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

Protein crystallography data

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

Iron Binding Sites:

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 6qkg

Go back to Iron Binding Sites List in 6qkg
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 6qkg

Go back to Iron Binding Sites List in 6qkg
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 6qkg

Go back to Iron Binding Sites List in 6qkg
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 6qkg

Go back to Iron Binding Sites List in 6qkg
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 6qkg

Go back to Iron Binding Sites List in 6qkg
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 6qkg

Go back to Iron Binding Sites List in 6qkg
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 6qkg

Go back to Iron Binding Sites List in 6qkg
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 6qkg

Go back to Iron Binding Sites List in 6qkg
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

Reference:

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
Page generated: Wed Aug 7 07:57:54 2024

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