Iron in PDB 5odr: Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 Minutes.

All present enzymatic activity of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 Minutes.:
1.12.99.6; 1.8.98.1;

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 Minutes., PDB code: 5odr 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)	90.26 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	366.219, 96.920, 134.450, 90.00, 108.30, 90.00
R / Rfree (%)	20.4 / 22.5

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 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 2 Minutes. (pdb code 5odr). 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 2 Minutes., PDB code: 5odr:
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 2 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 2 Minutes. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:27.4 occ:1.00 FE1 A:SF4702 0.0 27.4 1.0 SG A:CYS399 2.3 25.5 1.0 S4 A:SF4702 2.3 28.2 1.0 S3 A:SF4702 2.3 29.1 1.0 S2 A:SF4702 2.3 28.5 1.0 FE3 A:SF4702 2.7 29.6 1.0 FE4 A:SF4702 2.8 28.4 1.0 FE2 A:SF4702 2.9 28.2 1.0 CB A:CYS399 3.6 22.1 1.0 CD A:ARG431 3.9 30.3 1.0 NH2 A:ARG431 3.9 22.1 1.0 CA A:CYS399 3.9 23.3 1.0 S1 A:SF4702 3.9 29.5 1.0 N A:SER400 4.0 24.7 1.0 N A:ASN401 4.2 29.3 1.0 CD A:ARG390 4.2 28.4 1.0 C A:CYS399 4.3 26.9 1.0 NE A:ARG431 4.7 32.9 1.0 CZ A:ARG431 4.7 39.7 1.0 CA A:ASN401 4.7 28.3 1.0 CG A:ARG431 4.7 30.5 1.0 CG A:ARG390 4.7 23.8 1.0 SG A:CYS386 4.8 30.2 1.0 CB A:ARG431 4.9 23.8 1.0 SG A:CYS403 4.9 29.7 1.0 SG A:CYS404 5.0 29.4 1.0

Iron binding site 2 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 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 2 Minutes. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:28.2 occ:1.00 FE2 A:SF4702 0.0 28.2 1.0 S3 A:SF4702 2.3 29.1 1.0 S1 A:SF4702 2.3 29.5 1.0 SG A:CYS404 2.3 29.4 1.0 S4 A:SF4702 2.4 28.2 1.0 FE4 A:SF4702 2.7 28.4 1.0 FE3 A:SF4702 2.8 29.6 1.0 FE1 A:SF4702 2.9 27.4 1.0 CB A:CYS404 3.2 26.2 1.0 N A:CYS404 3.4 26.6 1.0 CA A:CYS404 3.7 26.3 1.0 S2 A:SF4702 4.0 28.5 1.0 O A:ASP429 4.3 29.2 1.0 C A:CYS403 4.3 29.1 1.0 CB A:ARG431 4.3 23.8 1.0 O A:HOH941 4.4 19.8 1.0 CB A:CYS403 4.5 25.9 1.0 N A:ARG431 4.6 24.3 1.0 CG A:ARG431 4.6 30.5 1.0 O A:HOH834 4.6 24.8 1.0 CD A:ARG431 4.7 30.3 1.0 SG A:CYS386 4.7 30.2 1.0 NE2 A:GLN385 4.7 28.5 1.0 CA A:CYS403 4.8 26.4 1.0 SG A:CYS403 4.8 29.7 1.0 SG A:CYS399 4.8 25.5 1.0 N A:CYS403 4.9 26.6 1.0

Iron binding site 3 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 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 2 Minutes. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:29.6 occ:1.00 FE3 A:SF4702 0.0 29.6 1.0 S2 A:SF4702 2.2 28.5 1.0 S1 A:SF4702 2.3 29.5 1.0 S4 A:SF4702 2.3 28.2 1.0 SG A:CYS386 2.3 30.2 1.0 FE4 A:SF4702 2.7 28.4 1.0 FE1 A:SF4702 2.7 27.4 1.0 FE2 A:SF4702 2.8 28.2 1.0 CB A:CYS386 3.4 26.7 1.0 CA A:CYS386 3.5 26.8 1.0 N A:CYS386 3.6 27.9 1.0 S3 A:SF4702 3.9 29.1 1.0 CD A:ARG390 3.9 28.4 1.0 O A:HOH941 4.0 19.8 1.0 O A:HOH922 4.5 21.3 1.0 CG A:ARG390 4.6 23.8 1.0 NH1 A:ARG390 4.7 28.4 1.0 SG A:CYS403 4.7 29.7 1.0 SG A:CYS404 4.7 29.4 1.0 C A:GLN385 4.7 32.5 1.0 CB A:GLN385 4.8 29.2 1.0 SG A:CYS399 4.9 25.5 1.0 CB A:SER389 5.0 32.2 1.0 CB A:CYS403 5.0 25.9 1.0 C A:CYS386 5.0 29.8 1.0

Iron binding site 4 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 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 2 Minutes. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:28.4 occ:1.00 FE4 A:SF4702 0.0 28.4 1.0 S1 A:SF4702 2.3 29.5 1.0 SG A:CYS403 2.3 29.7 1.0 S3 A:SF4702 2.3 29.1 1.0 S2 A:SF4702 2.4 28.5 1.0 FE3 A:SF4702 2.7 29.6 1.0 FE2 A:SF4702 2.7 28.2 1.0 FE1 A:SF4702 2.8 27.4 1.0 CB A:CYS403 2.9 25.9 1.0 N A:CYS403 3.6 26.6 1.0 CA A:CYS403 3.6 26.4 1.0 O A:HOH922 3.8 21.3 1.0 S4 A:SF4702 3.8 28.2 1.0 N A:CYS404 3.9 26.6 1.0 C A:CYS403 4.1 29.1 1.0 N A:ASN401 4.3 29.3 1.0 N A:SER400 4.3 24.7 1.0 CB A:SER400 4.5 28.2 1.0 SG A:CYS399 4.6 25.5 1.0 C A:SER400 4.6 29.7 1.0 CA A:SER400 4.7 24.4 1.0 N A:VAL402 4.8 27.7 1.0 N A:CYS386 4.8 27.9 1.0 SG A:CYS404 4.8 29.4 1.0 C A:VAL402 4.8 31.0 1.0 C A:ASN401 4.9 31.8 1.0 CA A:CYS386 4.9 26.8 1.0 SG A:CYS386 4.9 30.2 1.0 CA A:ASN401 5.0 28.3 1.0

Iron binding site 5 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 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 2 Minutes. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:0.6 occ:1.00 FE1 A:SF4703 0.0 0.6 1.0 S3 A:SF4703 2.3 0.9 1.0 S2 A:SF4703 2.3 0.4 1.0 S4 A:SF4703 2.3 0.4 1.0 SG A:CYS303 2.8 0.8 1.0 FE4 A:SF4703 2.8 0.1 1.0 FE3 A:SF4703 2.8 0.8 1.0 FE2 A:SF4703 2.8 0.0 1.0 S1 A:SF4703 4.0 0.0 1.0 CD A:PRO305 4.2 0.3 1.0 CB A:CYS303 4.2 0.1 1.0 CG A:PRO305 4.4 0.8 1.0 SG A:CYS252 4.4 0.7 1.0 CB A:ALA307 4.7 0.8 1.0 CA A:CYS303 4.7 0.4 1.0 CB A:PRO305 4.8 0.4 1.0 SG A:CYS249 4.9 0.9 1.0

Iron binding site 6 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 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 2 Minutes. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:0.0 occ:1.00 FE2 A:SF4703 0.0 0.0 1.0 SG A:CYS249 2.3 0.9 1.0 S1 A:SF4703 2.3 0.0 1.0 S4 A:SF4703 2.3 0.4 1.0 S3 A:SF4703 2.3 0.9 1.0 FE4 A:SF4703 2.8 0.1 1.0 FE3 A:SF4703 2.8 0.8 1.0 FE1 A:SF4703 2.8 0.6 1.0 OG1 A:THR247 3.0 0.9 1.0 N A:CYS249 3.7 0.1 1.0 CB A:CYS249 3.8 0.3 1.0 N A:GLY250 3.8 0.5 1.0 S2 A:SF4703 4.0 0.4 1.0 CA A:CYS249 4.1 0.3 1.0 N A:GLY248 4.2 0.4 1.0 CB A:THR247 4.4 0.1 1.0 C A:CYS249 4.5 0.1 1.0 N A:GLN251 4.6 0.9 1.0 N A:THR247 4.7 0.3 1.0 CA A:GLY250 4.7 0.6 1.0 C A:GLY248 4.7 0.8 1.0 CA A:GLY248 4.9 0.6 1.0 CA A:THR247 4.9 0.8 1.0

