Iron in PDB 5exd: Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate

All present enzymatic activity of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate:
1.2.7.10;

The structure of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate, PDB code: 5exd was solved by M.I.Gibson, P.Y.-T.Chen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.94 / 2.50
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	138.430, 138.430, 217.069, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.9

The structure of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate also contains other interesting chemical elements:

Magnesium

(Mg)

4 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 - 48;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate (pdb code 5exd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 48 binding sites of Iron where determined in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate, PDB code: 5exd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 48 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:27.0 occ:1.00 FE1 B:SF4401 0.0 27.0 1.0 S2 B:SF4401 2.3 24.8 1.0 SG B:CYS290 2.3 23.9 1.0 S3 B:SF4401 2.3 23.4 1.0 S4 B:SF4401 2.3 28.1 1.0 FE4 B:SF4401 2.7 25.9 1.0 FE2 B:SF4401 2.7 28.7 1.0 FE3 B:SF4401 2.7 24.6 1.0 CB B:CYS290 3.6 26.9 1.0 S1 B:SF4401 3.9 28.3 1.0 N B:GLY292 4.0 26.3 1.0 CA B:CYS290 4.0 26.1 1.0 CG B:PRO254 4.1 29.4 1.0 N B:LYS291 4.2 25.8 1.0 CD B:PRO254 4.3 28.8 1.0 CA B:GLY292 4.3 26.5 1.0 C B:CYS290 4.5 26.2 1.0 N B:CYS293 4.7 27.1 1.0 CB B:CYS275 4.7 27.5 1.0 SG B:CYS296 4.7 27.5 1.0 SG B:CYS271 4.8 28.8 1.0 SG B:CYS293 5.0 27.5 1.0

Iron binding site 2 out of 48 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:28.7 occ:1.00 FE2 B:SF4401 0.0 28.7 1.0 S1 B:SF4401 2.3 28.3 1.0 S4 B:SF4401 2.3 28.1 1.0 S3 B:SF4401 2.3 23.4 1.0 SG B:CYS296 2.3 27.5 1.0 FE3 B:SF4401 2.7 24.6 1.0 FE4 B:SF4401 2.7 25.9 1.0 FE1 B:SF4401 2.7 27.0 1.0 CB B:CYS296 3.3 28.1 1.0 S2 B:SF4401 3.9 24.8 1.0 N B:CYS296 3.9 28.4 1.0 CG B:PRO254 4.2 29.4 1.0 CA B:CYS296 4.2 27.4 1.0 SG B:CYS293 4.5 27.5 1.0 N B:LEU295 4.6 26.0 1.0 CE2 B:PHE285 4.6 30.8 1.0 CB B:PRO254 4.7 29.9 1.0 N B:GLY294 4.7 27.2 1.0 SG B:CYS271 4.7 28.8 1.0 SG B:CYS290 4.8 23.9 1.0 CD1 B:ILE276 4.8 27.9 1.0 CD2 B:PHE285 4.9 30.4 1.0 CD B:PRO254 4.9 28.8 1.0

Iron binding site 3 out of 48 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:24.6 occ:1.00 FE3 B:SF4401 0.0 24.6 1.0 S1 B:SF4401 2.3 28.3 1.0 S4 B:SF4401 2.3 28.1 1.0 SG B:CYS293 2.3 27.5 1.0 S2 B:SF4401 2.3 24.8 1.0 FE2 B:SF4401 2.7 28.7 1.0 FE1 B:SF4401 2.7 27.0 1.0 FE4 B:SF4401 2.7 25.9 1.0 N B:CYS293 3.3 27.1 1.0 CB B:CYS293 3.4 25.9 1.0 N B:GLY294 3.7 27.2 1.0 CA B:CYS293 3.8 25.8 1.0 S3 B:SF4401 3.9 23.4 1.0 C B:CYS293 4.2 26.9 1.0 C B:GLY292 4.3 27.5 1.0 N B:GLY292 4.3 26.3 1.0 N B:LEU295 4.3 26.0 1.0 CA B:GLY292 4.4 26.5 1.0 SG B:CYS290 4.7 23.9 1.0 SG B:CYS296 4.7 27.5 1.0 CA B:GLY294 4.7 26.3 1.0 SG B:CYS271 4.8 28.8 1.0 CD B:PRO272 4.9 25.7 1.0 CB B:LEU295 4.9 25.6 1.0

