Iron in PDB 6qkg: 2-Naphthoyl-Coa Reductase(Ncr)

The structure of 2-Naphthoyl-Coa Reductase(Ncr), PDB code: 6qkg was solved by K.Kayastha, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.94 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.450, 86.840, 96.870, 90.00, 90.71, 90.00
R / Rfree (%)	18.7 / 21.8

The binding sites of Iron atom in the 2-Naphthoyl-Coa Reductase(Ncr) (pdb code 6qkg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the 2-Naphthoyl-Coa Reductase(Ncr), PDB code: 6qkg:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the 2-Naphthoyl-Coa Reductase(Ncr)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2-Naphthoyl-Coa Reductase(Ncr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:43.5 occ:1.00 FE1 A:SF4801 0.0 43.5 1.0 SG A:CYS374 2.3 42.5 1.0 S2 A:SF4801 2.3 51.1 1.0 S3 A:SF4801 2.3 46.0 1.0 S4 A:SF4801 2.3 43.1 1.0 FE3 A:SF4801 2.7 42.8 1.0 FE2 A:SF4801 2.8 42.3 1.0 FE4 A:SF4801 2.8 72.6 1.0 CB A:CYS374 3.2 39.4 1.0 N A:CYS374 3.9 43.0 1.0 S1 A:SF4801 3.9 50.6 1.0 CA A:CYS374 4.1 40.6 1.0 CG A:ARG344 4.3 31.0 1.0 N A:ASN371 4.3 42.8 1.0 CA A:ASN371 4.5 44.5 1.0 CD A:ARG344 4.5 39.4 1.0 SG A:CYS370 4.5 46.5 1.0 CB A:ARG344 4.6 28.7 1.0 SG A:CYS367 4.7 36.0 1.0 SG A:CYS386 4.7 38.5 1.0 N A:GLN372 4.8 48.1 1.0 C A:ASN371 4.9 50.7 1.0 C A:GLY373 5.0 49.2 1.0

Iron binding site 2 out of 8 in the 2-Naphthoyl-Coa Reductase(Ncr)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2-Naphthoyl-Coa Reductase(Ncr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:42.3 occ:1.00 FE2 A:SF4801 0.0 42.3 1.0 SG A:CYS386 2.2 38.5 1.0 S4 A:SF4801 2.3 43.1 1.0 S3 A:SF4801 2.3 46.0 1.0 S1 A:SF4801 2.4 50.6 1.0 FE1 A:SF4801 2.8 43.5 1.0 FE3 A:SF4801 2.8 42.8 1.0 FE4 A:SF4801 2.8 72.6 1.0 CB A:CYS386 3.3 33.6 1.0 CA A:CYS386 3.7 33.7 1.0 N A:MET387 3.7 34.2 1.0 S2 A:SF4801 4.0 51.1 1.0 C A:CYS386 4.1 37.5 1.0 CG2 A:VAL388 4.3 32.5 1.0 N A:VAL388 4.5 31.9 1.0 SG A:CYS370 4.6 46.5 1.0 CB A:ALA348 4.6 31.5 1.0 CG2 A:ILE347 4.6 30.6 1.0 CA A:MET387 4.7 36.2 1.0 CB A:MET387 4.7 39.8 1.0 CA A:ALA348 4.8 30.9 1.0 N A:ALA348 4.8 30.4 1.0 SG A:CYS374 5.0 42.5 1.0

Iron binding site 3 out of 8 in the 2-Naphthoyl-Coa Reductase(Ncr)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2-Naphthoyl-Coa Reductase(Ncr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:42.8 occ:1.00 FE3 A:SF4801 0.0 42.8 1.0 S2 A:SF4801 2.3 51.1 1.0 S4 A:SF4801 2.3 43.1 1.0 S1 A:SF4801 2.4 50.6 1.0 SG A:CYS367 2.4 36.0 1.0 FE1 A:SF4801 2.7 43.5 1.0 FE4 A:SF4801 2.8 72.6 1.0 FE2 A:SF4801 2.8 42.3 1.0 CB A:CYS367 3.3 33.5 1.0 CA A:CYS367 3.7 36.0 1.0 S3 A:SF4801 3.9 46.0 1.0 CB A:ARG344 4.0 28.7 1.0 N A:ALA369 4.1 44.0 1.0 N A:THR368 4.1 42.3 1.0 C A:CYS367 4.2 43.8 1.0 CA A:ALA369 4.4 42.6 1.0 O A:ARG344 4.6 30.5 1.0 CB A:ALA348 4.6 31.5 1.0 N A:CYS370 4.6 41.1 1.0 CG A:ARG344 4.7 31.0 1.0 SG A:CYS374 4.7 42.5 1.0 SG A:CYS386 4.7 38.5 1.0 C A:ARG344 4.8 32.4 1.0 CA A:ARG344 4.8 27.3 1.0 SG A:CYS370 4.9 46.5 1.0 CD A:ARG344 4.9 39.4 1.0

Iron binding site 4 out of 8 in the 2-Naphthoyl-Coa Reductase(Ncr)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 2-Naphthoyl-Coa Reductase(Ncr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:72.6 occ:1.00 FE4 A:SF4801 0.0 72.6 1.0 SG A:CYS370 2.1 46.5 1.0 S1 A:SF4801 2.3 50.6 1.0 S3 A:SF4801 2.3 46.0 1.0 S2 A:SF4801 2.4 51.1 1.0 FE1 A:SF4801 2.8 43.5 1.0 FE3 A:SF4801 2.8 42.8 1.0 FE2 A:SF4801 2.8 42.3 1.0 CB A:CYS370 3.4 42.4 1.0 N A:CYS370 3.4 41.1 1.0 N A:ASN371 3.6 42.8 1.0 CA A:CYS370 3.8 41.8 1.0 S4 A:SF4801 4.0 43.1 1.0 C A:CYS370 4.1 45.2 1.0 CB A:MET387 4.3 39.8 1.0 N A:GLN372 4.4 48.1 1.0 C A:ALA369 4.5 46.1 1.0 OG1 A:THR368 4.5 45.6 1.0 CA A:ASN371 4.5 44.5 1.0 N A:MET387 4.6 34.2 1.0 N A:ALA369 4.6 44.0 1.0 SG A:CYS374 4.6 42.5 1.0 CA A:ALA369 4.8 42.6 1.0 SG A:CYS367 4.8 36.0 1.0 CE A:MET387 4.8 49.8 1.0 SG A:CYS386 4.9 38.5 1.0 C A:ASN371 4.9 50.7 1.0

Iron binding site 5 out of 8 in the 2-Naphthoyl-Coa Reductase(Ncr)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 2-Naphthoyl-Coa Reductase(Ncr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:49.9 occ:1.00 FE1 B:SF4801 0.0 49.9 1.0 S2 B:SF4801 2.3 54.2 1.0 S4 B:SF4801 2.3 51.5 1.0 S3 B:SF4801 2.3 55.5 1.0 SG B:CYS374 2.4 50.4 1.0 FE3 B:SF4801 2.8 53.1 1.0 FE2 B:SF4801 2.8 51.3 1.0 FE4 B:SF4801 2.8 76.2 1.0 CB B:CYS374 3.1 48.0 1.0 N B:CYS374 3.9 50.6 1.0 S1 B:SF4801 3.9 58.3 1.0 CA B:CYS374 4.2 49.3 1.0 CG B:ARG344 4.2 44.0 1.0 N B:ASN371 4.4 50.5 1.0 CA B:ASN371 4.5 50.4 1.0 CD B:ARG344 4.5 44.7 1.0 CB B:ARG344 4.5 38.4 1.0 SG B:CYS370 4.7 57.4 1.0 SG B:CYS367 4.7 46.0 1.0 SG B:CYS386 4.7 49.2 1.0 N B:GLN372 4.9 49.6 1.0 C B:ASN371 4.9 53.9 1.0