Iron binding site 7 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 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 2 Minutes. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:0.8 occ:1.00 FE3 A:SF4703 0.0 0.8 1.0 S4 A:SF4703 2.3 0.4 1.0 S1 A:SF4703 2.3 0.0 1.0 S2 A:SF4703 2.3 0.4 1.0 FE4 A:SF4703 2.8 0.1 1.0 FE2 A:SF4703 2.8 0.0 1.0 FE1 A:SF4703 2.8 0.6 1.0 SG A:CYS246 3.2 0.4 1.0 N A:THR247 3.8 0.3 1.0 CA A:CYS246 3.9 0.4 1.0 S3 A:SF4703 3.9 0.9 1.0 N A:GLY248 3.9 0.4 1.0 CB A:CYS246 4.0 1.0 1.0 OG1 A:THR247 4.2 0.9 1.0 C A:CYS246 4.3 1.0 1.0 CA A:GLY248 4.6 0.6 1.0 CG2 A:ILE241 4.7 0.9 1.0 CB A:TYR286 4.8 82.9 1.0 CA A:THR247 4.8 0.8 1.0 C A:THR247 4.9 0.8 1.0 N A:CYS249 4.9 0.1 1.0 SG A:CYS249 4.9 0.9 1.0 CD1 A:TYR286 5.0 86.0 1.0

Iron binding site 8 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 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 2 Minutes. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:0.1 occ:1.00 FE4 A:SF4703 0.0 0.1 1.0 S3 A:SF4703 2.3 0.9 1.0 S1 A:SF4703 2.3 0.0 1.0 S2 A:SF4703 2.3 0.4 1.0 FE3 A:SF4703 2.8 0.8 1.0 SG A:CYS252 2.8 0.7 1.0 FE1 A:SF4703 2.8 0.6 1.0 FE2 A:SF4703 2.8 0.0 1.0 S4 A:SF4703 3.9 0.4 1.0 N A:GLY250 4.2 0.5 1.0 CB A:CYS252 4.2 0.2 1.0 CA A:GLY250 4.2 0.6 1.0 N A:GLN251 4.3 0.9 1.0 N A:CYS252 4.3 0.9 1.0 SG A:CYS249 4.6 0.9 1.0 C A:GLY250 4.6 0.9 1.0 CG A:TYR286 4.7 84.8 1.0 CB A:TYR286 4.8 82.9 1.0 SG A:CYS303 4.8 0.8 1.0 CA A:CYS252 4.9 0.9 1.0 CD2 A:TYR286 5.0 86.3 1.0

Iron binding site 9 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 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 2 Minutes. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe704 b:0.5 occ:1.00 FE1 A:SF4704 0.0 0.5 1.0 SG A:CYS299 2.2 0.1 1.0 S2 A:SF4704 2.3 0.5 1.0 S3 A:SF4704 2.3 0.8 1.0 S4 A:SF4704 2.3 0.6 1.0 FE4 A:SF4704 2.7 0.4 1.0 FE2 A:SF4704 2.8 0.8 1.0 FE3 A:SF4704 2.9 0.7 1.0 CB A:CYS299 3.0 0.4 1.0 N A:CYS299 3.9 0.6 1.0 S1 A:SF4704 4.0 0.6 1.0 CA A:CYS299 4.1 0.6 1.0 CG2 A:ILE274 4.6 96.5 1.0 CZ A:PHE310 4.7 0.3 1.0 N A:LEU298 4.9 0.7 1.0 SG A:CYS256 4.9 0.9 1.0 SG A:CYS293 4.9 0.2 1.0

Iron binding site 10 out of 113 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus Soaked with Heterodisulfide For 2 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 2 Minutes. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe704 b:0.8 occ:1.00 FE2 A:SF4704 0.0 0.8 1.0 S4 A:SF4704 2.3 0.6 1.0 S3 A:SF4704 2.3 0.8 1.0 S1 A:SF4704 2.3 0.6 1.0 SG A:CYS293 2.4 0.2 1.0 FE4 A:SF4704 2.8 0.4 1.0 FE3 A:SF4704 2.8 0.7 1.0 FE1 A:SF4704 2.8 0.5 1.0 CB A:CYS293 3.6 0.3 1.0 S2 A:SF4704 3.9 0.5 1.0 CA A:CYS293 4.1 0.2 1.0 N A:GLU295 4.1 0.8 1.0 N A:ILE294 4.2 0.4 1.0 CB A:ALA273 4.3 94.3 1.0 CG2 A:ILE288 4.5 99.3 1.0 C A:CYS293 4.5 0.4 1.0 CE1 A:PHE310 4.6 0.2 1.0 CA A:GLU295 4.6 0.8 1.0 SG A:CYS299 4.8 0.1 1.0 CZ A:PHE310 4.9 0.3 1.0 SG A:CYS256 4.9 0.9 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