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Iron in PDB 5jfc: Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus

Enzymatic activity of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus

All present enzymatic activity of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus:
1.6.1.4;

Protein crystallography data

The structure of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus, PDB code: 5jfc was solved by O.A.Zadvornyy, G.J.Schut, D.M.Nguyen, J.H.Artz, M.Tokmina-Lukaszewska, G.Lipscomb, P.W.King, M.W.Adams, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.59 / 1.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 179.927, 179.927, 80.792, 90.00, 90.00, 120.00
R / Rfree (%) 14.7 / 15.9

Other elements in 5jfc:

The structure of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus (pdb code 5jfc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus, PDB code: 5jfc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 5jfc

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Iron binding site 1 out of 10 in the Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe501

b:11.4
occ:1.00
 FE1 L:SF4501 0.0 11.4 1.0
OE1 L:GLU126 1.9 15.3 1.0
S4 L:SF4501 2.1 10.8 1.0
S3 L:SF4501 2.1 9.5 1.0
S2 L:SF4501 2.1 11.5 1.0
CD L:GLU126 2.8 15.6 1.0
FE3 L:SF4501 3.0 10.8 1.0
FE2 L:SF4501 3.0 10.5 1.0
FE4 L:SF4501 3.0 10.7 1.0
OE2 L:GLU126 3.2 15.9 1.0
S1 L:SF4501 3.7 9.8 1.0
CD1 L:ILE60 3.9 11.6 1.0
OG1 L:THR97 4.0 10.5 1.0
CG L:GLU126 4.1 10.1 1.0
CB L:GLU126 4.3 10.4 1.0
CB L:THR97 4.6 11.6 1.0
ND2 L:ASN91 4.8 11.4 1.0
N L:GLY98 4.8 9.3 1.0
C L:THR97 4.8 9.6 1.0
SG L:CYS101 4.9 9.7 1.0
CA L:GLY98 4.9 10.4 1.0
O L:THR97 4.9 10.0 1.0
CG2 L:ILE122 5.0 11.1 1.0
SG L:CYS56 5.0 10.8 1.0

Iron binding site 2 out of 10 in 5jfc

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Iron binding site 2 out of 10 in the Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe501

b:10.5
occ:1.00
 FE2 L:SF4501 0.0 10.5 1.0
S3 L:SF4501 2.1 9.5 1.0
S4 L:SF4501 2.1 10.8 1.0
S1 L:SF4501 2.1 9.8 1.0
SG L:CYS101 2.2 9.7 1.0
FE4 L:SF4501 3.0 10.7 1.0
FE3 L:SF4501 3.0 10.8 1.0
FE1 L:SF4501 3.0 11.4 1.0
CB L:CYS101 3.0 9.4 1.0
S2 L:SF4501 3.7 11.5 1.0
NE2 L:GLN106 3.8 10.6 1.0
CB L:THR97 4.1 11.6 1.0
O L:THR97 4.3 10.0 1.0
CA L:CYS101 4.5 9.9 1.0
OE1 L:GLU126 4.5 15.3 1.0
OG1 L:THR97 4.5 10.5 1.0
CB L:ILE453 4.6 8.6 1.0
CG1 L:ILE453 4.6 9.4 1.0
C L:THR97 4.7 9.6 1.0
CG2 L:ILE453 4.7 9.6 1.0
SG L:CYS107 4.9 11.5 1.0
CA L:THR97 4.9 9.7 1.0
CG L:GLN103 5.0 10.5 1.0
CD1 L:ILE453 5.0 11.3 1.0
SG L:CYS56 5.0 10.8 1.0

Iron binding site 3 out of 10 in 5jfc

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Iron binding site 3 out of 10 in the Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe501

b:10.8
occ:1.00
 FE3 L:SF4501 0.0 10.8 1.0
S2 L:SF4501 2.1 11.5 1.0
S1 L:SF4501 2.1 9.8 1.0
S4 L:SF4501 2.1 10.8 1.0
SG L:CYS107 2.1 11.5 1.0
FE1 L:SF4501 3.0 11.4 1.0
FE2 L:SF4501 3.0 10.5 1.0
FE4 L:SF4501 3.0 10.7 1.0
CB L:CYS107 3.1 10.9 1.0
S3 L:SF4501 3.7 9.5 1.0
CG L:GLN103 4.1 10.5 1.0
CG2 L:ILE122 4.2 11.1 1.0
N L:CYS107 4.3 10.9 1.0
CA L:CYS107 4.3 11.1 1.0
OE1 L:GLU126 4.6 15.3 1.0
CB L:ILE122 4.8 11.4 1.0
CB L:CYS56 4.8 11.3 1.0
SG L:CYS56 4.9 10.8 1.0
CB L:GLN103 4.9 11.9 1.0
SG L:CYS101 4.9 9.7 1.0
CB L:CYS101 5.0 9.4 1.0

Iron binding site 4 out of 10 in 5jfc

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Iron binding site 4 out of 10 in the Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe501

b:10.7
occ:1.00
 FE4 L:SF4501 0.0 10.7 1.0
S1 L:SF4501 2.1 9.8 1.0
S3 L:SF4501 2.1 9.5 1.0
S2 L:SF4501 2.1 11.5 1.0
SG L:CYS56 2.2 10.8 1.0
FE2 L:SF4501 3.0 10.5 1.0
FE3 L:SF4501 3.0 10.8 1.0
FE1 L:SF4501 3.0 11.4 1.0
CB L:CYS56 3.1 11.3 1.0
S4 L:SF4501 3.7 10.8 1.0
CD1 L:ILE60 3.8 11.6 1.0
CA L:CYS56 3.8 11.4 1.0
CD L:PRO57 4.3 11.1 1.0
CG1 L:ILE60 4.5 10.5 1.0
C L:CYS56 4.5 10.2 1.0
N L:PRO57 4.6 9.9 1.0
CB L:ILE60 4.8 11.4 1.0
OE1 L:GLU126 4.8 15.3 1.0
CB L:CYS107 4.8 10.9 1.0
CG1 L:ILE453 4.8 9.4 1.0
SG L:CYS107 4.8 11.5 1.0
CD1 L:ILE453 5.0 11.3 1.0
CG2 L:VAL58 5.0 12.1 1.0

Iron binding site 5 out of 10 in 5jfc

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Iron binding site 5 out of 10 in the Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe502

b:14.6
occ:1.00
 FE1 L:SF4502 0.0 14.6 1.0
S3 L:SF4502 2.1 13.8 1.0
S2 L:SF4502 2.1 14.2 1.0
S4 L:SF4502 2.1 14.3 1.0
SG L:CYS45 2.3 21.6 1.0
FE2 L:SF4502 3.0 13.2 1.0
FE4 L:SF4502 3.0 13.7 1.0
FE3 L:SF4502 3.0 13.7 1.0
CB L:CYS45 3.4 17.8 1.0
S1 L:SF4502 3.7 12.9 1.0
N L:CYS45 3.9 18.6 1.0
CA L:CYS45 4.3 18.2 1.0
CB L:LEU43 4.6 15.6 1.0
N L:GLN44 4.6 15.5 1.0
CG2 L:VAL112 4.6 24.2 1.0
N L:LEU43 4.8 15.1 1.0
CD L:PRO51 4.8 15.5 1.0
SG L:CYS42 4.8 13.9 1.0
SG L:CYS52 4.8 12.9 1.0
CB L:VAL112 4.9 16.2 1.0
N L:VAL112 4.9 14.2 1.0
C L:LEU43 5.0 15.3 1.0

Iron binding site 6 out of 10 in 5jfc

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Iron binding site 6 out of 10 in the Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe502

b:13.2
occ:1.00
 FE2 L:SF4502 0.0 13.2 1.0
SG L:CYS52 2.1 12.9 1.0
S1 L:SF4502 2.1 12.9 1.0
S4 L:SF4502 2.1 14.3 1.0
S3 L:SF4502 2.1 13.8 1.0
FE4 L:SF4502 3.0 13.7 1.0
FE1 L:SF4502 3.0 14.6 1.0
FE3 L:SF4502 3.0 13.7 1.0
CB L:CYS52 3.0 12.7 1.0
S2 L:SF4502 3.7 14.2 1.0
N L:CYS52 4.1 12.3 1.0
CA L:CYS52 4.2 11.9 1.0
CD L:PRO63 4.4 12.4 1.0
CB L:ALA50 4.4 15.9 1.0
CG2 L:ILE62 4.5 11.8 1.0
SG L:CYS42 4.9 13.9 1.0
SG L:CYS45 4.9 21.6 1.0
SG L:CYS111 4.9 13.6 1.0
CG L:PRO63 5.0 12.8 1.0
CD1 L:ILE122 5.0 11.8 1.0

Iron binding site 7 out of 10 in 5jfc

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Iron binding site 7 out of 10 in the Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe502

b:13.7
occ:1.00
 FE3 L:SF4502 0.0 13.7 1.0
S4 L:SF4502 2.1 14.3 1.0
S2 L:SF4502 2.1 14.2 1.0
S1 L:SF4502 2.1 12.9 1.0
SG L:CYS42 2.2 13.9 1.0
FE2 L:SF4502 3.0 13.2 1.0
FE4 L:SF4502 3.0 13.7 1.0
FE1 L:SF4502 3.0 14.6 1.0
CB L:CYS42 3.3 14.2 1.0
S3 L:SF4502 3.7 13.8 1.0
CA L:CYS42 3.8 14.7 1.0
N L:LEU43 3.8 15.1 1.0
N L:GLN44 4.0 15.5 1.0
CG1 L:ILE120 4.1 13.8 1.0
C L:CYS42 4.2 15.3 1.0
CA L:LEU43 4.8 15.5 1.0
CA L:GLN44 4.8 14.7 1.0
C L:LEU43 4.9 15.3 1.0
CD1 L:ILE66 4.9 15.3 1.0
N L:CYS45 4.9 18.6 1.0
CB L:ILE120 4.9 13.4 1.0
SG L:CYS52 4.9 12.9 1.0
SG L:CYS45 5.0 21.6 1.0

Iron binding site 8 out of 10 in 5jfc

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Iron binding site 8 out of 10 in the Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe502

b:13.7
occ:1.00
 FE4 L:SF4502 0.0 13.7 1.0
S3 L:SF4502 2.1 13.8 1.0
S1 L:SF4502 2.1 12.9 1.0
S2 L:SF4502 2.1 14.2 1.0
SG L:CYS111 2.2 13.6 1.0
FE2 L:SF4502 3.0 13.2 1.0
FE1 L:SF4502 3.0 14.6 1.0
FE3 L:SF4502 3.0 13.7 1.0
CB L:CYS111 3.3 13.2 1.0
S4 L:SF4502 3.7 14.3 1.0
CA L:CYS111 3.7 13.3 1.0
CG1 L:ILE120 3.8 13.8 1.0
N L:VAL112 3.9 14.2 1.0
C L:CYS111 4.2 13.9 1.0
CB L:ILE120 4.4 13.4 1.0
N L:VAL113 4.6 15.0 1.0
CG2 L:VAL113 4.6 17.3 1.0
CB L:CYS52 4.8 12.7 1.0
SG L:CYS52 4.8 12.9 1.0
CA L:VAL112 4.9 14.8 1.0
N L:ILE120 5.0 13.7 1.0

Iron binding site 9 out of 10 in 5jfc

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Iron binding site 9 out of 10 in the Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe501

b:9.3
occ:1.00
 FE1 S:FES501 0.0 9.3 1.0
SG S:CYS243 2.2 9.8 1.0
S1 S:FES501 2.2 10.2 1.0
S2 S:FES501 2.2 10.1 1.0
SG S:CYS231 2.3 10.4 1.0
FE2 S:FES501 3.1 10.5 1.0
CB S:CYS243 3.2 9.1 1.0
CB S:CYS231 3.5 9.7 1.0
N S:CYS243 4.1 8.9 1.0
CA S:CYS243 4.2 9.1 1.0
CA S:GLY224 4.3 9.1 1.0
N S:GLY226 4.3 9.4 1.0
N S:CYS231 4.4 9.8 1.0
N S:GLY224 4.4 9.3 1.0
CA S:CYS231 4.6 8.9 1.0
C S:GLY224 4.6 10.3 1.0
OD1 S:ASP223 4.6 10.1 1.0
CB S:PHE241 4.6 11.0 1.0
N S:THR225 4.6 10.3 1.0
CA S:GLY226 4.6 9.5 1.0
N S:GLY229 4.9 10.6 1.0
CG S:MET221 4.9 9.9 1.0
SG S:CYS228 5.0 11.5 1.0

Iron binding site 10 out of 10 in 5jfc

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Iron binding site 10 out of 10 in the Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Nadh-Dependent Ferredoxin:Nadp Oxidoreductase (Nfni) From Pyrococcus Furiosus within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe501

b:10.5
occ:1.00
 FE2 S:FES501 0.0 10.5 1.0
OD1 S:ASP223 1.9 10.1 1.0
S2 S:FES501 2.2 10.1 1.0
S1 S:FES501 2.2 10.2 1.0
SG S:CYS228 2.3 11.5 1.0
CG S:ASP223 2.9 10.1 1.0
FE1 S:FES501 3.1 9.3 1.0
CB S:CYS228 3.4 11.3 1.0
OD2 S:ASP223 3.4 11.0 1.0
N S:CYS228 3.5 9.5 1.0
CA S:CYS228 3.9 11.6 1.0
N S:ASP223 3.9 9.2 1.0
N S:GLY229 3.9 10.6 1.0
N S:GLY224 3.9 9.3 1.0
N S:MET227 4.2 9.5 1.0
CB S:ASP223 4.2 9.1 1.0
C S:CYS228 4.2 13.3 1.0
O S:HOH900 4.3 18.1 1.0
N S:ALA230 4.4 10.8 1.0
CA S:ASP223 4.4 8.6 1.0
C S:MET227 4.5 14.5 1.0
N S:GLY226 4.6 9.4 1.0
N S:VAL222 4.6 7.8 1.0
SG S:CYS243 4.6 9.8 1.0
C S:ASP223 4.7 9.8 1.0
CB S:ALA230 4.7 10.1 1.0
CA S:MET227 4.8 10.6 1.0
CA S:GLY224 4.8 9.1 1.0
N S:THR225 4.8 10.3 1.0
C S:GLY226 4.8 9.4 1.0
C S:VAL222 4.9 9.0 1.0
SG S:CYS231 4.9 10.4 1.0
CB S:VAL222 4.9 9.2 1.0
CA S:GLY229 5.0 10.6 1.0
CA S:GLY226 5.0 9.5 1.0

Reference:

C.E.Lubner, D.P.Jennings, D.W.Mulder, G.J.Schut, O.A.Zadvornyy, J.P.Hoben, M.Tokmina-Lukaszewska, L.Berry, D.M.Nguyen, G.L.Lipscomb, B.Bothner, A.K.Jones, A.F.Miller, P.W.King, M.W.W.Adams, J.W.Peters. Mechanistic Insights Into Energy Conservation By Flavin-Based Electron Bifurcation. Nat. Chem. Biol. V. 13 655 2017.
ISSN: ESSN 1552-4469
PubMed: 28394885
DOI: 10.1038/NCHEMBIO.2348
Page generated: Sun Dec 13 16:04:11 2020

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