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Iron in PDB 8fo0: The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule

Enzymatic activity of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule

All present enzymatic activity of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule:
1.97.1.4;

Protein crystallography data

The structure of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule, PDB code: 8fo0 was solved by J.D.Moody, A.J.Saxton, A.Galambas, C.M.Lawrence, J.B.Broderick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.26 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.58, 58.551, 84.484, 90, 90, 90
R / Rfree (%) 16.4 / 18.8

Other elements in 8fo0:

The structure of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule also contains other interesting chemical elements:

Potassium (K) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule (pdb code 8fo0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule, PDB code: 8fo0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8fo0

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Iron binding site 1 out of 4 in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:22.9
occ:1.00
 FE1 A:SF4301 0.0 22.9 1.0
S3 A:SF4301 2.3 22.4 1.0
SG A:CYS33 2.3 22.6 1.0
S2 A:SF4301 2.3 21.3 1.0
S4 A:SF4301 2.3 27.0 1.0
FE3 A:SF4301 2.7 23.8 1.0
FE4 A:SF4301 2.7 22.0 1.0
FE2 A:SF4301 2.8 27.3 1.0
HB2 A:CYS33 3.0 27.6 1.0
HZ3 A:LYS131 3.1 33.9 1.0
CB A:CYS33 3.2 23.0 1.0
H A:CYS33 3.3 29.0 1.0
HZ2 A:LYS131 3.4 33.9 1.0
HE3 A:LYS131 3.5 30.6 1.0
NZ A:LYS131 3.6 28.2 1.0
HB2 A:MET31 3.7 29.3 1.0
S1 A:SF4301 3.9 22.4 1.0
HB3 A:CYS33 3.9 27.6 1.0
HB3 A:MET31 3.9 29.3 1.0
HB2 A:CYS36 3.9 31.8 1.0
N A:CYS33 4.0 24.2 1.0
CE A:LYS131 4.0 25.5 1.0
O A:SAM302 4.2 31.1 0.4
O A:SAM302 4.2 31.2 0.6
CB A:MET31 4.3 24.4 1.0
CA A:CYS33 4.3 21.7 1.0
HZ1 A:LYS131 4.4 33.9 1.0
HD3 A:LYS131 4.6 25.4 1.0
HN1 A:SAM302 4.6 39.5 0.6
HN1 A:SAM302 4.6 38.6 0.4
SG A:CYS36 4.6 25.1 1.0
HG13 A:VAL142 4.6 36.9 1.0
CB A:CYS36 4.6 26.5 1.0
HA A:CYS36 4.7 33.6 1.0
SG A:CYS29 4.7 22.0 1.0
HD22 A:ASN106 4.7 36.7 1.0
HE2 A:LYS131 4.8 30.6 1.0
HE1 A:TYR35 4.8 29.2 1.0
HO2' A:SAM302 4.8 48.6 0.6
HA A:CYS33 4.8 26.0 1.0
SD A:MET31 4.9 30.5 1.0
CD A:LYS131 4.9 21.2 1.0
HE1 A:TRP42 4.9 32.1 1.0
N A:SAM302 5.0 32.2 0.4
C A:MET31 5.0 25.5 1.0
N A:ARG32 5.0 23.9 1.0

Iron binding site 2 out of 4 in 8fo0

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Iron binding site 2 out of 4 in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:27.3
occ:1.00
 FE2 A:SF4301 0.0 27.3 1.0
S3 A:SF4301 2.3 22.4 1.0
S4 A:SF4301 2.3 27.0 1.0
S1 A:SF4301 2.3 22.4 1.0
N A:SAM302 2.4 32.2 0.4
HN1 A:SAM302 2.4 39.5 0.6
HN1 A:SAM302 2.4 38.6 0.4
O A:SAM302 2.4 31.1 0.4
O A:SAM302 2.4 31.2 0.6
N A:SAM302 2.5 32.9 0.6
FE1 A:SF4301 2.8 22.9 1.0
FE3 A:SF4301 2.8 23.8 1.0
FE4 A:SF4301 2.8 22.0 1.0
SD A:SAM302 2.9 51.4 0.6
HN2 A:SAM302 3.0 38.6 0.4
HN2 A:SAM302 3.0 39.5 0.6
C A:SAM302 3.2 40.9 0.6
C A:SAM302 3.2 40.6 0.4
HE2 A:SAM302 3.3 60.4 0.4
CA A:SAM302 3.3 41.2 0.4
CA A:SAM302 3.3 41.4 0.6
HZ2 A:LYS131 3.4 33.9 1.0
HE3 A:SAM302 3.4 60.4 0.4
SD A:SAM302 3.5 54.6 0.4
CE A:SAM302 3.6 50.3 0.4
HE2 A:SAM302 3.6 59.9 0.6
HE3 A:SAM302 3.7 59.9 0.6
CE A:SAM302 3.7 49.9 0.6
H2' A:SAM302 3.8 43.5 0.4
H2' A:SAM302 3.9 43.1 0.6
S2 A:SF4301 3.9 21.3 1.0
CG A:SAM302 4.0 44.6 0.6
HA A:SAM302 4.0 49.7 0.6
HA A:SAM302 4.0 49.5 0.4
HG2 A:SAM302 4.1 53.5 0.6
HZ3 A:LYS131 4.1 33.9 1.0
NZ A:LYS131 4.1 28.2 1.0
HO2' A:SAM302 4.2 48.6 0.6
CG A:SAM302 4.2 44.2 0.4
CB A:SAM302 4.2 41.3 0.6
CB A:SAM302 4.3 41.2 0.4
HG2 A:SAM302 4.3 53.0 0.4
OXT A:SAM302 4.3 41.1 0.6
H8 A:SAM302 4.4 45.6 0.4
OXT A:SAM302 4.4 41.0 0.4
H8 A:SAM302 4.4 45.5 0.6
HE3 A:LYS131 4.5 30.6 1.0
HB3 A:ASN106 4.5 32.6 1.0
H3' A:SAM302 4.6 52.6 0.4
HE1 A:SAM302 4.6 59.9 0.6
SG A:CYS29 4.6 22.0 1.0
HD22 A:ASN106 4.6 36.7 1.0
H A:GLY78 4.6 29.7 1.0
HE1 A:SAM302 4.7 60.4 0.4
HB2 A:SAM302 4.7 49.5 0.6
O A:GLY78 4.7 26.4 1.0
C2' A:SAM302 4.7 36.2 0.4
H3' A:SAM302 4.7 52.6 0.6
C2' A:SAM302 4.8 35.9 0.6
HZ1 A:LYS131 4.8 33.9 1.0
HO2' A:SAM302 4.8 48.5 0.4
SG A:CYS33 4.8 22.6 1.0
SG A:CYS36 4.8 25.1 1.0
CE A:LYS131 4.9 25.5 1.0
HG1 A:SAM302 4.9 53.5 0.6
O2' A:SAM302 4.9 40.5 0.6
HB2 A:SAM302 5.0 49.5 0.4

Iron binding site 3 out of 4 in 8fo0

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Iron binding site 3 out of 4 in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:23.8
occ:1.00
 FE3 A:SF4301 0.0 23.8 1.0
SG A:CYS36 2.2 25.1 1.0
S1 A:SF4301 2.3 22.4 1.0
S2 A:SF4301 2.3 21.3 1.0
S4 A:SF4301 2.3 27.0 1.0
FE1 A:SF4301 2.7 22.9 1.0
FE4 A:SF4301 2.7 22.0 1.0
FE2 A:SF4301 2.8 27.3 1.0
HB2 A:CYS36 2.9 31.8 1.0
HE1 A:TRP42 3.2 32.1 1.0
CB A:CYS36 3.2 26.5 1.0
HA A:CYS36 3.6 33.6 1.0
HE3 A:SAM302 3.8 60.4 0.4
HE3 A:SAM302 3.8 59.9 0.6
S3 A:SF4301 3.8 22.4 1.0
HB3 A:CYS36 3.9 31.8 1.0
HB2 A:CYS33 4.0 27.6 1.0
CA A:CYS36 4.0 28.0 1.0
NE1 A:TRP42 4.0 26.7 1.0
HE2 A:SAM302 4.1 60.4 0.4
HE2 A:SAM302 4.1 59.9 0.6
H A:ASN38 4.3 34.2 1.0
CE A:SAM302 4.3 49.9 0.6
CE A:SAM302 4.4 50.3 0.4
HB2 A:ASN38 4.5 37.8 1.0
H8 A:SAM302 4.5 45.5 0.6
HD1 A:TRP42 4.6 29.2 1.0
H A:CYS33 4.6 29.0 1.0
H8 A:SAM302 4.6 45.6 0.4
HN1 A:SAM302 4.6 39.5 0.6
HN1 A:SAM302 4.6 38.6 0.4
SG A:CYS33 4.7 22.6 1.0
H A:HIS37 4.7 35.5 1.0
SD A:SAM302 4.7 51.4 0.6
CD1 A:TRP42 4.7 24.4 1.0
CB A:CYS33 4.7 23.0 1.0
HD2 A:HIS37 4.8 49.1 1.0
N A:SAM302 4.8 32.2 0.4
H A:GLY78 4.8 29.7 1.0
C A:CYS36 4.8 28.4 1.0
HG1 A:THR41 4.8 32.0 1.0
N A:SAM302 4.9 32.9 0.6
SG A:CYS29 4.9 22.0 1.0
HZ2 A:TRP42 4.9 31.2 1.0
O A:ASN38 5.0 27.8 1.0
O A:SAM302 5.0 31.1 0.4
HN2 A:SAM302 5.0 38.6 0.4
HN2 A:SAM302 5.0 39.5 0.6
N A:HIS37 5.0 29.6 1.0

Iron binding site 4 out of 4 in 8fo0

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Iron binding site 4 out of 4 in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to A Partially Cleaved Sam Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:22.0
occ:1.00
 FE4 A:SF4301 0.0 22.0 1.0
SG A:CYS29 2.3 22.0 1.0
S2 A:SF4301 2.3 21.3 1.0
S1 A:SF4301 2.3 22.4 1.0
S3 A:SF4301 2.3 22.4 1.0
FE3 A:SF4301 2.7 23.8 1.0
FE1 A:SF4301 2.7 22.9 1.0
FE2 A:SF4301 2.8 27.3 1.0
HB2 A:MET31 3.3 29.3 1.0
HN1 A:SAM302 3.3 39.5 0.6
HN1 A:SAM302 3.3 38.6 0.4
CB A:CYS29 3.4 21.1 1.0
HB3 A:CYS29 3.4 25.4 1.0
HB2 A:CYS29 3.5 25.4 1.0
S4 A:SF4301 3.9 27.0 1.0
HD22 A:ASN106 3.9 36.7 1.0
N A:SAM302 4.0 32.9 0.6
N A:SAM302 4.0 32.2 0.4
H A:MET31 4.1 23.9 1.0
HE1 A:TRP42 4.1 32.1 1.0
CB A:MET31 4.2 24.4 1.0
O A:MET31 4.3 24.5 1.0
HN2 A:SAM302 4.4 38.6 0.4
HN2 A:SAM302 4.4 39.5 0.6
HB3 A:MET31 4.5 29.3 1.0
HD1 A:TRP42 4.5 29.2 1.0
NE1 A:TRP42 4.5 26.7 1.0
HA2 A:GLY78 4.6 30.9 1.0
C A:MET31 4.6 25.5 1.0
ND2 A:ASN106 4.6 30.6 1.0
H A:CYS33 4.7 29.0 1.0
SG A:CYS36 4.7 25.1 1.0
N A:MET31 4.7 19.9 1.0
HB2 A:GLU79 4.7 33.8 1.0
H A:GLY78 4.7 29.7 1.0
CA A:MET31 4.8 19.2 1.0
HD21 A:ASN106 4.8 36.7 1.0
CD1 A:TRP42 4.8 24.4 1.0
CA A:CYS29 4.8 19.2 1.0
SG A:CYS33 4.8 22.6 1.0
O A:SAM302 4.9 31.1 0.4
O A:SAM302 4.9 31.2 0.6
HA A:CYS29 5.0 23.1 1.0

Reference:

J.D.Moody, S.Hill, M.N.Lundahl, A.J.Saxton, A.Galambas, W.E.Broderick, C.M.Lawrence, J.B.Broderick. Computational Engineering of Previously Crystallized Pyruvate Formate-Lyase Activating Enzyme Reveals Insights Into Sam Binding and Reductive Cleavage. J.Biol.Chem. 04791 2023.
ISSN: ESSN 1083-351X
PubMed: 37156396
DOI: 10.1016/J.JBC.2023.104791
Page generated: Sat Aug 10 04:26:59 2024

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