Atomistry » Iron » PDB 1fca-1fnp » 1fdo
Atomistry »
  Iron »
    PDB 1fca-1fnp »
      1fdo »

Iron in PDB 1fdo: Oxidized Form of Formate Dehydrogenase H From E. Coli

Enzymatic activity of Oxidized Form of Formate Dehydrogenase H From E. Coli

All present enzymatic activity of Oxidized Form of Formate Dehydrogenase H From E. Coli:
1.2.1.2;

Protein crystallography data

The structure of Oxidized Form of Formate Dehydrogenase H From E. Coli, PDB code: 1fdo was solved by P.D.Sun, J.C.Boyington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 146.600, 146.600, 81.100, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 28.1

Other elements in 1fdo:

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

Molybdenum (Mo) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Oxidized Form of Formate Dehydrogenase H From E. Coli (pdb code 1fdo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Oxidized Form of Formate Dehydrogenase H From E. Coli, PDB code: 1fdo:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1fdo

Go back to Iron Binding Sites List in 1fdo
Iron binding site 1 out of 4 in the Oxidized Form of Formate Dehydrogenase H 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 Oxidized Form of Formate Dehydrogenase H From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe800

b:11.2
occ:1.00
FE1 A:SF4800 0.0 11.2 1.0
S2 A:SF4800 2.3 13.9 1.0
S4 A:SF4800 2.3 14.9 1.0
S3 A:SF4800 2.3 14.6 1.0
SG A:CYS42 2.4 15.3 1.0
FE4 A:SF4800 2.5 13.3 1.0
FE2 A:SF4800 2.7 14.2 1.0
FE3 A:SF4800 2.8 12.9 1.0
CB A:CYS42 3.5 12.8 1.0
S1 A:SF4800 3.9 14.3 1.0
N A:CYS42 3.9 12.3 1.0
CA A:CYS42 4.2 13.2 1.0
N A:GLY45 4.3 18.8 1.0
SG A:CYS11 4.6 10.7 1.0
CD A:PRO182 4.6 14.3 1.0
CE A:LYS44 4.6 20.6 1.0
O A:CYS42 4.7 14.2 1.0
C A:CYS42 4.7 13.1 1.0
CG A:PRO182 4.8 13.7 1.0
CA A:GLY45 4.8 18.2 1.0
O A:HOH831 4.8 19.7 1.0
CB A:PRO182 4.8 13.1 1.0
SG A:CYS8 4.9 15.4 1.0
SG A:CYS15 4.9 9.6 1.0

Iron binding site 2 out of 4 in 1fdo

Go back to Iron Binding Sites List in 1fdo
Iron binding site 2 out of 4 in the Oxidized Form of Formate Dehydrogenase H 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 Oxidized Form of Formate Dehydrogenase H From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe800

b:14.2
occ:1.00
FE2 A:SF4800 0.0 14.2 1.0
S3 A:SF4800 2.3 14.6 1.0
S1 A:SF4800 2.3 14.3 1.0
S4 A:SF4800 2.3 14.9 1.0
SG A:CYS8 2.3 15.4 1.0
FE4 A:SF4800 2.6 13.3 1.0
FE3 A:SF4800 2.7 12.9 1.0
FE1 A:SF4800 2.7 11.2 1.0
CB A:CYS8 3.0 13.1 1.0
S2 A:SF4800 3.9 13.9 1.0
CB A:TYR10 4.1 9.1 1.0
CA A:GLY45 4.2 18.2 1.0
N A:CYS11 4.3 7.5 1.0
N A:GLY45 4.4 18.8 1.0
CA A:CYS8 4.5 13.6 1.0
CB A:CYS15 4.6 10.5 1.0
SG A:CYS11 4.7 10.7 1.0
N A:TYR10 4.7 10.4 1.0
SG A:CYS42 4.7 15.3 1.0
SG A:CYS15 4.7 9.6 1.0
CD2 A:TYR10 4.8 10.9 1.0
C A:CYS8 4.8 13.3 1.0
CA A:TYR10 4.8 8.2 1.0
CG A:TYR10 5.0 7.6 1.0

