Iron in PDB 3p4s: Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct

The structure of Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct, PDB code: 3p4s was solved by T.M.Tomasiak, T.L.Archuleta, J.Andrell, C.Luna-Chavez, T.A.Davis, M.Sarwar, A.J.Ham, W.H.Mcdonald, V.Yankowskaya, H.A.Stern, J.N.Johnston, E.Maklashina, G.Cecchini, T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.065, 139.006, 276.476, 90.00, 90.00, 90.00
R / Rfree (%)	25.5 / 27.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct (pdb code 3p4s). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct, PDB code: 3p4s:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 18 in the Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe244 b:60.4 occ:1.00 FE1 B:FES244 0.0 60.4 1.0 S2 B:FES244 2.2 59.1 1.0 S1 B:FES244 2.3 61.5 1.0 CB B:CYS77 2.4 47.7 1.0 CB B:CYS65 2.6 48.1 1.0 SG B:CYS65 2.7 49.1 1.0 SG B:CYS77 2.8 49.0 1.0 FE2 B:FES244 2.9 61.9 1.0 CA B:CYS77 3.7 48.1 1.0 CA B:CYS65 4.0 48.3 1.0 N B:CYS77 4.2 48.0 1.0 SG B:CYS57 4.2 43.0 1.0 N B:CYS65 4.3 48.1 1.0 N B:ALA60 4.3 44.6 1.0 CA B:ALA60 4.5 45.2 1.0 CB B:LEU75 4.5 47.4 1.0 SG B:CYS62 4.6 43.3 1.0 C B:CYS77 4.9 48.9 1.0 N B:ARG58 4.9 42.1 1.0 CD2 B:LEU37 5.0 47.0 1.0 N B:GLY63 5.0 46.3 1.0

Iron binding site 2 out of 18 in the Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe244 b:61.9 occ:1.00 FE2 B:FES244 0.0 61.9 1.0 SG B:CYS57 2.1 43.0 1.0 S1 B:FES244 2.1 61.5 1.0 SG B:CYS62 2.2 43.3 1.0 S2 B:FES244 2.3 59.1 1.0 FE1 B:FES244 2.9 60.4 1.0 CB B:CYS57 3.2 42.8 1.0 CB B:CYS62 3.3 45.5 1.0 N B:CYS62 3.4 46.0 1.0 N B:CYS57 3.5 42.4 1.0 N B:GLY63 3.5 46.3 1.0 CA B:CYS62 3.7 45.9 1.0 CA B:CYS57 3.8 42.6 1.0 N B:ARG58 4.0 42.1 1.0 C B:CYS62 4.1 46.2 1.0 N B:ILE61 4.2 46.2 1.0 N B:ALA60 4.3 44.6 1.0 C B:CYS57 4.4 42.5 1.0 SG B:CYS77 4.4 49.0 1.0 N B:SER56 4.5 42.7 1.0 N B:SER64 4.5 47.4 1.0 OG B:SER64 4.5 48.2 1.0 C B:SER56 4.6 42.5 1.0 CA B:GLY63 4.6 47.2 1.0 N B:MET59 4.6 43.3 1.0 C B:ILE61 4.6 46.9 1.0 CA B:ALA60 4.6 45.2 1.0 CB B:CYS65 4.8 48.1 1.0 C B:ALA60 4.9 46.0 1.0 CB B:CYS77 5.0 47.7 1.0 CA B:SER56 5.0 42.6 1.0

Iron binding site 3 out of 18 in the Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe245 b:0.9 occ:1.00 FE1 B:F3S245 0.0 0.9 1.0 SG B:CYS204 1.7 55.1 1.0 S2 B:F3S245 2.2 0.3 1.0 S3 B:F3S245 2.3 0.2 1.0 S1 B:F3S245 2.4 0.4 1.0 FE4 B:F3S245 2.7 0.1 1.0 FE3 B:F3S245 2.9 0.7 1.0 CB B:CYS204 2.9 56.0 1.0 CA B:CYS204 3.5 57.3 1.0 CD1 B:ILE224 4.1 55.5 1.0 S4 B:F3S245 4.1 0.7 1.0 N B:PHE206 4.1 61.2 1.0 N B:THR205 4.2 60.5 1.0 C B:CYS204 4.2 59.2 1.0 N B:VAL207 4.3 62.0 1.0 CA B:PHE206 4.4 61.7 1.0 SG B:CYS158 4.4 57.3 1.0 N B:CYS204 4.8 57.4 1.0 C B:PHE206 4.9 63.2 1.0 N B:GLY208 4.9 61.3 1.0 SG B:CYS210 5.0 54.0 1.0

