Atomistry » Iron » PDB 5ve3-5vuv » 5vj7
Atomistry »
  Iron »
    PDB 5ve3-5vuv »
      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: Sun Dec 13 16:14:47 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy