2 out of 112 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh


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 Cocrystallized with Com-Sh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:24.6 occ:1.00 FE2 A:SF4703 0.0 24.6 1.0 S3 A:SF4703 2.1 16.9 1.0 S1 A:SF4703 2.1 18.7 1.0 S4 A:SF4703 2.2 20.9 1.0 SG A:CYS404 2.3 21.5 1.0 FE4 A:SF4703 2.9 18.7 1.0 FE1 A:SF4703 2.9 15.5 1.0 FE3 A:SF4703 3.1 19.6 1.0 CB A:CYS404 3.1 17.3 1.0 N A:CYS404 3.4 17.0 1.0 S2 A:SF4703 3.5 13.8 1.0 CA A:CYS404 3.6 17.9 1.0 O A:HOH831 3.7 31.3 1.0 O A:ASP429 4.0 26.6 1.0 C A:CYS403 4.3 25.4 1.0 O A:HOH812 4.5 3.0 1.0 CB A:ARG431 4.5 16.3 1.0 CB A:CYS403 4.5 25.3 1.0 CD A:ARG431 4.6 34.1 1.0 N A:ARG431 4.7 19.7 1.0 SG A:CYS386 4.7 19.2 1.0 NE2 A:GLN385 4.8 43.5 1.0 CA A:CYS403 4.8 22.3 1.0 SG A:CYS399 4.9 15.1 1.0 SG A:CYS403 5.0 29.4 1.0 N A:CYS403 5.0 21.4 1.0

Iron binding site 3 out of 112 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh


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 Cocrystallized with Com-Sh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:19.6 occ:1.00 FE3 A:SF4703 0.0 19.6 1.0 S2 A:SF4703 2.1 13.8 1.0 SG A:CYS386 2.1 19.2 1.0 S4 A:SF4703 2.1 20.9 1.0 S1 A:SF4703 2.1 18.7 1.0 CB A:CYS386 3.0 16.3 1.0 FE1 A:SF4703 3.1 15.5 1.0 FE2 A:SF4703 3.1 24.6 1.0 FE4 A:SF4703 3.1 18.7 1.0 CA A:CYS386 3.2 16.1 1.0 N A:CYS386 3.4 19.3 1.0 O A:HOH831 3.4 31.3 1.0 S3 A:SF4703 3.8 16.9 1.0 CD A:ARG390 3.8 23.1 1.0 O A:HOH847 4.2 7.4 1.0 C A:GLN385 4.5 29.8 1.0 CG A:ARG390 4.5 25.4 1.0 NH1 A:ARG390 4.6 29.5 1.0 CB A:GLN385 4.6 23.0 1.0 C A:CYS386 4.7 22.9 1.0 CB A:SER389 4.8 29.8 1.0 SG A:CYS404 4.9 21.5 1.0 NE A:ARG390 5.0 10.9 1.0

Iron binding site 4 out of 112 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh


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 Cocrystallized with Com-Sh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:18.7 occ:1.00 FE4 A:SF4703 0.0 18.7 1.0 S3 A:SF4703 2.1 16.9 1.0 S2 A:SF4703 2.1 13.8 1.0 S1 A:SF4703 2.1 18.7 1.0 SG A:CYS403 2.2 29.4 1.0 CB A:CYS403 2.5 25.3 1.0 FE2 A:SF4703 2.9 24.6 1.0 FE1 A:SF4703 3.1 15.5 1.0 FE3 A:SF4703 3.1 19.6 1.0 CA A:CYS403 3.4 22.3 1.0 O A:HOH847 3.5 7.4 1.0 N A:CYS403 3.6 21.4 1.0 S4 A:SF4703 3.7 20.9 1.0 N A:CYS404 3.7 17.0 1.0 C A:CYS403 3.9 25.4 1.0 N A:SER400 4.3 21.7 1.0 N A:ASN401 4.5 28.1 1.0 CB A:SER400 4.5 24.6 1.0 CA A:SER400 4.7 22.2 1.0 C A:SER400 4.7 27.2 1.0 C A:VAL402 4.7 20.2 1.0 N A:CYS386 4.7 19.3 1.0 SG A:CYS399 4.8 15.1 1.0 CA A:CYS404 4.9 17.9 1.0 CA A:CYS386 4.9 16.1 1.0 SG A:CYS404 4.9 21.5 1.0 N A:VAL402 4.9 13.7 1.0 O A:CYS403 4.9 25.5 1.0 OG A:SER389 5.0 22.3 1.0

Iron binding site 5 out of 112 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh


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 Cocrystallized with Com-Sh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe704 b:31.9 occ:1.00 FE1 A:SF4704 0.0 31.9 1.0 S3 A:SF4704 2.1 15.0 1.0 S4 A:SF4704 2.1 19.9 1.0 SG A:CYS11 2.1 44.0 1.0 S2 A:SF4704 2.2 12.8 1.0 FE4 A:SF4704 3.1 21.5 1.0 FE2 A:SF4704 3.1 28.0 1.0 FE3 A:SF4704 3.2 28.9 1.0 CB A:CYS11 3.3 38.0 1.0 S1 A:SF4704 3.7 21.4 1.0 N A:MET45 3.8 39.2 1.0 CB A:CYS13 3.8 28.0 1.0 CA A:CYS13 3.8 31.1 1.0 N A:CYS13 4.0 37.7 1.0 CB A:ALA70 4.1 34.3 1.0 SG A:CYS13 4.2 27.4 1.0 CA A:TYR44 4.3 33.2 1.0 C A:TYR44 4.5 38.7 1.0 CB A:MET45 4.6 38.8 1.0 O A:LYS43 4.6 37.9 1.0 CA A:CYS11 4.6 35.9 1.0 N A:CYS46 4.7 34.4 1.0 CA A:MET45 4.7 37.5 1.0 CD1 A:ILE17 4.9 41.9 1.0 N A:HIS12 4.9 34.9 1.0 C A:CYS11 5.0 36.1 1.0

Iron binding site 6 out of 112 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh


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 Cocrystallized with Com-Sh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe704 b:28.0 occ:1.00 FE2 A:SF4704 0.0 28.0 1.0 S4 A:SF4704 2.1 19.9 1.0 S3 A:SF4704 2.1 15.0 1.0 S1 A:SF4704 2.1 21.4 1.0 SG A:CYS46 2.2 31.4 1.0 CB A:CYS46 3.0 30.7 1.0 FE1 A:SF4704 3.1 31.9 1.0 FE3 A:SF4704 3.2 28.9 1.0 FE4 A:SF4704 3.2 21.5 1.0 N A:CYS46 3.5 34.4 1.0 S2 A:SF4704 3.8 12.8 1.0 CA A:CYS46 3.8 33.0 1.0 CA G:CYS197 4.1 44.2 1.0 N A:MET45 4.4 39.2 1.0 SG G:CYS197 4.4 53.6 1.0 CD2 A:HIS76 4.5 45.7 1.0 CB G:CYS197 4.6 48.4 1.0 NE2 A:HIS76 4.6 45.5 1.0 C A:CYS46 4.7 33.1 1.0 C A:MET45 4.7 37.6 1.0 N G:CYS197 4.7 43.1 1.0 C A:TYR44 4.8 38.7 1.0 N A:ALA47 4.8 27.3 1.0 CA A:TYR44 4.8 33.2 1.0 O G:CYS197 4.8 32.3 1.0 CB A:TYR44 4.9 35.9 1.0 SG A:CYS11 4.9 44.0 1.0

Iron binding site 7 out of 112 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh


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 Cocrystallized with Com-Sh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe704 b:28.9 occ:1.00 FE3 A:SF4704 0.0 28.9 1.0 S1 A:SF4704 2.1 21.4 1.0 S4 A:SF4704 2.1 19.9 1.0 S2 A:SF4704 2.2 12.8 1.0 SG G:CYS197 2.3 53.6 1.0 SG A:CYS13 2.3 27.4 1.0 FE2 A:SF4704 3.2 28.0 1.0 FE1 A:SF4704 3.2 31.9 1.0 FE4 A:SF4704 3.2 21.5 1.0 NH1 A:ARG100 3.4 20.2 1.0 CB A:CYS13 3.5 28.0 1.0 CB G:CYS197 3.6 48.4 1.0 S3 A:SF4704 3.7 15.0 1.0 CA A:CYS13 4.0 31.1 1.0 CA G:CYS197 4.1 44.2 1.0 CZ A:ARG100 4.4 40.6 1.0 CB G:CYS194 4.5 36.0 1.0 N G:CYS197 4.7 43.1 1.0 SG A:CYS71 4.9 38.4 1.0 CB A:CYS71 4.9 34.3 1.0

Iron binding site 8 out of 112 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh


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 Cocrystallized with Com-Sh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe704 b:21.5 occ:1.00 FE4 A:SF4704 0.0 21.5 1.0 S2 A:SF4704 2.1 12.8 1.0 S3 A:SF4704 2.2 15.0 1.0 S1 A:SF4704 2.2 21.4 1.0 SG A:CYS71 2.3 38.4 1.0 FE1 A:SF4704 3.1 31.9 1.0 CB A:CYS71 3.2 34.3 1.0 FE3 A:SF4704 3.2 28.9 1.0 FE2 A:SF4704 3.2 28.0 1.0 S4 A:SF4704 3.7 19.9 1.0 N A:CYS71 3.7 34.1 1.0 CB A:ALA70 3.9 34.3 1.0 CD2 A:HIS76 4.0 45.7 1.0 CA A:CYS71 4.1 32.9 1.0 C A:ALA70 4.7 34.8 1.0 NH1 A:ARG100 4.8 20.2 1.0 SG A:CYS13 4.9 27.4 1.0 CA A:ALA70 4.9 33.1 1.0 NE2 A:HIS76 4.9 45.5 1.0 CG A:HIS76 4.9 44.9 1.0

Iron binding site 9 out of 112 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh


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 Cocrystallized with Com-Sh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe705 b:35.9 occ:1.00 FE1 A:SF4705 0.0 35.9 1.0 S2 A:SF4705 2.1 31.3 1.0 S4 A:SF4705 2.1 35.3 1.0 S3 A:SF4705 2.1 24.3 1.0 SG A:CYS617 2.2 37.2 1.0 CB A:CYS617 3.1 34.2 1.0 FE2 A:SF4705 3.1 36.3 1.0 FE4 A:SF4705 3.1 29.5 1.0 FE3 A:SF4705 3.2 41.8 1.0 CA A:CYS617 3.7 32.2 1.0 S1 A:SF4705 3.7 32.4 1.0 N A:GLY619 3.8 26.9 1.0 N A:LYS618 4.0 24.9 1.0 CB A:ALA577 4.1 45.3 1.0 CA A:GLY619 4.2 25.9 1.0 C A:CYS617 4.2 30.7 1.0 N A:CYS620 4.3 21.5 1.0 N A:ALA577 4.5 43.9 1.0 C A:GLY619 4.7 24.6 1.0 C A:LYS618 4.8 29.8 1.0 CB A:ALA598 4.9 32.0 1.0 SG A:CYS623 5.0 33.6 1.0 CA A:ALA577 5.0 44.4 1.0 N A:CYS617 5.0 32.9 1.0

Iron binding site 10 out of 112 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Cocrystallized with Com-Sh


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 Cocrystallized with Com-Sh within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe705 b:36.3 occ:1.00 FE2 A:SF4705 0.0 36.3 1.0 S1 A:SF4705 2.1 32.4 1.0 S3 A:SF4705 2.1 24.3 1.0 S4 A:SF4705 2.1 35.3 1.0 SG A:CYS623 2.2 33.6 1.0 FE3 A:SF4705 3.1 41.8 1.0 FE1 A:SF4705 3.1 35.9 1.0 CB A:CYS623 3.1 28.8 1.0 FE4 A:SF4705 3.2 29.5 1.0 N A:CYS623 3.6 24.2 1.0 S2 A:SF4705 3.6 31.3 1.0 CD A:PRO624 3.8 23.4 1.0 CA A:CYS623 3.9 27.2 1.0 CB A:ALA577 4.3 45.3 1.0 N A:THR622 4.6 31.7 1.0 N A:PRO624 4.6 27.0 1.0 CG A:PRO624 4.7 27.6 1.0 C A:CYS623 4.7 33.5 1.0 CG A:PRO599 4.7 44.8 1.0 C A:THR622 4.8 23.2 1.0 CB A:CYS594 4.8 40.4 1.0 SG A:CYS620 4.8 23.6 1.0 N A:GLY621 4.9 26.8 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