Iron in PDB 1kqf: Formate Dehydrogenase N From E. Coli

All present enzymatic activity of Formate Dehydrogenase N From E. Coli:
1.2.1.2;

The structure of Formate Dehydrogenase N From E. Coli, PDB code: 1kqf was solved by M.Jormakka, S.Tornroth, B.Byrne, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.60
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	203.000, 203.000, 203.000, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 19.5

The structure of Formate Dehydrogenase N From E. Coli also contains other interesting chemical elements:

Molybdenum

(Mo)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Iron atom in the Formate Dehydrogenase N From E. Coli (pdb code 1kqf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 22 binding sites of Iron where determined in the Formate Dehydrogenase N From E. Coli, PDB code: 1kqf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 22 in the Formate Dehydrogenase N From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Formate Dehydrogenase N From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1017 b:12.1 occ:1.00 FE1 A:SF41017 0.0 12.1 1.0 S3 A:SF41017 2.3 12.3 1.0 S4 A:SF41017 2.3 11.8 1.0 S2 A:SF41017 2.3 12.7 1.0 SG A:CYS92 2.4 12.4 1.0 FE2 A:SF41017 2.7 11.4 1.0 FE4 A:SF41017 2.7 12.3 1.0 FE3 A:SF41017 2.7 12.2 1.0 CB A:CYS92 3.4 12.1 1.0 S1 A:SF41017 3.8 12.3 1.0 N A:CYS92 3.9 12.3 1.0 CA A:CYS92 4.2 12.0 1.0 N A:GLY95 4.2 10.4 1.0 O A:HOH1031 4.3 11.2 1.0 NZ A:LYS94 4.4 13.2 1.0 CG2 A:VAL239 4.5 10.2 1.0 CG A:PRO238 4.5 15.9 1.0 SG A:CYS53 4.7 12.6 1.0 CB A:LYS94 4.7 10.8 1.0 CE A:LYS94 4.8 13.5 1.0 CA A:GLY95 4.8 11.3 1.0 C A:CYS92 4.8 12.3 1.0 SG A:CYS50 4.8 11.6 1.0 SG A:CYS57 4.9 11.8 1.0 CD A:PRO238 4.9 13.0 1.0

Iron binding site 2 out of 22 in the Formate Dehydrogenase N From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Formate Dehydrogenase N From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1017 b:11.4 occ:1.00 FE2 A:SF41017 0.0 11.4 1.0 S4 A:SF41017 2.3 11.8 1.0 S1 A:SF41017 2.3 12.3 1.0 S3 A:SF41017 2.3 12.3 1.0 SG A:CYS50 2.3 11.6 1.0 FE1 A:SF41017 2.7 12.1 1.0 FE3 A:SF41017 2.7 12.2 1.0 FE4 A:SF41017 2.7 12.3 1.0 CB A:CYS50 3.1 10.0 1.0 S2 A:SF41017 3.8 12.7 1.0 CA A:GLY95 4.2 11.3 1.0 N A:GLY95 4.2 10.4 1.0 CB A:TYR52 4.4 11.6 1.0 N A:CYS53 4.4 12.6 1.0 CA A:CYS50 4.5 10.3 1.0 SG A:CYS92 4.6 12.4 1.0 SG A:CYS57 4.7 11.8 1.0 CD2 A:TYR52 4.7 10.6 1.0 N A:TYR52 4.8 11.4 1.0 CB A:CYS57 4.8 10.1 1.0 SG A:CYS53 4.9 12.6 1.0 C A:CYS50 5.0 11.1 1.0 CA A:TYR52 5.0 10.7 1.0

Iron binding site 3 out of 22 in the Formate Dehydrogenase N From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Formate Dehydrogenase N From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1017 b:12.2 occ:1.00 FE3 A:SF41017 0.0 12.2 1.0 S4 A:SF41017 2.2 11.8 1.0 S1 A:SF41017 2.3 12.3 1.0 S2 A:SF41017 2.3 12.7 1.0 SG A:CYS57 2.4 11.8 1.0 FE4 A:SF41017 2.6 12.3 1.0 FE1 A:SF41017 2.7 12.1 1.0 FE2 A:SF41017 2.7 11.4 1.0 CB A:CYS57 3.3 10.1 1.0 S3 A:SF41017 3.8 12.3 1.0 CG2 A:VAL239 4.0 10.2 1.0 CB A:VAL55 4.0 12.5 1.0 CB A:VAL239 4.1 10.8 1.0 N A:CYS57 4.2 10.9 1.0 CG1 A:VAL55 4.3 11.9 1.0 CA A:CYS57 4.4 10.0 1.0 CB A:CYS50 4.6 10.0 1.0 SG A:CYS50 4.7 11.6 1.0 CG2 A:VAL55 4.7 12.3 1.0 SG A:CYS53 4.7 12.6 1.0 CG1 A:VAL239 4.9 11.6 1.0 SG A:CYS92 4.9 12.4 1.0 N A:CYS92 4.9 12.3 1.0