Iron binding site 3 out of 4 in 1fdo

Go back to Iron Binding Sites List in 1fdo
Iron binding site 3 out of 4 in the Oxidized Form of Formate Dehydrogenase H 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 Oxidized Form of Formate Dehydrogenase H From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe800

b:12.9
occ:1.00
FE3 A:SF4800 0.0 12.9 1.0
S1 A:SF4800 2.2 14.3 1.0
SG A:CYS15 2.2 9.6 1.0
S4 A:SF4800 2.3 14.9 1.0
S2 A:SF4800 2.4 13.9 1.0
FE4 A:SF4800 2.7 13.3 1.0
FE2 A:SF4800 2.7 14.2 1.0
FE1 A:SF4800 2.8 11.2 1.0
CB A:CYS15 2.9 10.5 1.0
CB A:SER13 3.9 8.2 1.0
S3 A:SF4800 4.0 14.6 1.0
CA A:CYS15 4.2 11.9 1.0
N A:CYS15 4.2 11.4 1.0
CD1 A:ILE183 4.2 11.3 1.0
OG A:SER13 4.4 11.9 1.0
CG1 A:ILE183 4.5 13.5 1.0
CB A:CYS8 4.5 13.1 1.0
CD2 A:LEU41 4.6 12.9 1.0
CB A:ILE183 4.6 14.3 1.0
SG A:CYS11 4.7 10.7 1.0
SG A:CYS8 4.7 15.4 1.0

Iron binding site 4 out of 4 in 1fdo

Go back to Iron Binding Sites List in 1fdo
Iron binding site 4 out of 4 in the Oxidized Form of Formate Dehydrogenase H 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 Oxidized Form of Formate Dehydrogenase H From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe800

b:13.3
occ:1.00
FE4 A:SF4800 0.0 13.3 1.0
S2 A:SF4800 2.2 13.9 1.0
S3 A:SF4800 2.3 14.6 1.0
S1 A:SF4800 2.3 14.3 1.0
SG A:CYS11 2.3 10.7 1.0
FE1 A:SF4800 2.5 11.2 1.0
FE2 A:SF4800 2.6 14.2 1.0
FE3 A:SF4800 2.7 12.9 1.0
CB A:CYS11 3.5 8.8 1.0
OG A:SER13 3.7 11.9 1.0
S4 A:SF4800 3.7 14.9 1.0
N A:CYS11 3.8 7.5 1.0
CB A:SER13 3.9 8.2 1.0
CA A:CYS11 4.0 6.6 1.0
O A:HOH831 4.3 19.7 1.0
C A:CYS11 4.4 5.8 1.0
O A:CYS11 4.5 4.8 1.0
CD A:PRO182 4.6 14.3 1.0
SG A:CYS42 4.6 15.3 1.0
N A:SER13 4.6 6.3 1.0
SG A:CYS15 4.7 9.6 1.0
SG A:CYS8 4.7 15.4 1.0
CA A:SER13 4.9 7.0 1.0
CB A:TYR10 4.9 9.1 1.0
C A:TYR10 5.0 8.7 1.0

Reference:

J.C.Boyington, V.N.Gladyshev, S.V.Khangulov, T.C.Stadtman, P.D.Sun. Crystal Structure of Formate Dehydrogenase H: Catalysis Involving Mo, Molybdopterin, Selenocysteine, and An FE4S4 Cluster. Science V. 275 1305 1997.
ISSN: ISSN 0036-8075
PubMed: 9036855
DOI: 10.1126/SCIENCE.275.5304.1305
Page generated: Sat Aug 3 04:51:41 2024

Last articles

Ca in 5NMR
Ca in 5NN9
Ca in 5NM8
Ca in 5NH8
Ca in 5NL7
Ca in 5NIN
Ca in 5NGQ
Ca in 5NH5
Ca in 5NGY
Ca in 5NG1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy