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Iron in PDB 1fdi: Oxidized Form of Formate Dehydrogenase H From E. Coli Complexed with the Inhibitor Nitrite

Enzymatic activity of Oxidized Form of Formate Dehydrogenase H From E. Coli Complexed with the Inhibitor Nitrite

All present enzymatic activity of Oxidized Form of Formate Dehydrogenase H From E. Coli Complexed with the Inhibitor Nitrite:
1.2.1.2;

Protein crystallography data

The structure of Oxidized Form of Formate Dehydrogenase H From E. Coli Complexed with the Inhibitor Nitrite, PDB code: 1fdi 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 / 2.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 146.800, 146.800, 81.800, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 28.4

Other elements in 1fdi:

The structure of Oxidized Form of Formate Dehydrogenase H From E. Coli Complexed with the Inhibitor Nitrite 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 Complexed with the Inhibitor Nitrite (pdb code 1fdi). 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 Complexed with the Inhibitor Nitrite, PDB code: 1fdi:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1fdi

Go back to Iron Binding Sites List in 1fdi
Iron binding site 1 out of 4 in the Oxidized Form of Formate Dehydrogenase H From E. Coli Complexed with the Inhibitor Nitrite


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 Complexed with the Inhibitor Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe800

b:13.7
occ:1.00
 FE1 A:SF4800 0.0 13.7 1.0
S2 A:SF4800 2.2 14.1 1.0
S3 A:SF4800 2.3 14.7 1.0
S4 A:SF4800 2.3 14.5 1.0
FE4 A:SF4800 2.3 13.9 1.0
SG A:CYS42 2.4 15.3 1.0
FE2 A:SF4800 2.6 13.4 1.0
FE3 A:SF4800 2.7 13.6 1.0
CB A:CYS42 3.5 12.8 1.0
S1 A:SF4800 3.8 14.3 1.0
N A:CYS42 3.8 13.3 1.0
CA A:CYS42 4.2 13.9 1.0
N A:GLY45 4.4 18.3 1.0
SG A:CYS11 4.4 13.9 1.0
CD A:PRO182 4.6 13.1 1.0
CE A:LYS44 4.7 22.2 1.0
SG A:CYS8 4.7 15.8 1.0
CG A:PRO182 4.8 12.4 1.0
O A:HOH832 4.8 21.4 1.0
C A:CYS42 4.8 14.4 1.0
SG A:CYS15 4.8 11.6 1.0
CB A:PRO182 4.9 12.2 1.0
CA A:GLY45 4.9 19.2 1.0
C A:LEU41 5.0 13.7 1.0
CD1 A:ILE183 5.0 13.6 1.0

Iron binding site 2 out of 4 in 1fdi

Go back to Iron Binding Sites List in 1fdi
Iron binding site 2 out of 4 in the Oxidized Form of Formate Dehydrogenase H From E. Coli Complexed with the Inhibitor Nitrite


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 Complexed with the Inhibitor Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe800

b:13.4
occ:1.00
 FE2 A:SF4800 0.0 13.4 1.0
S1 A:SF4800 2.2 14.3 1.0
SG A:CYS8 2.3 15.8 1.0
S3 A:SF4800 2.3 14.7 1.0
S4 A:SF4800 2.3 14.5 1.0
FE4 A:SF4800 2.5 13.9 1.0
FE1 A:SF4800 2.6 13.7 1.0
FE3 A:SF4800 2.8 13.6 1.0
CB A:CYS8 3.1 14.3 1.0
CB A:TYR10 3.9 9.9 1.0
S2 A:SF4800 3.9 14.1 1.0
N A:CYS11 4.2 9.5 1.0
CA A:GLY45 4.3 19.2 1.0
N A:GLY45 4.3 18.3 1.0
N A:TYR10 4.5 11.1 1.0
CA A:CYS8 4.5 14.3 1.0
CD2 A:TYR10 4.5 10.8 1.0
CA A:TYR10 4.6 10.7 1.0
SG A:CYS11 4.6 13.9 1.0
SG A:CYS42 4.7 15.3 1.0
CG A:TYR10 4.7 9.5 1.0
SG A:CYS15 4.7 11.6 1.0
CB A:CYS15 4.7 10.0 1.0
C A:TYR10 4.8 10.5 1.0
C A:CYS8 4.8 13.4 1.0

Iron binding site 3 out of 4 in 1fdi

Go back to Iron Binding Sites List in 1fdi
Iron binding site 3 out of 4 in the Oxidized Form of Formate Dehydrogenase H From E. Coli Complexed with the Inhibitor Nitrite


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 Complexed with the Inhibitor Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe800

b:13.6
occ:1.00
 FE3 A:SF4800 0.0 13.6 1.0
S1 A:SF4800 2.2 14.3 1.0
S4 A:SF4800 2.2 14.5 1.0
SG A:CYS15 2.3 11.6 1.0
S2 A:SF4800 2.3 14.1 1.0
FE4 A:SF4800 2.5 13.9 1.0
FE1 A:SF4800 2.7 13.7 1.0
FE2 A:SF4800 2.8 13.4 1.0
CB A:CYS15 3.2 10.0 1.0
CB A:SER13 3.9 8.7 1.0
S3 A:SF4800 4.0 14.7 1.0
CD1 A:ILE183 4.1 13.6 1.0
N A:CYS15 4.2 10.5 1.0
CA A:CYS15 4.3 10.3 1.0
CG1 A:ILE183 4.3 15.1 1.0
OG A:SER13 4.4 12.8 1.0
SG A:CYS11 4.5 13.9 1.0
CB A:ILE183 4.5 15.0 1.0
CB A:CYS8 4.6 14.3 1.0
SG A:CYS8 4.7 15.8 1.0
CD2 A:LEU41 4.8 15.9 1.0
N A:CYS42 4.9 13.3 1.0
SG A:CYS42 5.0 15.3 1.0
CA A:LEU41 5.0 13.5 1.0

Iron binding site 4 out of 4 in 1fdi

Go back to Iron Binding Sites List in 1fdi
Iron binding site 4 out of 4 in the Oxidized Form of Formate Dehydrogenase H From E. Coli Complexed with the Inhibitor Nitrite


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 Complexed with the Inhibitor Nitrite within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe800

b:13.9
occ:1.00
 FE4 A:SF4800 0.0 13.9 1.0
S2 A:SF4800 2.3 14.1 1.0
S3 A:SF4800 2.3 14.7 1.0
FE1 A:SF4800 2.3 13.7 1.0
SG A:CYS11 2.3 13.9 1.0
S1 A:SF4800 2.3 14.3 1.0
FE3 A:SF4800 2.5 13.6 1.0
FE2 A:SF4800 2.5 13.4 1.0
S4 A:SF4800 3.5 14.5 1.0
CB A:CYS11 3.6 10.7 1.0
OG A:SER13 3.7 12.8 1.0
N A:CYS11 3.7 9.5 1.0
CB A:SER13 4.0 8.7 1.0
CA A:CYS11 4.1 9.6 1.0
O A:HOH832 4.3 21.4 1.0
C A:CYS11 4.5 9.3 1.0
SG A:CYS42 4.5 15.3 1.0
SG A:CYS15 4.6 11.6 1.0
CD A:PRO182 4.6 13.1 1.0
SG A:CYS8 4.6 15.8 1.0
O A:CYS11 4.6 8.4 1.0
N A:SER13 4.7 8.3 1.0
CB A:TYR10 4.8 9.9 1.0
C A:TYR10 4.9 10.5 1.0
CA A:SER13 4.9 7.8 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: Sun Dec 13 14:13:35 2020

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