Iron binding site 6 out of 8 in the 2-Naphthoyl-Coa Reductase(Ncr)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 2-Naphthoyl-Coa Reductase(Ncr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:51.3 occ:1.00 FE2 B:SF4801 0.0 51.3 1.0 SG B:CYS386 2.2 49.2 1.0 S4 B:SF4801 2.3 51.5 1.0 S3 B:SF4801 2.3 55.5 1.0 S1 B:SF4801 2.4 58.3 1.0 FE1 B:SF4801 2.8 49.9 1.0 FE3 B:SF4801 2.8 53.1 1.0 FE4 B:SF4801 2.8 76.2 1.0 CB B:CYS386 3.4 45.6 1.0 N B:MET387 3.7 46.3 1.0 CA B:CYS386 3.7 45.5 1.0 S2 B:SF4801 4.0 54.2 1.0 C B:CYS386 4.1 48.7 1.0 CG2 B:VAL388 4.3 50.5 1.0 N B:VAL388 4.5 47.8 1.0 CB B:ALA348 4.6 43.2 1.0 CG2 B:ILE347 4.6 45.2 1.0 CA B:MET387 4.7 46.4 1.0 CB B:MET387 4.7 48.2 1.0 SG B:CYS370 4.7 57.4 1.0 CA B:ALA348 4.8 42.9 1.0 N B:ALA348 4.9 42.2 1.0

Iron binding site 7 out of 8 in the 2-Naphthoyl-Coa Reductase(Ncr)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 2-Naphthoyl-Coa Reductase(Ncr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:53.1 occ:1.00 FE3 B:SF4801 0.0 53.1 1.0 SG B:CYS367 2.3 46.0 1.0 S2 B:SF4801 2.3 54.2 1.0 S4 B:SF4801 2.3 51.5 1.0 S1 B:SF4801 2.3 58.3 1.0 FE1 B:SF4801 2.8 49.9 1.0 FE4 B:SF4801 2.8 76.2 1.0 FE2 B:SF4801 2.8 51.3 1.0 CB B:CYS367 3.2 43.7 1.0 CA B:CYS367 3.7 44.8 1.0 S3 B:SF4801 4.0 55.5 1.0 CB B:ARG344 4.0 38.4 1.0 N B:ALA369 4.1 51.1 1.0 N B:THR368 4.1 47.9 1.0 C B:CYS367 4.2 49.9 1.0 CA B:ALA369 4.5 50.8 1.0 O B:ARG344 4.6 41.8 1.0 CB B:ALA348 4.6 43.2 1.0 CG B:ARG344 4.6 44.0 1.0 N B:CYS370 4.7 52.1 1.0 SG B:CYS386 4.8 49.2 1.0 C B:ARG344 4.8 41.6 1.0 SG B:CYS374 4.8 50.4 1.0 CA B:ARG344 4.8 38.0 1.0 CD B:ARG344 4.9 44.7 1.0

Iron binding site 8 out of 8 in the 2-Naphthoyl-Coa Reductase(Ncr)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 2-Naphthoyl-Coa Reductase(Ncr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:76.2 occ:1.00 FE4 B:SF4801 0.0 76.2 1.0 SG B:CYS370 2.3 57.4 1.0 S1 B:SF4801 2.3 58.3 1.0 S3 B:SF4801 2.3 55.5 1.0 S2 B:SF4801 2.4 54.2 1.0 FE1 B:SF4801 2.8 49.9 1.0 FE3 B:SF4801 2.8 53.1 1.0 FE2 B:SF4801 2.8 51.3 1.0 N B:CYS370 3.5 52.1 1.0 CB B:CYS370 3.5 53.0 1.0 N B:ASN371 3.6 50.5 1.0 CA B:CYS370 3.9 52.1 1.0 S4 B:SF4801 4.0 51.5 1.0 C B:CYS370 4.2 55.2 1.0 CB B:MET387 4.3 48.2 1.0 N B:GLN372 4.4 49.6 1.0 OG1 B:THR368 4.5 59.3 1.0 CA B:ASN371 4.5 50.4 1.0 C B:ALA369 4.6 53.9 1.0 N B:ALA369 4.6 51.1 1.0 N B:MET387 4.6 46.3 1.0 SG B:CYS374 4.7 50.4 1.0 SG B:CYS367 4.8 46.0 1.0 CA B:ALA369 4.8 50.8 1.0 SG B:CYS386 4.9 49.2 1.0 C B:ASN371 5.0 53.9 1.0

M.Willistein, D.F.Bechtel, C.S.Muller, U.Demmer, L.Heimann, K.Kayastha, V.Schunemann, A.J.Pierik, G.M.Ullmann, U.Ermler, M.Boll. Low Potential Enzymatic Hydride Transfer Via Highly Cooperative and Inversely Functionalized Flavin Cofactors. Nat Commun V. 10 2074 2019.
ISSN: ESSN 2041-1723
PubMed: 31061390
DOI: 10.1038/S41467-019-10078-3