Iron in PDB 4ylf: Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure

Protein crystallography data

The structure of Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure, PDB code: 4ylf was solved by U.Ermler, R.K.Thauer, J.K.Demmer, H.Huang, S.Wang, U.Demmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.29 / 2.30
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 81.420, 81.420, 311.480, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.9

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iron atom in the Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure (pdb code 4ylf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure, PDB code: 4ylf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 4ylf

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Iron binding site 1 out of 20 in the Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:42.2
occ:1.00
 FE1 A:FES501 0.0 42.2 1.0
S1 A:FES501 2.2 36.5 1.0
S2 A:FES501 2.2 82.2 1.0
SG A:CYS228 2.3 53.2 1.0
SG A:CYS240 2.3 35.5 1.0
FE2 A:FES501 3.1 60.4 1.0
CB A:CYS240 3.3 40.5 1.0
OD1 A:ASP220 3.5 73.9 1.0
CB A:CYS228 3.7 23.7 1.0
N A:GLY223 4.2 43.8 1.0
CA A:GLY223 4.2 49.6 1.0
N A:CYS240 4.3 35.8 1.0
CA A:GLY221 4.4 30.4 1.0
N A:GLY221 4.4 40.8 1.0
CA A:CYS240 4.4 30.1 1.0
N A:CYS228 4.5 42.3 1.0
N A:GLY226 4.5 58.0 1.0
CG A:ASP220 4.6 69.3 1.0
CB A:PHE238 4.6 47.1 1.0
CA A:CYS228 4.7 50.0 1.0
CA A:GLY226 4.7 68.1 1.0
C A:GLY221 4.7 32.8 1.0
N A:THR222 4.8 38.9 1.0
OD2 A:ASP220 4.9 70.2 1.0
N A:ALA227 4.9 71.5 1.0

Iron binding site 2 out of 20 in 4ylf

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Iron binding site 2 out of 20 in the Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:60.4
occ:1.00
 FE2 A:FES501 0.0 60.4 1.0
OD1 A:ASP220 2.1 73.9 1.0
S2 A:FES501 2.2 82.2 1.0
S1 A:FES501 2.2 36.5 1.0
SG A:CYS225 2.3 26.1 1.0
OD2 A:ASP220 2.3 70.2 1.0
CG A:ASP220 2.5 69.3 1.0
FE1 A:FES501 3.1 42.2 1.0
N A:GLY226 3.2 58.0 1.0
CB A:CYS225 3.4 40.5 1.0
N A:CYS225 3.6 51.2 1.0
CA A:CYS225 3.8 45.0 1.0
N A:ALA227 3.9 71.5 1.0
CB A:ASP220 3.9 33.4 1.0
C A:CYS225 4.0 62.6 1.0
N A:ASP220 4.0 23.1 1.0
N A:GLY221 4.1 40.8 1.0
CA A:GLY226 4.1 68.1 1.0
N A:MET224 4.4 40.2 1.0
CA A:ASP220 4.5 28.4 1.0
C A:GLY226 4.5 64.5 1.0
SG A:CYS228 4.6 53.2 1.0
CB A:ALA227 4.6 41.2 1.0
N A:VAL219 4.7 39.7 1.0
N A:GLY223 4.7 43.8 1.0
C A:MET224 4.7 53.4 1.0
CB A:VAL219 4.8 44.6 1.0
C A:ASP220 4.8 49.4 1.0
CA A:ALA227 4.8 49.6 1.0
N A:CYS228 4.9 42.3 1.0
CA A:GLY223 4.9 49.6 1.0
SG A:CYS240 4.9 35.5 1.0
C A:GLY223 5.0 49.4 1.0

Iron binding site 3 out of 20 in 4ylf

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Iron binding site 3 out of 20 in the Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:0.5
occ:1.00
 FE1 B:SF4501 0.0 0.5 1.0
SG B:CYS100 2.2 62.4 1.0
S2 B:SF4501 2.2 39.6 1.0
S4 B:SF4501 2.2 86.7 1.0
S3 B:SF4501 2.2 83.1 1.0
FE2 B:SF4501 3.0 0.7 1.0
FE4 B:SF4501 3.1 33.1 1.0
FE3 B:SF4501 3.1 30.2 1.0
CB B:CYS100 3.3 46.4 1.0
CA B:CYS100 3.6 40.1 1.0
CG2 B:VAL111 3.7 43.6 1.0
S1 B:SF4501 3.8 42.3 1.0
N B:VAL101 3.8 40.5 1.0
C B:CYS100 4.1 36.6 1.0
CB B:VAL111 4.1 36.0 1.0
N B:VAL102 4.5 54.1 1.0
CG1 B:VAL102 4.6 36.6 1.0
CB B:CYS47 4.6 67.3 1.0
CG2 B:VAL102 4.7 58.1 1.0
CA B:VAL101 4.8 56.6 1.0
N B:VAL111 4.9 57.8 1.0
SG B:CYS47 4.9 21.6 1.0
CB B:VAL101 4.9 46.8 1.0
N B:CYS100 4.9 23.6 1.0

Iron binding site 4 out of 20 in 4ylf

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Iron binding site 4 out of 20 in the Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:0.7
occ:1.00
 FE2 B:SF4501 0.0 0.7 1.0
SG B:CYS47 2.0 21.6 1.0
S1 B:SF4501 2.2 42.3 1.0
S3 B:SF4501 2.2 83.1 1.0
S4 B:SF4501 2.2 86.7 1.0
CB B:CYS47 2.6 67.3 1.0
FE1 B:SF4501 3.0 0.5 1.0
FE4 B:SF4501 3.1 33.1 1.0
FE3 B:SF4501 3.1 30.2 1.0
S2 B:SF4501 3.8 39.6 1.0
CA B:CYS47 3.9 48.7 1.0
N B:CYS47 3.9 64.8 1.0
CG2 B:ILE57 4.3 22.0 1.0
CD1 B:ILE113 4.7 68.6 1.0
SG B:CYS100 4.7 62.4 1.0
CA B:HIS45 4.8 47.1 1.0
C B:HIS45 4.9 51.6 1.0
CD B:PRO46 4.9 25.6 1.0
C B:CYS47 4.9 36.5 1.0
N B:PRO46 5.0 34.2 1.0
CD B:PRO58 5.0 31.5 1.0
CB B:HIS45 5.0 38.7 1.0
CA B:CYS100 5.0 40.1 1.0

Iron binding site 5 out of 20 in 4ylf

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Iron binding site 5 out of 20 in the Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:30.2
occ:1.00
 FE3 B:SF4501 0.0 30.2 1.0
S4 B:SF4501 2.2 86.7 1.0
S2 B:SF4501 2.2 39.6 1.0
S1 B:SF4501 2.2 42.3 1.0
SG B:CYS42 2.3 45.3 1.0
FE4 B:SF4501 3.0 33.1 1.0
FE2 B:SF4501 3.1 0.7 1.0
FE1 B:SF4501 3.1 0.5 1.0
CB B:CYS42 3.2 24.9 1.0
N B:CYS42 3.7 38.9 1.0
S3 B:SF4501 3.8 83.1 1.0
CA B:CYS42 4.1 42.2 1.0
CG2 B:VAL101 4.4 60.8 1.0
CB B:VAL101 4.4 46.8 1.0
CD B:PRO46 4.5 25.6 1.0
N B:GLN41 4.6 46.9 1.0
N B:VAL101 4.7 40.5 1.0
SG B:CYS47 4.8 21.6 1.0
N B:LEU40 4.8 39.0 1.0
C B:GLN41 4.9 61.5 1.0
SG B:CYS39 4.9 40.1 1.0
CA B:HIS45 4.9 47.1 1.0

Iron binding site 6 out of 20 in 4ylf

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Iron binding site 6 out of 20 in the Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:33.1
occ:1.00
 FE4 B:SF4501 0.0 33.1 1.0
S1 B:SF4501 2.2 42.3 1.0
S3 B:SF4501 2.2 83.1 1.0
S2 B:SF4501 2.2 39.6 1.0
SG B:CYS39 2.3 40.1 1.0
FE3 B:SF4501 3.0 30.2 1.0
FE2 B:SF4501 3.1 0.7 1.0
FE1 B:SF4501 3.1 0.5 1.0
CB B:CYS39 3.2 46.5 1.0
CA B:CYS39 3.6 47.5 1.0
S4 B:SF4501 3.8 86.7 1.0
N B:LEU40 3.8 39.0 1.0
C B:CYS39 4.0 52.7 1.0
N B:GLN41 4.1 46.9 1.0
CG2 B:VAL111 4.4 43.6 1.0
CA B:GLN41 4.8 60.6 1.0
SG B:CYS47 4.8 21.6 1.0
N B:CYS42 4.9 38.9 1.0
CA B:LEU40 4.9 38.3 1.0
N B:CYS39 4.9 32.2 1.0
CD1 B:ILE61 4.9 34.4 1.0
C B:LEU40 5.0 58.8 1.0
CB B:PRO58 5.0 49.3 1.0
SG B:CYS42 5.0 45.3 1.0
CB B:VAL111 5.0 36.0 1.0
O B:CYS39 5.0 48.5 1.0

Iron binding site 7 out of 20 in 4ylf

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Iron binding site 7 out of 20 in the Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:22.0
occ:1.00
 FE1 B:SF4502 0.0 22.0 1.0
OE1 B:GLU117 1.8 51.1 1.0
S3 B:SF4502 2.2 26.9 1.0
S2 B:SF4502 2.2 53.4 1.0
S4 B:SF4502 2.2 39.2 1.0
CD B:GLU117 2.9 45.0 1.0
FE4 B:SF4502 3.1 71.6 1.0
FE2 B:SF4502 3.1 53.5 1.0
FE3 B:SF4502 3.1 0.8 1.0
OE2 B:GLU117 3.3 26.1 1.0
CD1 B:ILE55 3.7 43.5 1.0
S1 B:SF4502 3.8 56.4 1.0
CG B:GLU117 4.2 33.7 1.0
CB B:GLU117 4.3 20.4 1.0
ND2 B:ASN80 4.6 20.9 1.0
CB B:CYS86 4.8 19.3 1.0
N B:GLY87 4.9 38.6 1.0
CG1 B:ILE55 4.9 38.4 1.0
CG2 B:ILE113 5.0 20.6 1.0
SG B:CYS90 5.0 20.8 1.0

Iron binding site 8 out of 20 in 4ylf

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Iron binding site 8 out of 20 in the Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:53.5
occ:1.00
 FE2 B:SF4502 0.0 53.5 1.0
S1 B:SF4502 2.2 56.4 1.0
S4 B:SF4502 2.2 39.2 1.0
S3 B:SF4502 2.2 26.9 1.0
SG B:CYS90 2.2 20.8 1.0
FE4 B:SF4502 3.0 71.6 1.0
CB B:CYS90 3.0 59.5 1.0
FE3 B:SF4502 3.0 0.8 1.0
FE1 B:SF4502 3.1 22.0 1.0
OE1 B:GLN95 3.5 47.2 1.0
CD1 B:ILE442 3.7 43.4 1.0
S2 B:SF4502 3.7 53.4 1.0
CB B:CYS86 4.4 19.3 1.0
OE1 B:GLU117 4.5 51.1 1.0
CA B:CYS90 4.5 57.1 1.0
O B:CYS86 4.5 32.5 1.0
CD B:GLN95 4.7 30.6 1.0
C B:CYS86 4.8 33.3 1.0
CG1 B:ILE442 4.8 34.1 1.0
CB B:ILE442 4.9 32.5 1.0
SG B:CYS51 5.0 23.9 1.0

Iron binding site 9 out of 20 in 4ylf

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Iron binding site 9 out of 20 in the Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:0.8
occ:1.00
 FE3 B:SF4502 0.0 0.8 1.0
S1 B:SF4502 2.2 56.4 1.0
S2 B:SF4502 2.2 53.4 1.0
S4 B:SF4502 2.2 39.2 1.0
SG B:CYS96 2.2 31.1 1.0
CB B:CYS96 3.0 45.1 1.0
FE2 B:SF4502 3.0 53.5 1.0
FE4 B:SF4502 3.1 71.6 1.0
FE1 B:SF4502 3.1 22.0 1.0
S3 B:SF4502 3.8 26.9 1.0
CG B:GLN92 4.2 41.6 1.0
N B:CYS96 4.2 62.6 1.0
CA B:CYS96 4.2 51.4 1.0
CG2 B:ILE113 4.3 20.6 1.0
OE1 B:GLU117 4.6 51.1 1.0
CB B:CYS51 4.7 53.5 1.0
OE1 B:GLN95 4.8 47.2 1.0
CB B:CYS90 4.9 59.5 1.0
SG B:CYS51 4.9 23.9 1.0
CB B:ILE113 5.0 49.0 1.0
CB B:GLN92 5.0 44.9 1.0

Iron binding site 10 out of 20 in 4ylf

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Iron binding site 10 out of 20 in the Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin-Nadp Oxidoreductase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:71.6
occ:1.00
 FE4 B:SF4502 0.0 71.6 1.0
S3 B:SF4502 2.2 26.9 1.0
S2 B:SF4502 2.2 53.4 1.0
S1 B:SF4502 2.2 56.4 1.0
SG B:CYS51 2.2 23.9 1.0
FE2 B:SF4502 3.0 53.5 1.0
CB B:CYS51 3.0 53.5 1.0
FE1 B:SF4502 3.1 22.0 1.0
FE3 B:SF4502 3.1 0.8 1.0
CD1 B:ILE442 3.5 43.4 1.0
S4 B:SF4502 3.7 39.2 1.0
CA B:CYS51 3.8 55.5 1.0
CD1 B:ILE55 3.8 43.5 1.0
CG1 B:ILE55 4.2 38.4 1.0
CD B:PRO52 4.4 42.1 1.0
C B:CYS51 4.5 46.0 1.0
N B:PRO52 4.6 33.5 1.0
CB B:ILE55 4.7 37.5 1.0
CG2 B:VAL53 4.8 52.4 1.0
CB B:CYS96 4.8 45.1 1.0
OE1 B:GLU117 4.8 51.1 1.0
N B:CYS51 4.9 34.6 1.0
SG B:CYS96 5.0 31.1 1.0
CG1 B:ILE442 5.0 34.1 1.0

Reference:

J.K.Demmer, H.Huang, S.Wang, U.Demmer, R.K.Thauer, U.Ermler. Insights Into Flavin-Based Electron Bifurcation Via the Nadh-Dependent Reduced Ferredoxin:Nadp Oxidoreductase Structure. J.Biol.Chem. V. 290 21985 2015.
ISSN: ESSN 1083-351X
PubMed: 26139605
DOI: 10.1074/JBC.M115.656520
Page generated: Sun Dec 13 15:53:11 2020

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