Atomistry » Iron » PDB 5ve4-5vuw » 5vj7
Atomistry »
  Iron »
    PDB 5ve4-5vuw »
      5vj7 »

Iron in PDB 5vj7: Ferredoxin Nadp Oxidoreductase (Xfn)

Enzymatic activity of Ferredoxin Nadp Oxidoreductase (Xfn)

All present enzymatic activity of Ferredoxin Nadp Oxidoreductase (Xfn):
1.18.1.2;

Protein crystallography data

The structure of Ferredoxin Nadp Oxidoreductase (Xfn), PDB code: 5vj7 was solved by O.A.Zadvornyy, D.M.N.Nguyen, G.J.Schut, G.L.Lipscomb, M.Tokmina-Lukaszewska, M.W.W.Adams, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.743, 73.140, 99.963, 90.00, 96.73, 90.00
R / Rfree (%) 18.3 / 25.1

Other elements in 5vj7:

The structure of Ferredoxin Nadp Oxidoreductase (Xfn) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Ferredoxin Nadp Oxidoreductase (Xfn) (pdb code 5vj7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Ferredoxin Nadp Oxidoreductase (Xfn), PDB code: 5vj7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 5vj7

Go back to Iron Binding Sites List in 5vj7
Iron binding site 1 out of 10 in the Ferredoxin Nadp Oxidoreductase (Xfn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ferredoxin Nadp Oxidoreductase (Xfn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:38.5
occ:1.00
 FE1 A:SF4501 0.0 38.5 1.0
OE1 A:GLU126 1.8 34.3 1.0
S3 A:SF4501 2.1 39.5 1.0
S2 A:SF4501 2.1 37.8 1.0
S4 A:SF4501 2.1 39.2 1.0
CD A:GLU126 2.8 60.4 1.0
FE4 A:SF4501 3.0 39.5 1.0
FE2 A:SF4501 3.0 40.2 1.0
FE3 A:SF4501 3.0 41.0 1.0
OE2 A:GLU126 3.3 54.3 1.0
S1 A:SF4501 3.7 39.6 1.0
OG1 A:THR97 4.1 33.1 1.0
CG A:GLU126 4.1 46.4 1.0
CD1 A:ILE60 4.1 34.5 1.0
SG A:CYS101 4.4 37.1 1.0
CB A:GLU126 4.4 35.0 1.0
CB A:THR97 4.5 29.7 1.0
N A:GLY98 4.6 27.7 1.0
ND2 A:ASN91 4.7 27.9 1.0
C A:THR97 4.7 31.9 1.0
CA A:GLY98 4.8 27.4 1.0
O A:THR97 4.9 31.5 1.0
SG A:CYS56 4.9 40.7 1.0

Iron binding site 2 out of 10 in 5vj7

Go back to Iron Binding Sites List in 5vj7
Iron binding site 2 out of 10 in the Ferredoxin Nadp Oxidoreductase (Xfn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ferredoxin Nadp Oxidoreductase (Xfn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:40.2
occ:1.00
 FE2 A:SF4501 0.0 40.2 1.0
S4 A:SF4501 2.1 39.2 1.0
S1 A:SF4501 2.1 39.6 1.0
S3 A:SF4501 2.1 39.5 1.0
SG A:CYS101 2.3 37.1 1.0
CB A:CYS101 2.9 33.3 1.0
FE1 A:SF4501 3.0 38.5 1.0
FE4 A:SF4501 3.0 39.5 1.0
FE3 A:SF4501 3.0 41.0 1.0
S2 A:SF4501 3.7 37.8 1.0
NE2 A:GLN106 3.8 40.1 1.0
O A:THR97 4.2 31.5 1.0
CB A:THR97 4.2 29.7 1.0
CA A:CYS101 4.4 33.0 1.0
CG1 A:ILE454 4.5 35.0 1.0
CB A:ILE454 4.6 35.0 1.0
OE1 A:GLU126 4.6 34.3 1.0
C A:THR97 4.6 31.9 1.0
CG2 A:ILE454 4.6 35.4 1.0
OG1 A:THR97 4.8 33.1 1.0
SG A:CYS56 4.9 40.7 1.0
CA A:THR97 4.9 28.4 1.0
NE2 A:GLN103 4.9 15.7 1.0
CD1 A:ILE454 4.9 32.8 1.0

Iron binding site 3 out of 10 in 5vj7

Go back to Iron Binding Sites List in 5vj7
Iron binding site 3 out of 10 in the Ferredoxin Nadp Oxidoreductase (Xfn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ferredoxin Nadp Oxidoreductase (Xfn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:41.0
occ:1.00
 FE3 A:SF4501 0.0 41.0 1.0
S2 A:SF4501 2.1 37.8 1.0
S1 A:SF4501 2.1 39.6 1.0
S4 A:SF4501 2.1 39.2 1.0
SG A:CYS107 2.2 41.8 1.0
FE1 A:SF4501 3.0 38.5 1.0
FE4 A:SF4501 3.0 39.5 1.0
FE2 A:SF4501 3.0 40.2 1.0
CB A:CYS107 3.2 38.0 1.0
S3 A:SF4501 3.7 39.5 1.0
CG A:GLN103 4.1 34.6 1.0
CG2 A:ILE122 4.2 36.3 1.0
CA A:CYS107 4.5 37.6 1.0
N A:CYS107 4.5 38.5 1.0
OE1 A:GLU126 4.6 34.3 1.0
SG A:CYS56 4.8 40.7 1.0
CB A:CYS56 4.8 36.9 1.0
CB A:ILE122 4.8 35.0 1.0
CB A:CYS101 4.9 33.3 1.0
NE2 A:GLN106 4.9 40.1 1.0
NE2 A:GLN103 4.9 15.7 1.0
N A:GLY123 5.0 31.6 1.0
SG A:CYS101 5.0 37.1 1.0

Iron binding site 4 out of 10 in 5vj7

Go back to Iron Binding Sites List in 5vj7
Iron binding site 4 out of 10 in the Ferredoxin Nadp Oxidoreductase (Xfn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ferredoxin Nadp Oxidoreductase (Xfn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:39.5
occ:1.00
 FE4 A:SF4501 0.0 39.5 1.0
SG A:CYS56 2.1 40.7 1.0
S1 A:SF4501 2.1 39.6 1.0
S2 A:SF4501 2.1 37.8 1.0
S3 A:SF4501 2.1 39.5 1.0
FE1 A:SF4501 3.0 38.5 1.0
FE2 A:SF4501 3.0 40.2 1.0
FE3 A:SF4501 3.0 41.0 1.0
CB A:CYS56 3.1 36.9 1.0
S4 A:SF4501 3.7 39.2 1.0
CD1 A:ILE60 3.8 34.5 1.0
CA A:CYS56 3.9 36.4 1.0
CD A:PRO57 4.5 38.7 1.0
CG1 A:ILE60 4.6 34.0 1.0
C A:CYS56 4.6 41.0 1.0
CG1 A:ILE454 4.7 35.0 1.0
OE1 A:GLU126 4.7 34.3 1.0
N A:PRO57 4.8 37.5 1.0
CD1 A:ILE454 4.8 32.8 1.0
CB A:CYS107 4.9 38.0 1.0
SG A:CYS107 4.9 41.8 1.0
CB A:ILE60 5.0 35.0 1.0

Iron binding site 5 out of 10 in 5vj7

Go back to Iron Binding Sites List in 5vj7
Iron binding site 5 out of 10 in the Ferredoxin Nadp Oxidoreductase (Xfn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ferredoxin Nadp Oxidoreductase (Xfn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:53.0
occ:1.00
 FE1 A:SF4502 0.0 53.0 1.0
S3 A:SF4502 2.1 46.8 1.0
S2 A:SF4502 2.1 45.2 1.0
S4 A:SF4502 2.1 45.1 1.0
SG A:CYS45 2.2 49.2 1.0
FE4 A:SF4502 3.0 43.1 1.0
FE2 A:SF4502 3.0 45.0 1.0
FE3 A:SF4502 3.0 41.6 1.0
CB A:CYS45 3.2 45.7 1.0
S1 A:SF4502 3.7 40.9 1.0
CG2 A:VAL112 3.8 52.6 1.0
N A:CYS45 3.9 45.3 1.0
CA A:CYS45 4.2 45.8 1.0
SG A:CYS52 4.7 44.0 1.0
SG A:CYS42 4.7 47.4 1.0
N A:LEU43 4.8 40.9 1.0
N A:GLN44 4.8 44.2 1.0
CB A:LEU43 4.9 41.2 1.0
CD A:PRO51 5.0 42.2 1.0

Iron binding site 6 out of 10 in 5vj7

Go back to Iron Binding Sites List in 5vj7
Iron binding site 6 out of 10 in the Ferredoxin Nadp Oxidoreductase (Xfn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ferredoxin Nadp Oxidoreductase (Xfn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:45.0
occ:1.00
 FE2 A:SF4502 0.0 45.0 1.0
SG A:CYS52 2.1 44.0 1.0
S4 A:SF4502 2.1 45.1 1.0
S3 A:SF4502 2.1 46.8 1.0
S1 A:SF4502 2.1 40.9 1.0
CB A:CYS52 2.9 39.8 1.0
FE1 A:SF4502 3.0 53.0 1.0
FE3 A:SF4502 3.0 41.6 1.0
FE4 A:SF4502 3.0 43.1 1.0
S2 A:SF4502 3.7 45.2 1.0
CG2 A:ILE62 4.1 36.2 1.0
CA A:CYS52 4.2 39.5 1.0
N A:CYS52 4.3 40.2 1.0
CD A:PRO63 4.6 41.9 1.0
CD1 A:ILE122 4.6 34.3 1.0
SG A:CYS42 4.7 47.4 1.0
CB A:ILE62 4.7 37.1 1.0
SG A:CYS111 4.8 43.4 1.0
CB A:ALA50 5.0 42.3 1.0

Iron binding site 7 out of 10 in 5vj7

Go back to Iron Binding Sites List in 5vj7
Iron binding site 7 out of 10 in the Ferredoxin Nadp Oxidoreductase (Xfn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Ferredoxin Nadp Oxidoreductase (Xfn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:41.6
occ:1.00
 FE3 A:SF4502 0.0 41.6 1.0
SG A:CYS42 2.0 47.4 1.0
S1 A:SF4502 2.1 40.9 1.0
S4 A:SF4502 2.1 45.1 1.0
S2 A:SF4502 2.1 45.2 1.0
FE4 A:SF4502 3.0 43.1 1.0
FE1 A:SF4502 3.0 53.0 1.0
FE2 A:SF4502 3.0 45.0 1.0
CB A:CYS42 3.2 43.4 1.0
CA A:CYS42 3.5 42.7 1.0
S3 A:SF4502 3.7 46.8 1.0
N A:LEU43 3.8 40.9 1.0
C A:CYS42 4.0 44.1 1.0
CG1 A:ILE120 4.2 40.9 1.0
N A:GLN44 4.3 44.2 1.0
SG A:CYS45 4.8 49.2 1.0
CA A:LEU43 4.8 41.2 1.0
CD1 A:ILE66 4.9 51.7 1.0
CB A:ILE120 4.9 40.4 1.0
N A:CYS42 4.9 43.0 1.0
CA A:GLN44 5.0 44.0 1.0
N A:CYS45 5.0 45.3 1.0
SG A:CYS52 5.0 44.0 1.0

Iron binding site 8 out of 10 in 5vj7

Go back to Iron Binding Sites List in 5vj7
Iron binding site 8 out of 10 in the Ferredoxin Nadp Oxidoreductase (Xfn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Ferredoxin Nadp Oxidoreductase (Xfn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:43.1
occ:1.00
 FE4 A:SF4502 0.0 43.1 1.0
S2 A:SF4502 2.1 45.2 1.0
S1 A:SF4502 2.1 40.9 1.0
S3 A:SF4502 2.1 46.8 1.0
SG A:CYS111 2.3 43.4 1.0
FE1 A:SF4502 3.0 53.0 1.0
FE3 A:SF4502 3.0 41.6 1.0
FE2 A:SF4502 3.0 45.0 1.0
CB A:CYS111 3.4 40.3 1.0
S4 A:SF4502 3.7 45.1 1.0
CG1 A:ILE120 3.8 40.9 1.0
CA A:CYS111 3.8 41.2 1.0
N A:VAL112 4.0 47.8 1.0
CG2 A:VAL113 4.2 47.9 1.0
C A:CYS111 4.2 48.4 1.0
CG2 A:VAL112 4.3 52.6 1.0
CB A:ILE120 4.4 40.4 1.0
N A:VAL113 4.6 47.2 1.0
CB A:CYS52 4.8 39.8 1.0
CB A:VAL113 4.9 48.9 1.0
N A:ILE120 4.9 37.9 1.0
SG A:CYS52 4.9 44.0 1.0
SG A:CYS42 5.0 47.4 1.0

Iron binding site 9 out of 10 in 5vj7

Go back to Iron Binding Sites List in 5vj7
Iron binding site 9 out of 10 in the Ferredoxin Nadp Oxidoreductase (Xfn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Ferredoxin Nadp Oxidoreductase (Xfn) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:35.9
occ:1.00
 FE1 B:FES302 0.0 35.9 1.0
SG B:CYS245 1.9 34.9 1.0
SG B:CYS233 2.2 35.9 1.0
S1 B:FES302 2.2 39.5 1.0
S2 B:FES302 2.2 35.4 1.0
CB B:CYS245 3.0 31.2 1.0
FE2 B:FES302 3.1 36.7 1.0
CB B:CYS233 3.6 32.4 1.0
N B:CYS245 4.0 31.2 1.0
CA B:CYS245 4.1 31.3 1.0
N B:GLY228 4.2 37.4 1.0
CA B:GLY226 4.3 36.2 1.0
CA B:GLY228 4.4 37.1 1.0
OD1 B:ASP225 4.4 34.3 1.0
N B:GLY226 4.5 36.2 1.0
OD2 B:ASP225 4.5 33.3 1.0
CB B:PHE243 4.5 29.7 1.0
N B:CYS233 4.6 33.1 1.0
N B:THR227 4.6 37.0 1.0
C B:GLY226 4.6 40.1 1.0
CA B:CYS233 4.7 32.6 1.0
SG B:CYS230 4.7 36.8 1.0
CG B:ASP225 4.8 34.7 1.0
C B:CYS245 4.8 37.8 1.0
CG B:MET223 5.0 32.1 1.0
CD2 B:PHE243 5.0 30.7 1.0
CG B:PHE243 5.0 29.7 1.0

Iron binding site 10 out of 10 in 5vj7

Go back to Iron Binding Sites List in 5vj7
Iron binding site 10 out of 10 in the Ferredoxin Nadp Oxidoreductase (Xfn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Ferredoxin Nadp Oxidoreductase (Xfn) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:36.7
occ:1.00
 FE2 B:FES302 0.0 36.7 1.0
SG B:CYS230 1.7 36.8 1.0
OD1 B:ASP225 2.0 34.3 1.0
S1 B:FES302 2.2 39.5 1.0
S2 B:FES302 2.2 35.4 1.0
CG B:ASP225 3.0 34.7 1.0
FE1 B:FES302 3.1 35.9 1.0
CB B:CYS230 3.4 33.3 1.0
OD2 B:ASP225 3.4 33.3 1.0
N B:GLY231 3.8 31.8 1.0
N B:CYS230 3.9 34.6 1.0
N B:ASP225 3.9 31.4 1.0
CA B:CYS230 3.9 33.5 1.0
N B:ALA232 4.1 34.4 1.0
C B:CYS230 4.2 36.1 1.0
N B:GLY226 4.2 36.2 1.0
N B:VAL224 4.2 29.5 1.0
CB B:ASP225 4.3 33.4 1.0
SG B:CYS233 4.4 35.9 1.0
CB B:ALA232 4.5 34.2 1.0
CA B:ASP225 4.6 31.9 1.0
SG B:CYS245 4.7 34.9 1.0
CB B:VAL224 4.7 35.4 1.0
CA B:VAL224 4.7 30.0 1.0
CA B:GLY231 4.7 32.2 1.0
C B:VAL224 4.8 34.5 1.0
N B:MET229 4.8 39.8 1.0
C B:MET229 4.9 40.6 1.0
CA B:ALA232 4.9 33.6 1.0
N B:CYS233 4.9 33.1 1.0
C B:ASP225 4.9 38.4 1.0
C B:GLY231 4.9 37.8 1.0

Reference:

D.M.N.Nguyen, G.J.Schut, O.A.Zadvornyy, M.Tokmina-Lukaszewska, S.Poudel, G.L.Lipscomb, L.A.Adams, J.T.Dinsmore, W.J.Nixon, E.S.Boyd, B.Bothner, J.W.Peters, M.W.W.Adams. Two Functionally Distinct Nadp(+)-Dependent Ferredoxin Oxidoreductases Maintain the Primary Redox Balance of Pyrococcus Furiosus. J. Biol. Chem. V. 292 14603 2017.
ISSN: ESSN 1083-351X
PubMed: 28705933
DOI: 10.1074/JBC.M117.794172
Page generated: Tue Aug 6 10:26:26 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy