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Iron in PDB 3dnf: Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway

Enzymatic activity of Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway

All present enzymatic activity of Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway:
1.17.1.2;

Protein crystallography data

The structure of Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway, PDB code: 3dnf was solved by I.Rekittke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.90 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.370, 87.760, 72.400, 90.00, 95.13, 90.00
R / Rfree (%) 19.3 / 22.6

Iron Binding Sites:

The binding sites of Iron atom in the Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway (pdb code 3dnf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway, PDB code: 3dnf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3dnf

Go back to Iron Binding Sites List in 3dnf
Iron binding site 1 out of 6 in the Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2302

b:29.1
occ:1.00
 FE1 A:F3S2302 0.0 29.1 1.0
S1 A:F3S2302 2.3 26.0 1.0
S2 A:F3S2302 2.3 35.8 1.0
S3 A:F3S2302 2.3 25.3 1.0
SG A:CYS193 2.4 35.9 0.8
FE4 A:F3S2302 2.4 28.1 1.0
SG A:CYS193 2.5 31.1 0.2
FE3 A:F3S2302 2.7 21.7 1.0
CB A:CYS193 3.2 33.1 0.2
CB A:CYS193 3.2 33.8 0.8
S4 A:F3S2302 3.9 25.9 1.0
CB A:ALA195 4.0 34.6 1.0
O A:HOH3970 4.3 45.6 1.0
O A:HOH3892 4.6 83.9 1.0
CA A:CYS193 4.6 33.0 0.2
CA A:CYS193 4.7 33.3 0.8
OG1 A:THR165 4.7 33.0 1.0
SG A:CYS13 4.7 29.3 1.0
O A:HOH3762 4.7 29.5 1.0
SG A:CYS96 4.7 32.3 1.0
CB A:THR165 4.8 30.9 1.0
CB A:CYS13 4.8 27.5 1.0
CB A:TYR98 4.8 29.9 1.0
CD2 A:TYR98 4.8 29.5 1.0
CG A:TYR98 4.9 32.5 1.0
N A:ALA195 5.0 36.1 1.0

Iron binding site 2 out of 6 in 3dnf

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Iron binding site 2 out of 6 in the Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2302

b:21.7
occ:1.00
 FE3 A:F3S2302 0.0 21.7 1.0
S1 A:F3S2302 2.2 26.0 1.0
S4 A:F3S2302 2.2 25.9 1.0
S3 A:F3S2302 2.3 25.3 1.0
SG A:CYS96 2.3 32.3 1.0
FE4 A:F3S2302 2.4 28.1 1.0
FE1 A:F3S2302 2.7 29.1 1.0
CB A:CYS96 3.2 31.8 1.0
CA A:GLY15 3.8 31.2 1.0
N A:GLY15 3.9 30.5 1.0
S2 A:F3S2302 4.0 35.8 1.0
O A:HOH3970 4.1 45.6 1.0
CB A:TYR98 4.3 29.9 1.0
CD2 A:TYR98 4.4 29.5 1.0
SG A:CYS193 4.5 31.1 0.2
SG A:CYS13 4.6 29.3 1.0
CA A:CYS96 4.6 30.4 1.0
CG A:TYR98 4.8 32.5 1.0
C A:GLY15 4.9 30.6 1.0
SG A:CYS193 4.9 35.9 0.8

Iron binding site 3 out of 6 in 3dnf

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Iron binding site 3 out of 6 in the Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2302

b:28.1
occ:1.00
 FE4 A:F3S2302 0.0 28.1 1.0
S2 A:F3S2302 2.1 35.8 1.0
S4 A:F3S2302 2.1 25.9 1.0
S3 A:F3S2302 2.1 25.3 1.0
FE3 A:F3S2302 2.4 21.7 1.0
FE1 A:F3S2302 2.4 29.1 1.0
SG A:CYS13 2.5 29.3 1.0
CB A:CYS13 3.3 27.5 1.0
S1 A:F3S2302 3.5 26.0 1.0
N A:GLY15 4.0 30.5 1.0
CA A:GLY15 4.3 31.2 1.0
O A:HOH3970 4.4 45.6 1.0
O A:HOH3865 4.4 52.8 1.0
SG A:CYS96 4.6 32.3 1.0
CA A:CYS13 4.6 29.1 1.0
CB A:ALA195 4.6 34.6 1.0
N A:VAL16 4.6 30.6 1.0
SG A:CYS193 4.7 31.1 0.2
SG A:CYS193 4.7 35.9 0.8
C A:CYS13 4.7 28.2 1.0
N A:PHE14 4.8 31.0 1.0
C A:GLY15 4.9 30.6 1.0
CG2 A:VAL16 4.9 33.2 1.0
O A:HOH3891 4.9 52.8 1.0