Iron binding site 4 out of 22 in the Formate Dehydrogenase N From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Formate Dehydrogenase N From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1017 b:12.3 occ:1.00 FE4 A:SF41017 0.0 12.3 1.0 S2 A:SF41017 2.2 12.7 1.0 S1 A:SF41017 2.2 12.3 1.0 S3 A:SF41017 2.2 12.3 1.0 SG A:CYS53 2.4 12.6 1.0 FE3 A:SF41017 2.6 12.2 1.0 FE1 A:SF41017 2.7 12.1 1.0 FE2 A:SF41017 2.7 11.4 1.0 CB A:CYS53 3.5 13.4 1.0 O A:HOH1031 3.8 11.2 1.0 N A:CYS53 3.8 12.6 1.0 S4 A:SF41017 3.9 11.8 1.0 CB A:VAL55 4.0 12.5 1.0 CA A:CYS53 4.0 11.9 1.0 CG2 A:VAL55 4.1 12.3 1.0 C A:CYS53 4.2 12.3 1.0 O A:CYS53 4.2 13.5 1.0 N A:VAL55 4.5 12.0 1.0 SG A:CYS57 4.7 11.8 1.0 SG A:CYS92 4.8 12.4 1.0 SG A:CYS50 4.8 11.6 1.0 CA A:VAL55 4.8 10.8 1.0 N A:SER54 5.0 12.3 1.0

Iron binding site 5 out of 22 in the Formate Dehydrogenase N From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Formate Dehydrogenase N From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe805 b:13.5 occ:1.00 FE1 B:SF4805 0.0 13.5 1.0 S3 B:SF4805 2.3 13.7 1.0 S2 B:SF4805 2.3 13.6 1.0 S4 B:SF4805 2.3 14.2 1.0 SG B:CYS39 2.4 13.9 1.0 FE3 B:SF4805 2.7 13.4 1.0 FE2 B:SF4805 2.7 13.6 1.0 FE4 B:SF4805 2.7 13.1 1.0 CB B:CYS39 3.5 12.7 1.0 S1 B:SF4805 3.8 12.9 1.0 CA B:CYS39 3.9 13.4 1.0 CE B:MET80 3.9 13.0 1.0 N B:GLY41 4.0 13.0 1.0 N B:ILE40 4.0 12.8 1.0 O B:HOH823 4.3 16.5 1.0 C B:CYS39 4.3 13.6 1.0 CA B:GLY41 4.4 13.2 1.0 SD B:MET80 4.5 13.7 1.0 N B:CYS42 4.6 11.9 1.0 CB B:ALA183 4.7 14.7 1.0 SG B:CYS179 4.8 12.8 1.0 C B:ILE40 4.9 14.4 1.0 SG B:CYS42 5.0 13.1 1.0

Iron binding site 6 out of 22 in the Formate Dehydrogenase N From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Formate Dehydrogenase N From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe805 b:13.6 occ:1.00 FE2 B:SF4805 0.0 13.6 1.0 S4 B:SF4805 2.3 14.2 1.0 S1 B:SF4805 2.3 12.9 1.0 S3 B:SF4805 2.3 13.7 1.0 SG B:CYS45 2.5 13.5 1.0 FE1 B:SF4805 2.7 13.5 1.0 FE3 B:SF4805 2.7 13.4 1.0 FE4 B:SF4805 2.7 13.1 1.0 CB B:CYS45 3.4 11.7 1.0 SD B:MET80 3.6 13.7 1.0 S2 B:SF4805 3.9 13.6 1.0 N B:CYS45 4.0 11.1 1.0 CE B:MET80 4.3 13.0 1.0 CA B:CYS45 4.4 12.1 1.0 CD1 B:ILE184 4.5 15.0 1.0 CG B:MET80 4.5 13.0 1.0 CD B:LYS97 4.6 13.2 1.0 N B:LYS43 4.6 11.6 1.0 N B:ALA44 4.7 11.3 1.0 SG B:CYS42 4.8 13.1 1.0 SG B:CYS39 4.8 13.9 1.0 CA B:LYS43 4.8 11.9 1.0 C B:LYS43 5.0 10.7 1.0 CB B:LYS97 5.0 12.8 1.0

Iron binding site 7 out of 22 in the Formate Dehydrogenase N From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Formate Dehydrogenase N From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe805 b:13.4 occ:1.00 FE3 B:SF4805 0.0 13.4 1.0 S1 B:SF4805 2.2 12.9 1.0 S4 B:SF4805 2.2 14.2 1.0 S2 B:SF4805 2.3 13.6 1.0 SG B:CYS179 2.4 12.8 1.0 FE4 B:SF4805 2.6 13.1 1.0 FE1 B:SF4805 2.7 13.5 1.0 FE2 B:SF4805 2.7 13.6 1.0 CB B:CYS179 3.5 11.4 1.0 S3 B:SF4805 3.8 13.7 1.0 CA B:CYS179 3.9 11.0 1.0 CG1 B:ILE184 4.1 13.7 1.0 CD1 B:ILE184 4.2 15.0 1.0 CB B:ALA183 4.2 14.7 1.0 CD B:PRO180 4.4 10.4 1.0 C B:CYS179 4.6 10.5 1.0 SG B:CYS42 4.7 13.1 1.0 N B:PRO180 4.8 11.2 1.0 OG1 B:THR181 4.8 14.7 1.0 SG B:CYS39 4.9 13.9 1.0 N B:ILE184 4.9 13.9 1.0 SG B:CYS45 4.9 13.5 1.0