Iron binding site 4 out of 18 in the Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe245 b:0.7 occ:1.00 FE3 B:F3S245 0.0 0.7 1.0 SG B:CYS210 2.2 54.0 1.0 S1 B:F3S245 2.2 0.4 1.0 S4 B:F3S245 2.3 0.7 1.0 S3 B:F3S245 2.4 0.2 1.0 FE4 B:F3S245 2.8 0.1 1.0 FE1 B:F3S245 2.9 0.9 1.0 CB B:CYS210 3.3 54.0 1.0 S2 B:F3S245 3.8 0.3 1.0 N B:GLY208 4.2 61.3 1.0 N B:CYS210 4.2 57.3 1.0 SG B:CYS204 4.2 55.1 1.0 SG B:CYS158 4.3 57.3 1.0 CA B:CYS210 4.4 55.5 1.0 CA B:GLY208 4.4 61.3 1.0 CD1 B:ILE224 4.5 55.5 1.0 CB B:ALA221 4.6 60.6 1.0 N B:TYR209 4.7 61.0 1.0 CB B:PRO170 4.8 57.8 1.0 C B:GLY208 4.8 61.4 1.0 CB B:CYS158 4.8 56.2 1.0 CA B:ALA221 4.9 59.1 1.0

Iron binding site 5 out of 18 in the Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe245 b:0.1 occ:1.00 FE4 B:F3S245 0.0 0.1 1.0 S2 B:F3S245 2.0 0.3 1.0 SG B:CYS158 2.1 57.3 1.0 S4 B:F3S245 2.2 0.7 1.0 S3 B:F3S245 2.5 0.2 1.0 FE1 B:F3S245 2.7 0.9 1.0 FE3 B:F3S245 2.8 0.7 1.0 CB B:CYS158 3.3 56.2 1.0 S1 B:F3S245 3.7 0.4 1.0 CA B:CYS158 3.9 57.0 1.0 CD B:PRO159 4.0 60.6 1.0 SG B:CYS204 4.3 55.1 1.0 CB B:VAL207 4.5 62.4 1.0 CG B:GLN160 4.5 63.8 1.0 N B:PRO159 4.6 60.0 1.0 C B:CYS158 4.6 58.5 1.0 CG2 B:VAL207 4.6 62.5 1.0 CB B:GLN160 4.6 62.5 1.0 SG B:CYS210 4.7 54.0 1.0 N B:GLN160 4.9 61.9 1.0 N B:VAL207 4.9 62.0 1.0

Iron binding site 6 out of 18 in the Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe246 b:79.3 occ:1.00 FE1 B:SF4246 0.0 79.3 1.0 SG B:CYS151 1.5 44.4 1.0 S4 B:SF4246 2.1 79.3 1.0 S3 B:SF4246 2.2 80.5 1.0 S2 B:SF4246 2.3 79.2 1.0 FE2 B:SF4246 2.6 79.2 1.0 FE3 B:SF4246 2.7 80.2 1.0 FE4 B:SF4246 2.8 79.9 1.0 CB B:CYS151 3.0 46.2 1.0 N B:CYS151 3.3 45.8 1.0 CA B:CYS151 3.6 46.1 1.0 N B:GLY152 3.8 46.7 1.0 S1 B:SF4246 3.8 80.2 1.0 C B:CYS151 4.1 46.7 1.0 N B:LEU153 4.2 48.7 1.0 CD B:PRO215 4.3 55.2 1.0 C B:ASN150 4.4 45.7 1.0 CB B:LEU153 4.5 49.8 1.0 SG B:CYS214 4.6 53.3 1.0 N B:ASN150 4.6 45.6 1.0 SG B:CYS148 4.6 44.5 1.0 SG B:CYS154 4.6 48.6 1.0 CG B:PRO215 4.7 55.4 1.0 CG1 B:ILE149 4.7 47.2 1.0 CA B:ASN150 4.8 45.5 1.0 N B:CYS154 4.8 50.3 1.0 CA B:GLY152 4.8 47.5 1.0 C B:GLY152 4.9 48.3 1.0 CA B:LEU153 4.9 49.8 1.0

Iron binding site 7 out of 18 in the Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe246 b:79.2 occ:1.00 FE2 B:SF4246 0.0 79.2 1.0 S3 B:SF4246 2.1 80.5 1.0 S4 B:SF4246 2.2 79.3 1.0 SG B:CYS148 2.2 44.5 1.0 S1 B:SF4246 2.4 80.2 1.0 FE1 B:SF4246 2.6 79.3 1.0 FE3 B:SF4246 2.6 80.2 1.0 FE4 B:SF4246 2.7 79.9 1.0 CB B:CYS148 3.4 46.8 1.0 S2 B:SF4246 3.7 79.2 1.0 N B:ILE149 4.0 46.4 1.0 N B:ASN150 4.0 45.6 1.0 SG B:CYS151 4.0 44.4 1.0 CA B:CYS148 4.0 46.7 1.0 C B:CYS148 4.4 46.4 1.0 N B:CYS151 4.4 45.8 1.0 SG B:CYS214 4.5 53.3 1.0 CA B:ASN150 4.5 45.5 1.0 CB B:ALA171 4.6 62.1 1.0 CG2 B:VAL218 4.7 59.4 1.0 SG B:CYS154 4.7 48.6 1.0 C B:ILE149 4.8 46.0 1.0 CA B:ILE149 5.0 46.1 1.0