Iron binding site 4 out of 6 in 3dnf

Go back to Iron Binding Sites List in 3dnf
Iron binding site 4 out of 6 in the Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3302

b:28.6
occ:1.00
 FE1 B:F3S3302 0.0 28.6 1.0
S1 B:F3S3302 2.3 25.2 1.0
S2 B:F3S3302 2.3 37.1 1.0
S3 B:F3S3302 2.3 27.3 1.0
SG B:CYS193 2.3 35.7 1.0
FE4 B:F3S3302 2.4 33.5 1.0
FE3 B:F3S3302 2.7 24.5 1.0
CB B:CYS193 3.1 32.6 1.0
S4 B:F3S3302 4.0 27.7 1.0
CB B:ALA195 4.0 35.6 1.0
CD2 B:TYR98 4.3 43.8 1.0
O B:HOH3961 4.3 34.3 1.0
O B:HOH4163 4.4 41.7 1.0
O B:HOH3998 4.5 43.9 1.0
CB B:CYS13 4.6 28.0 1.0
CA B:CYS193 4.6 33.4 1.0
SG B:CYS96 4.7 33.3 1.0
SG B:CYS13 4.7 26.7 1.0
CB B:THR165 5.0 30.4 1.0

Iron binding site 5 out of 6 in 3dnf

Go back to Iron Binding Sites List in 3dnf
Iron binding site 5 out of 6 in the Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3302

b:24.5
occ:1.00
 FE3 B:F3S3302 0.0 24.5 1.0
SG B:CYS96 2.2 33.3 1.0
S1 B:F3S3302 2.3 25.2 1.0
S3 B:F3S3302 2.3 27.3 1.0
S4 B:F3S3302 2.3 27.7 1.0
FE4 B:F3S3302 2.5 33.5 1.0
FE1 B:F3S3302 2.7 28.6 1.0
CB B:CYS96 3.1 31.2 1.0
CA B:GLY15 3.9 30.6 1.0
CD2 B:TYR98 4.0 43.8 1.0
S2 B:F3S3302 4.1 37.1 1.0
N B:GLY15 4.1 31.2 1.0
O B:HOH3961 4.2 34.3 1.0
CB B:TYR98 4.4 36.4 1.0
CA B:CYS96 4.6 32.3 1.0
SG B:CYS13 4.6 26.7 1.0
CG B:TYR98 4.6 40.6 1.0
SG B:CYS193 4.7 35.7 1.0
CE2 B:TYR98 4.9 45.0 1.0
C B:GLY15 5.0 31.9 1.0

Iron binding site 6 out of 6 in 3dnf

Go back to Iron Binding Sites List in 3dnf
Iron binding site 6 out of 6 in the Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3302

b:33.5
occ:1.00
 FE4 B:F3S3302 0.0 33.5 1.0
S3 B:F3S3302 2.2 27.3 1.0
S2 B:F3S3302 2.2 37.1 1.0
S4 B:F3S3302 2.2 27.7 1.0
FE1 B:F3S3302 2.4 28.6 1.0
FE3 B:F3S3302 2.5 24.5 1.0
SG B:CYS13 2.5 26.7 1.0
CB B:CYS13 3.2 28.0 1.0
S1 B:F3S3302 3.5 25.2 1.0
O B:HOH3961 4.1 34.3 1.0
N B:GLY15 4.1 31.2 1.0
CA B:GLY15 4.4 30.6 1.0
O B:HOH3977 4.4 38.3 1.0
SG B:CYS96 4.5 33.3 1.0
CA B:CYS13 4.6 28.3 1.0
N B:VAL16 4.6 31.1 1.0
SG B:CYS193 4.7 35.7 1.0
C B:CYS13 4.8 29.6 1.0
CB B:ALA195 4.8 35.6 1.0
N B:PHE14 4.8 31.5 1.0
CG2 B:VAL16 5.0 32.7 1.0
C B:GLY15 5.0 31.9 1.0

Reference:

I.Rekittke, J.Wiesner, U.Demmer, E.Warkentin, W.Xu, K.Troschke, M.Hintz, J.H.No, E.C.Duin, E.Oldfield, H.Jomaa, U.Ermler. Structure of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway. J.Am.Chem.Soc. 2008.
ISSN: ESSN 1520-5126
PubMed: 19035630
DOI: 10.1021/JA806668Q
Page generated: Tue Aug 5 00:38:43 2025

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