Iron binding site 4 out of 48 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:25.9 occ:1.00 FE4 B:SF4401 0.0 25.9 1.0 S3 B:SF4401 2.3 23.4 1.0 S2 B:SF4401 2.3 24.8 1.0 S1 B:SF4401 2.3 28.3 1.0 SG B:CYS271 2.3 28.8 1.0 FE2 B:SF4401 2.7 28.7 1.0 FE1 B:SF4401 2.7 27.0 1.0 FE3 B:SF4401 2.7 24.6 1.0 CB B:CYS271 3.5 26.9 1.0 S4 B:SF4401 3.9 28.1 1.0 CA B:CYS271 4.1 27.4 1.0 CB B:CYS275 4.3 27.5 1.0 CD B:PRO272 4.4 25.7 1.0 SG B:CYS293 4.5 27.5 1.0 C B:CYS271 4.8 26.9 1.0 SG B:CYS275 4.8 28.0 1.0 N B:PRO272 4.8 25.9 1.0 SG B:CYS290 4.9 23.9 1.0 SG B:CYS296 4.9 27.5 1.0 N B:ASP273 4.9 24.2 1.0 CB B:ASP273 4.9 23.6 1.0 CG1 B:ILE276 4.9 29.3 1.0 CD1 B:ILE276 5.0 27.9 1.0 N B:CYS275 5.0 27.0 1.0 OD2 B:ASP273 5.0 23.5 1.0

Iron binding site 5 out of 48 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:28.0 occ:1.00 FE1 B:SF4402 0.0 28.0 1.0 S2 B:SF4402 2.3 34.6 1.0 SG B:CYS261 2.3 34.0 1.0 S3 B:SF4402 2.3 29.2 1.0 S4 B:SF4402 2.3 31.8 1.0 FE4 B:SF4402 2.7 32.6 1.0 FE3 B:SF4402 2.7 28.5 1.0 FE2 B:SF4402 2.7 33.5 1.0 CB B:CYS261 3.4 32.6 1.0 CA B:CYS261 3.7 32.9 1.0 N B:GLU263 3.7 32.0 1.0 N B:THR262 3.8 32.6 1.0 S1 B:SF4402 3.9 29.8 1.0 C B:CYS261 4.2 33.4 1.0 CA B:GLU263 4.2 32.1 1.0 CG B:PRO283 4.2 33.2 1.0 N B:CYS264 4.5 31.3 1.0 CD B:PRO283 4.5 34.2 1.0 C B:THR262 4.7 31.8 1.0 OG1 B:THR262 4.8 33.2 1.0 CA B:THR262 4.8 31.7 1.0 CB B:ALA304 4.9 32.9 1.0 SG B:CYS264 4.9 29.1 1.0 C B:GLU263 4.9 31.5 1.0 SG B:CYS267 4.9 27.6 1.0 SG B:CYS300 4.9 28.9 1.0 CD1 B:ILE256 4.9 32.3 1.0

Iron binding site 6 out of 48 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:33.5 occ:1.00 FE2 B:SF4402 0.0 33.5 1.0 S4 B:SF4402 2.3 31.8 1.0 S1 B:SF4402 2.3 29.8 1.0 SG B:CYS264 2.3 29.1 1.0 S3 B:SF4402 2.3 29.2 1.0 FE4 B:SF4402 2.7 32.6 1.0 FE3 B:SF4402 2.7 28.5 1.0 FE1 B:SF4402 2.7 28.0 1.0 N B:CYS264 3.5 31.3 1.0 N B:TYR265 3.6 31.2 1.0 CB B:CYS264 3.6 31.7 1.0 S2 B:SF4402 3.9 34.6 1.0 CA B:CYS264 3.9 31.0 1.0 OG1 B:THR262 4.1 33.2 1.0 C B:CYS264 4.1 30.1 1.0 N B:THR266 4.1 28.4 1.0 SG B:CYS300 4.4 28.9 1.0 CA B:TYR265 4.4 29.1 1.0 N B:GLU263 4.4 32.0 1.0 C B:GLU263 4.5 31.5 1.0 SG B:CYS267 4.5 27.6 1.0 CA B:GLU263 4.7 32.1 1.0 SG B:CYS261 4.8 34.0 1.0 CB B:THR266 4.8 29.9 1.0 OG1 B:THR266 4.8 30.6 1.0 CD B:PRO301 4.8 31.1 1.0 C B:TYR265 4.8 28.4 1.0 N B:CYS267 4.9 29.7 1.0 N B:THR262 4.9 32.6 1.0

Iron binding site 7 out of 48 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:28.5 occ:1.00 FE3 B:SF4402 0.0 28.5 1.0 SG B:CYS300 2.3 28.9 1.0 S4 B:SF4402 2.3 31.8 1.0 S2 B:SF4402 2.3 34.6 1.0 S1 B:SF4402 2.3 29.8 1.0 FE1 B:SF4402 2.7 28.0 1.0 FE4 B:SF4402 2.7 32.6 1.0 FE2 B:SF4402 2.7 33.5 1.0 CB B:CYS300 3.5 29.0 1.0 S3 B:SF4402 3.9 29.2 1.0 CB B:ALA304 4.2 32.9 1.0 CA B:CYS300 4.4 30.4 1.0 CG B:LEU305 4.5 30.4 1.0 CD1 B:LEU305 4.6 28.9 1.0 SG B:CYS264 4.6 29.1 1.0 CB B:SER302 4.7 32.6 1.0 N B:ALA304 4.8 31.9 1.0 SG B:CYS267 4.8 27.6 1.0 SG B:CYS261 4.9 34.0 1.0 CD B:PRO301 4.9 31.1 1.0 CA B:ALA304 5.0 31.8 1.0

Iron binding site 8 out of 48 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:32.6 occ:1.00 FE4 B:SF4402 0.0 32.6 1.0 S3 B:SF4402 2.3 29.2 1.0 S1 B:SF4402 2.3 29.8 1.0 S2 B:SF4402 2.3 34.6 1.0 SG B:CYS267 2.3 27.6 1.0 FE1 B:SF4402 2.7 28.0 1.0 FE2 B:SF4402 2.7 33.5 1.0 FE3 B:SF4402 2.7 28.5 1.0 CB B:CYS267 3.5 28.9 1.0 S4 B:SF4402 3.9 31.8 1.0 CG B:PRO283 3.9 33.2 1.0 N B:CYS267 4.2 29.7 1.0 CA B:CYS267 4.5 28.8 1.0 CD1 B:LEU305 4.6 28.9 1.0 CB B:PRO283 4.6 33.8 1.0 N B:TYR265 4.6 31.2 1.0 SG B:CYS261 4.7 34.0 1.0 SG B:CYS300 4.7 28.9 1.0 CA B:TYR265 4.7 29.1 1.0 SG B:CYS264 4.8 29.1 1.0 N B:THR266 4.8 28.4 1.0 CD B:PRO283 5.0 34.2 1.0 CG B:LEU305 5.0 30.4 1.0

Iron binding site 9 out of 48 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:23.7 occ:1.00 FE1 C:SF4401 0.0 23.7 1.0 S3 C:SF4401 2.3 22.9 1.0 SG C:CYS225 2.3 23.2 1.0 S4 C:SF4401 2.3 25.7 1.0 S2 C:SF4401 2.3 21.1 1.0 FE2 C:SF4401 2.7 23.4 1.0 FE3 C:SF4401 2.7 24.9 1.0 FE4 C:SF4401 2.7 23.9 1.0 CB C:CYS225 3.4 23.2 1.0 S1 C:SF4401 3.9 23.8 1.0 CA C:CYS225 4.1 22.8 1.0 CB C:ALA142 4.2 22.2 1.0 ND2 C:ASN138 4.4 23.4 1.0 SG C:CYS52 4.5 24.2 1.0 CB C:LYS227 4.7 23.4 1.0 C C:CYS225 4.8 23.1 1.0 SG C:CYS24 4.9 23.1 1.0 SG C:CYS27 4.9 22.0 1.0 CB C:ASN138 4.9 23.2 1.0 N C:GLY228 5.0 22.5 1.0

Iron binding site 10 out of 48 in the Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Oxalate Oxidoreductase From Moorella Thermoacetica Bound with Carboxy-Di-Oxido-Methyl-Tpp (Coom-Tpp) Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:23.4 occ:1.00 FE2 C:SF4401 0.0 23.4 1.0 SG C:CYS27 2.3 22.0 1.0 S3 C:SF4401 2.3 22.9 1.0 S4 C:SF4401 2.3 25.7 1.0 S1 C:SF4401 2.3 23.8 1.0 FE1 C:SF4401 2.7 23.7 1.0 FE3 C:SF4401 2.7 24.9 1.0 FE4 C:SF4401 2.7 23.9 1.0 CB C:CYS27 3.4 23.1 1.0 S2 C:SF4401 3.9 21.1 1.0 CA C:CYS27 4.0 23.0 1.0 CD C:PRO29 4.1 23.2 1.0 CE C:MET53 4.2 22.6 1.0 CB C:CYS24 4.3 24.3 1.0 CG C:PRO29 4.4 23.0 1.0 N C:CYS24 4.5 23.3 1.0 SG C:CYS24 4.6 23.1 1.0 C C:CYS27 4.7 23.7 1.0 CB C:PRO29 4.7 23.1 1.0 N C:GLY28 4.8 23.2 1.0 SG C:CYS225 4.8 23.2 1.0 SG C:CYS52 4.9 24.2 1.0 CB C:CYS52 4.9 23.1 1.0 N C:PRO29 5.0 23.0 1.0 CB C:THR23 5.0 23.0 1.0

M.I.Gibson, P.Y.Chen, A.C.Johnson, E.Pierce, M.Can, S.W.Ragsdale, C.L.Drennan. One-Carbon Chemistry of Oxalate Oxidoreductase Captured By X-Ray Crystallography. Proc.Natl.Acad.Sci.Usa V. 113 320 2016.
ISSN: ESSN 1091-6490
PubMed: 26712008
DOI: 10.1073/PNAS.1518537113