Iron binding site 8 out of 18 in the Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe246 b:80.2 occ:1.00 FE3 B:SF4246 0.0 80.2 1.0 S1 B:SF4246 2.0 80.2 1.0 S2 B:SF4246 2.1 79.2 1.0 S4 B:SF4246 2.2 79.3 1.0 SG B:CYS154 2.4 48.6 1.0 FE4 B:SF4246 2.6 79.9 1.0 FE2 B:SF4246 2.6 79.2 1.0 FE1 B:SF4246 2.7 79.3 1.0 CB B:CYS154 3.2 50.4 1.0 S3 B:SF4246 3.6 80.5 1.0 N B:CYS154 3.9 50.3 1.0 SG B:CYS151 3.9 44.4 1.0 CA B:CYS154 4.2 50.8 1.0 CB B:ALA171 4.2 62.1 1.0 SG B:CYS214 4.4 53.3 1.0 SG B:CYS148 4.6 44.5 1.0 CA B:ALA171 4.8 59.5 1.0 N B:LEU153 4.8 48.7 1.0 N B:GLY152 4.9 46.7 1.0

Iron binding site 9 out of 18 in the Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe246 b:79.9 occ:1.00 FE4 B:SF4246 0.0 79.9 1.0 SG B:CYS214 2.0 53.3 1.0 S1 B:SF4246 2.1 80.2 1.0 S3 B:SF4246 2.2 80.5 1.0 S2 B:SF4246 2.3 79.2 1.0 FE3 B:SF4246 2.6 80.2 1.0 FE2 B:SF4246 2.7 79.2 1.0 FE1 B:SF4246 2.8 79.3 1.0 CB B:CYS214 3.4 56.4 1.0 S4 B:SF4246 3.7 79.3 1.0 CA B:CYS214 3.9 56.5 1.0 SG B:CYS151 4.0 44.4 1.0 CG2 B:VAL218 4.1 59.4 1.0 CD B:PRO215 4.2 55.2 1.0 CB B:VAL218 4.5 59.5 1.0 SG B:CYS148 4.7 44.5 1.0 C B:CYS214 4.7 58.5 1.0 N B:PRO215 4.7 57.6 1.0 SG B:CYS154 4.8 48.6 1.0 N B:LYS216 5.0 60.2 1.0

Iron binding site 10 out of 18 in the Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Menaquinol:Fumarate Oxidoreductase in Complex with A 3-Nitropropionate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe244 b:0.9 occ:1.00 FE1 N:FES244 0.0 0.9 1.0 S2 N:FES244 2.1 0.3 1.0 SG N:CYS65 2.4 0.4 1.0 S1 N:FES244 2.4 0.4 1.0 SG N:CYS77 2.7 0.1 1.0 FE2 N:FES244 2.9 0.2 1.0 CB N:CYS77 3.4 0.3 1.0 CB N:CYS65 3.5 0.3 1.0 N N:CYS65 3.7 0.3 1.0 CA N:CYS65 4.2 0.9 1.0 N N:SER64 4.3 0.1 1.0 CD1 N:LEU37 4.4 0.7 1.0 SG N:CYS62 4.4 0.4 1.0 N N:CYS77 4.4 0.4 1.0 N N:ALA60 4.5 0.1 1.0 CA N:ALA60 4.6 0.5 1.0 CA N:CYS77 4.6 0.5 1.0 CD2 N:LEU75 4.6 1.0 1.0 SG N:CYS57 4.7 0.5 1.0 C N:SER64 4.8 0.1 1.0 N N:GLY63 4.8 0.7 1.0 CA N:SER64 4.9 0.1 1.0 CB N:LEU75 4.9 0.8 1.0 CB N:SER64 4.9 0.9 1.0 C N:GLY63 5.0 0.7 1.0

T.M.Tomasiak, T.L.Archuleta, J.Andrell, C.Luna-Chavez, T.A.Davis, M.Sarwar, A.J.Ham, W.H.Mcdonald, V.Yankovskaya, H.A.Stern, J.N.Johnston, E.Maklashina, G.Cecchini, T.M.Iverson. Geometric Restraint Drives on- and Off-Pathway Catalysis By the Escherichia Coli Menaquinol:Fumarate Reductase. J.Biol.Chem. V. 286 3047 2011.
ISSN: ISSN 0021-9258
PubMed: 21098488
DOI: 10.1074/JBC.M110.192849