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Iron in PDB 6qkr: 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex)

Protein crystallography data

The structure of 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex), PDB code: 6qkr 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) 30.24 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.670, 86.050, 96.900, 90.00, 90.67, 90.00
R / Rfree (%) 17.8 / 21.8

Iron Binding Sites:

The binding sites of Iron atom in the 2-Naphthoyl-Coa Reductase-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) (pdb code 6qkr). 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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex), PDB code: 6qkr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6qkr

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


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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:60.4
occ:1.00
 FE1 A:SF4801 0.0 60.4 1.0
SG A:CYS374 2.3 62.1 1.0
S2 A:SF4801 2.3 62.0 1.0
S4 A:SF4801 2.3 56.8 1.0
S3 A:SF4801 2.3 61.8 1.0
FE3 A:SF4801 2.8 57.0 1.0
FE2 A:SF4801 2.8 59.1 1.0
FE4 A:SF4801 2.8 83.1 1.0
CB A:CYS374 3.3 58.8 1.0
N A:CYS374 3.9 60.0 1.0
S1 A:SF4801 4.0 65.4 1.0
CG A:ARG344 4.1 48.1 1.0
CA A:CYS374 4.2 59.3 1.0
CD A:ARG344 4.4 48.8 1.0
N A:ASN371 4.4 63.1 1.0
CA A:ASN371 4.5 63.0 1.0
CB A:ARG344 4.6 47.2 1.0
N A:GLN372 4.8 67.1 1.0
SG A:CYS367 4.8 55.0 1.0
SG A:CYS386 4.8 55.0 1.0
SG A:CYS370 4.8 65.4 1.0
C A:ASN371 4.9 69.6 1.0
N A:GLY373 4.9 62.8 1.0
CG2 A:ILE347 5.0 46.9 1.0
C A:GLY373 5.0 63.8 1.0

Iron binding site 2 out of 8 in 6qkr

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


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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:59.1
occ:1.00
 FE2 A:SF4801 0.0 59.1 1.0
SG A:CYS386 2.3 55.0 1.0
S4 A:SF4801 2.3 56.8 1.0
S3 A:SF4801 2.3 61.8 1.0
S1 A:SF4801 2.4 65.4 1.0
FE3 A:SF4801 2.8 57.0 1.0
FE1 A:SF4801 2.8 60.4 1.0
FE4 A:SF4801 2.8 83.1 1.0
CB A:CYS386 3.4 49.8 1.0
N A:MET387 3.7 50.1 1.0
CA A:CYS386 3.8 49.1 1.0
S2 A:SF4801 4.0 62.0 1.0
C A:CYS386 4.2 54.8 1.0
CG2 A:VAL388 4.3 55.4 1.0
N A:VAL388 4.4 49.5 1.0
CG2 A:ILE347 4.6 46.9 1.0
CB A:ALA348 4.6 50.9 1.0
CB A:MET387 4.7 54.7 1.0
CA A:MET387 4.7 51.7 1.0
CA A:ALA348 4.7 49.8 1.0
N A:ALA348 4.8 48.5 1.0
SG A:CYS370 4.8 65.4 1.0

Iron binding site 3 out of 8 in 6qkr

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


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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:57.0
occ:1.00
 FE3 A:SF4801 0.0 57.0 1.0
S2 A:SF4801 2.3 62.0 1.0
S4 A:SF4801 2.3 56.8 1.0
S1 A:SF4801 2.4 65.4 1.0
SG A:CYS367 2.4 55.0 1.0
FE1 A:SF4801 2.8 60.4 1.0
FE4 A:SF4801 2.8 83.1 1.0
FE2 A:SF4801 2.8 59.1 1.0
CB A:CYS367 3.3 52.0 1.0
CA A:CYS367 3.8 53.6 1.0
S3 A:SF4801 4.0 61.8 1.0
CB A:ARG344 4.0 47.2 1.0
N A:THR368 4.1 57.8 1.0
N A:ALA369 4.1 63.9 1.0
C A:CYS367 4.3 59.9 1.0
CG A:ARG344 4.5 48.1 1.0
CA A:ALA369 4.5 63.1 1.0
O A:ARG344 4.6 53.6 1.0
CB A:ALA348 4.6 50.9 1.0
N A:CYS370 4.6 62.6 1.0
CD A:ARG344 4.7 48.8 1.0
SG A:CYS374 4.8 62.1 1.0
C A:ARG344 4.8 51.7 1.0
SG A:CYS386 4.8 55.0 1.0
CA A:ARG344 4.8 46.2 1.0

Iron binding site 4 out of 8 in 6qkr

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


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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:83.1
occ:1.00
 FE4 A:SF4801 0.0 83.1 1.0
S1 A:SF4801 2.3 65.4 1.0
S3 A:SF4801 2.4 61.8 1.0
S2 A:SF4801 2.4 62.0 1.0
SG A:CYS370 2.4 65.4 1.0
FE3 A:SF4801 2.8 57.0 1.0
FE1 A:SF4801 2.8 60.4 1.0
FE2 A:SF4801 2.8 59.1 1.0
N A:CYS370 3.5 62.6 1.0
CB A:CYS370 3.5 61.4 1.0
N A:ASN371 3.7 63.1 1.0
CA A:CYS370 3.8 62.0 1.0
S4 A:SF4801 4.0 56.8 1.0
C A:CYS370 4.1 65.3 1.0
OG1 A:THR368 4.3 69.9 1.0
CB A:MET387 4.3 54.7 1.0
N A:GLN372 4.4 67.1 1.0
C A:ALA369 4.6 68.2 1.0
CA A:ASN371 4.6 63.0 1.0
N A:ALA369 4.7 63.9 1.0
N A:MET387 4.7 50.1 1.0
CE A:MET387 4.7 61.8 1.0
SG A:CYS374 4.7 62.1 1.0
SG A:CYS367 4.8 55.0 1.0
CA A:ALA369 4.9 63.1 1.0
SG A:CYS386 4.9 55.0 1.0
C A:ASN371 5.0 69.6 1.0
N A:THR368 5.0 57.8 1.0

Iron binding site 5 out of 8 in 6qkr

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


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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:54.2
occ:1.00
 FE1 B:SF4801 0.0 54.2 1.0
S2 B:SF4801 2.3 61.8 1.0
S4 B:SF4801 2.3 53.6 1.0
S3 B:SF4801 2.3 57.7 1.0
SG B:CYS374 2.3 54.5 1.0
FE3 B:SF4801 2.8 54.0 1.0
FE4 B:SF4801 2.8 80.2 1.0
FE2 B:SF4801 2.8 55.2 1.0
CB B:CYS374 3.3 51.8 1.0
N B:CYS374 4.0 55.1 1.0
S1 B:SF4801 4.0 61.3 1.0
CG B:ARG344 4.1 49.6 1.0
CA B:CYS374 4.2 52.8 1.0
CD B:ARG344 4.3 45.9 1.0
N B:ASN371 4.4 54.2 1.0
CA B:ASN371 4.4 54.1 1.0
CB B:ARG344 4.6 42.7 1.0
SG B:CYS367 4.7 50.8 1.0
SG B:CYS370 4.7 58.5 1.0
N B:GLN372 4.8 57.1 1.0
SG B:CYS386 4.8 50.5 1.0
C B:ASN371 4.8 59.2 1.0
N B:GLY373 4.9 58.0 1.0
CG2 B:ILE347 5.0 47.4 1.0

Iron binding site 6 out of 8 in 6qkr

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


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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:55.2
occ:1.00
 FE2 B:SF4801 0.0 55.2 1.0
SG B:CYS386 2.2 50.5 1.0
S4 B:SF4801 2.4 53.6 1.0
S1 B:SF4801 2.4 61.3 1.0
S3 B:SF4801 2.4 57.7 1.0
FE1 B:SF4801 2.8 54.2 1.0
FE3 B:SF4801 2.8 54.0 1.0
FE4 B:SF4801 2.8 80.2 1.0
CB B:CYS386 3.4 47.0 1.0
N B:MET387 3.7 50.5 1.0
CA B:CYS386 3.8 47.8 1.0
S2 B:SF4801 4.0 61.8 1.0
C B:CYS386 4.2 52.5 1.0
CG2 B:VAL388 4.3 52.0 1.0
N B:VAL388 4.4 48.8 1.0
CG2 B:ILE347 4.6 47.4 1.0
CB B:ALA348 4.6 47.1 1.0
CA B:MET387 4.6 52.5 1.0
CB B:MET387 4.6 55.9 1.0
CA B:ALA348 4.8 46.5 1.0
SG B:CYS370 4.8 58.5 1.0
N B:ALA348 4.8 46.6 1.0

Iron binding site 7 out of 8 in 6qkr

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


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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:54.0
occ:1.00
 FE3 B:SF4801 0.0 54.0 1.0
SG B:CYS367 2.3 50.8 1.0
S2 B:SF4801 2.3 61.8 1.0
S4 B:SF4801 2.3 53.6 1.0
S1 B:SF4801 2.4 61.3 1.0
FE1 B:SF4801 2.8 54.2 1.0
FE4 B:SF4801 2.8 80.2 1.0
FE2 B:SF4801 2.8 55.2 1.0
CB B:CYS367 3.3 48.7 1.0
CA B:CYS367 3.8 49.6 1.0
CB B:ARG344 4.0 42.7 1.0
S3 B:SF4801 4.0 57.7 1.0
N B:THR368 4.0 47.7 1.0
N B:ALA369 4.1 57.7 1.0
C B:CYS367 4.3 53.7 1.0
CG B:ARG344 4.5 49.6 1.0
CA B:ALA369 4.6 57.7 1.0
O B:ARG344 4.6 46.2 1.0
CB B:ALA348 4.7 47.1 1.0
N B:CYS370 4.7 54.7 1.0
CD B:ARG344 4.7 45.9 1.0
C B:ARG344 4.8 46.3 1.0
SG B:CYS374 4.8 54.5 1.0
CA B:ARG344 4.8 43.8 1.0
SG B:CYS386 4.8 50.5 1.0

Iron binding site 8 out of 8 in 6qkr

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


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-2-Naphthoyl-Coa Complex(Ncr-Ncoa-Soaked Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:80.2
occ:1.00
 FE4 B:SF4801 0.0 80.2 1.0
S1 B:SF4801 2.3 61.3 1.0
S3 B:SF4801 2.4 57.7 1.0
SG B:CYS370 2.4 58.5 1.0
S2 B:SF4801 2.4 61.8 1.0
FE1 B:SF4801 2.8 54.2 1.0
FE3 B:SF4801 2.8 54.0 1.0
FE2 B:SF4801 2.8 55.2 1.0
N B:CYS370 3.5 54.7 1.0
CB B:CYS370 3.5 54.7 1.0
N B:ASN371 3.6 54.2 1.0
CA B:CYS370 3.9 54.2 1.0
S4 B:SF4801 4.0 53.6 1.0
C B:CYS370 4.1 57.5 1.0
OG1 B:THR368 4.2 54.8 1.0
CB B:MET387 4.3 55.9 1.0
N B:GLN372 4.4 57.1 1.0
CA B:ASN371 4.5 54.1 1.0
C B:ALA369 4.6 61.7 1.0
N B:MET387 4.7 50.5 1.0
N B:ALA369 4.7 57.7 1.0
SG B:CYS374 4.7 54.5 1.0
SG B:CYS367 4.8 50.8 1.0
CA B:ALA369 4.9 57.7 1.0
SG B:CYS386 4.9 50.5 1.0
C B:ASN371 4.9 59.2 1.0
N B:THR368 5.0 47.7 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 08:03:14 2024

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