Iron binding site 8 out of 22 in the Formate Dehydrogenase N From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Formate Dehydrogenase N From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe805 b:13.1 occ:1.00 FE4 B:SF4805 0.0 13.1 1.0 S2 B:SF4805 2.2 13.6 1.0 S3 B:SF4805 2.2 13.7 1.0 S1 B:SF4805 2.2 12.9 1.0 SG B:CYS42 2.4 13.1 1.0 FE3 B:SF4805 2.6 13.4 1.0 FE1 B:SF4805 2.7 13.5 1.0 FE2 B:SF4805 2.7 13.6 1.0 N B:CYS42 3.6 11.9 1.0 CB B:CYS42 3.7 11.8 1.0 S4 B:SF4805 3.8 14.2 1.0 N B:LYS43 3.9 11.6 1.0 CA B:CYS42 4.0 11.9 1.0 CD B:PRO180 4.1 10.4 1.0 N B:ALA44 4.2 11.3 1.0 C B:CYS42 4.4 11.6 1.0 N B:GLY41 4.5 13.0 1.0 CG1 B:ILE40 4.6 12.7 1.0 CB B:ALA44 4.6 10.1 1.0 C B:GLY41 4.6 14.0 1.0 SG B:CYS179 4.6 12.8 1.0 CA B:LYS43 4.8 11.9 1.0 SG B:CYS39 4.8 13.9 1.0 CA B:GLY41 4.8 13.2 1.0 SG B:CYS45 4.8 13.5 1.0 N B:ILE40 4.9 12.8 1.0 N B:CYS45 4.9 11.1 1.0 CG B:PRO180 4.9 12.1 1.0 C B:LYS43 5.0 10.7 1.0 CA B:ALA44 5.0 12.1 1.0

Iron binding site 9 out of 22 in the Formate Dehydrogenase N From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Formate Dehydrogenase N From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe806 b:12.8 occ:1.00 FE1 B:SF4806 0.0 12.8 1.0 S3 B:SF4806 2.3 13.0 1.0 S4 B:SF4806 2.3 13.7 1.0 S2 B:SF4806 2.3 13.4 1.0 SG B:CYS49 2.4 13.6 1.0 FE4 B:SF4806 2.7 13.1 1.0 FE3 B:SF4806 2.7 13.6 1.0 FE2 B:SF4806 2.7 12.5 1.0 CB B:CYS49 3.2 12.6 1.0 ND2 B:ASN53 3.8 12.0 1.0 S1 B:SF4806 3.8 12.9 1.0 CA B:CYS49 4.0 11.8 1.0 SG B:CYS163 4.6 12.5 1.0 CG2 B:THR78 4.7 13.2 1.0 SG B:CYS160 4.8 12.7 1.0 CB B:TRP77 4.8 12.6 1.0 C B:CYS49 4.8 11.2 1.0 SG B:CYS175 4.9 13.2 1.0 O B:CYS49 5.0 11.1 1.0 CB B:CYS160 5.0 11.7 1.0

Iron binding site 10 out of 22 in the Formate Dehydrogenase N From E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Formate Dehydrogenase N From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe806 b:12.5 occ:1.00 FE2 B:SF4806 0.0 12.5 1.0 S4 B:SF4806 2.3 13.7 1.0 S1 B:SF4806 2.3 12.9 1.0 S3 B:SF4806 2.3 13.0 1.0 SG B:CYS163 2.3 12.5 1.0 FE1 B:SF4806 2.7 12.8 1.0 FE3 B:SF4806 2.7 13.6 1.0 FE4 B:SF4806 2.7 13.1 1.0 N B:CYS163 3.4 11.7 1.0 CB B:CYS163 3.4 11.7 1.0 CA B:CYS163 3.7 11.8 1.0 S2 B:SF4806 3.9 13.4 1.0 C B:LEU162 4.1 11.8 1.0 CB B:PRO173 4.2 12.1 1.0 ND2 B:ASN53 4.4 12.0 1.0 CA B:LEU162 4.4 12.6 1.0 N B:LEU162 4.5 11.1 1.0 N B:ALA174 4.5 11.4 1.0 SG B:CYS175 4.7 13.2 1.0 SG B:CYS49 4.8 13.6 1.0 CA B:PRO173 4.8 11.2 1.0 SG B:CYS160 4.8 12.7 1.0 O B:LEU162 4.9 12.0 1.0 OG1 B:THR161 4.9 13.2 1.0 N B:CYS175 5.0 11.5 1.0

M.Jormakka, S.Tornroth, B.Byrne, S.Iwata. Molecular Basis of Proton Motive Force Generation: Structure of Formate Dehydrogenase-N. Science V. 295 1863 2002.
ISSN: ISSN 0036-8075
PubMed: 11884747
DOI: 10.1126/SCIENCE.1068186