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Iron in PDB 6qkx: 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex)

Protein crystallography data

The structure of 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex), PDB code: 6qkx 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) 47.42 / 2.40
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 176.860, 176.860, 49.220, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.4

Iron Binding Sites:

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

Iron binding site 1 out of 4 in 6qkx

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Iron binding site 1 out of 4 in the 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized 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-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:77.5
occ:1.00
FE1 A:SF4801 0.0 77.5 1.0
S3 A:SF4801 2.3 67.4 1.0
S4 A:SF4801 2.3 78.0 1.0
S2 A:SF4801 2.3 65.1 0.8
SG A:CYS374 2.6 70.3 1.0
FE4 A:SF4801 2.7 76.2 0.8
FE2 A:SF4801 2.7 76.5 1.0
FE3 A:SF4801 2.7 65.3 0.8
CB A:CYS374 3.2 70.1 1.0
N A:CYS374 3.7 70.6 1.0
S1 A:SF4801 3.9 67.8 0.8
CA A:CYS374 4.1 65.3 1.0
CG A:ARG344 4.4 75.1 1.0
N A:ASN371 4.5 79.5 1.0
CD A:ARG344 4.5 73.4 1.0
CA A:ASN371 4.6 79.8 1.0
C A:GLY373 4.7 71.9 1.0
N A:GLY373 4.7 86.7 1.0
CB A:ARG344 4.7 75.9 1.0
SG A:CYS370 4.8 81.6 1.0
N A:GLN372 4.9 88.7 1.0
CA A:GLY373 5.0 82.3 1.0
SG A:CYS367 5.0 84.7 1.0

Iron binding site 2 out of 4 in 6qkx

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Iron binding site 2 out of 4 in the 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized 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-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:76.5
occ:1.00
FE2 A:SF4801 0.0 76.5 1.0
S4 A:SF4801 2.3 78.0 1.0
S1 A:SF4801 2.3 67.8 0.8
S3 A:SF4801 2.3 67.4 1.0
SG A:CYS386 2.6 77.4 1.0
FE1 A:SF4801 2.7 77.5 1.0
FE3 A:SF4801 2.7 65.3 0.8
FE4 A:SF4801 2.7 76.2 0.8
N A:MET387 3.6 85.0 1.0
CB A:CYS386 3.7 78.4 1.0
CA A:CYS386 3.9 83.7 1.0
S2 A:SF4801 3.9 65.1 0.8
C A:CYS386 4.2 83.7 1.0
CG2 A:VAL388 4.4 78.2 1.0
N A:VAL388 4.5 83.4 1.0
CB A:ALA348 4.6 89.5 1.0
CB A:MET387 4.6 88.8 1.0
CA A:MET387 4.6 85.8 1.0
CG2 A:ILE347 4.7 69.8 1.0
CA A:ALA348 4.8 86.6 1.0
SG A:CYS370 4.9 81.6 1.0
N A:ALA348 4.9 76.8 1.0

Iron binding site 3 out of 4 in 6qkx

Go back to Iron Binding Sites List in 6qkx
Iron binding site 3 out of 4 in the 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized 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-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:65.3
occ:0.80
FE3 A:SF4801 0.0 65.3 0.8
S4 A:SF4801 2.3 78.0 1.0
S2 A:SF4801 2.3 65.1 0.8
S1 A:SF4801 2.3 67.8 0.8
SG A:CYS367 2.5 84.7 1.0
FE1 A:SF4801 2.7 77.5 1.0
FE4 A:SF4801 2.7 76.2 0.8
FE2 A:SF4801 2.7 76.5 1.0
CB A:CYS367 3.5 85.0 1.0
S3 A:SF4801 3.9 67.4 1.0
CB A:ARG344 3.9 75.9 1.0
CA A:CYS367 3.9 86.0 1.0
N A:ALA369 4.1 81.8 1.0
N A:THR368 4.2 89.4 1.0
CG A:ARG344 4.4 75.1 1.0
C A:CYS367 4.4 87.5 1.0
CD A:ARG344 4.5 73.4 1.0
CA A:ALA369 4.5 80.3 1.0
O A:ARG344 4.5 72.3 1.0
CA A:ARG344 4.7 75.3 1.0
N A:CYS370 4.7 81.5 1.0
C A:ARG344 4.8 70.1 1.0
SG A:CYS374 4.8 70.3 1.0
CB A:ALA348 4.8 89.5 1.0

Iron binding site 4 out of 4 in 6qkx

Go back to Iron Binding Sites List in 6qkx
Iron binding site 4 out of 4 in the 2-Naphthoyl-Coa Reductase-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized 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-Dihydronaphthoyl-Coa Complex(Ncr-Dhncoa Co- Crystallized Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:76.2
occ:0.80
FE4 A:SF4801 0.0 76.2 0.8
S2 A:SF4801 2.3 65.1 0.8
S3 A:SF4801 2.3 67.4 1.0
S1 A:SF4801 2.3 67.8 0.8
SG A:CYS370 2.6 81.6 1.0
FE1 A:SF4801 2.7 77.5 1.0
FE3 A:SF4801 2.7 65.3 0.8
FE2 A:SF4801 2.7 76.5 1.0
N A:CYS370 3.4 81.5 1.0
CB A:CYS370 3.7 83.2 1.0
N A:ASN371 3.7 79.5 1.0
S4 A:SF4801 3.9 78.0 1.0
CA A:CYS370 3.9 81.6 1.0
C A:CYS370 4.2 79.4 1.0
CB A:MET387 4.2 88.8 1.0
OG1 A:THR368 4.3 88.8 1.0
N A:ALA369 4.4 81.8 1.0
C A:ALA369 4.4 79.5 1.0
N A:GLN372 4.5 88.7 1.0
N A:MET387 4.6 85.0 1.0
CA A:ASN371 4.6 79.8 1.0
CA A:ALA369 4.7 80.3 1.0
CE A:MET387 4.7 92.9 1.0
SG A:CYS374 4.8 70.3 1.0
SG A:CYS367 4.9 84.7 1.0
N A:GLY373 4.9 86.7 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: Sun Dec 13 16:57:28 2020

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