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Iron in PDB 8fol: The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam, Alternate Crystal Form

Enzymatic activity of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam, Alternate Crystal Form

All present enzymatic activity of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam, Alternate Crystal Form:
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 Sam, Alternate Crystal Form, PDB code: 8fol 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) 35.37 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.653, 59.011, 96.792, 90, 90, 90
R / Rfree (%) 19.5 / 21.4

Other elements in 8fol:

The structure of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam, Alternate Crystal Form also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 3 atoms

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 Sam, Alternate Crystal Form (pdb code 8fol). 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 Sam, Alternate Crystal Form, PDB code: 8fol:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8fol

Go back to Iron Binding Sites List in 8fol
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 Sam, Alternate Crystal Form


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 Sam, Alternate Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:47.2
occ:1.00
 FE1 A:SF4301 0.0 47.2 1.0
SG A:CYS33 2.3 45.0 1.0
S2 A:SF4301 2.3 41.2 1.0
S3 A:SF4301 2.3 44.4 1.0
S4 A:SF4301 2.3 39.6 1.0
FE3 A:SF4301 2.7 47.5 1.0
FE4 A:SF4301 2.7 46.3 1.0
FE2 A:SF4301 2.7 57.5 1.0
CB A:CYS33 3.2 41.1 1.0
NZ A:LYS131 3.6 44.4 1.0
S1 A:SF4301 3.9 45.2 1.0
N A:CYS33 4.0 39.3 1.0
CE A:LYS131 4.0 46.3 1.0
O A:SAM302 4.2 58.8 1.0
CA A:CYS33 4.2 46.1 1.0
CB A:MET31 4.3 35.4 1.0
CB A:CYS36 4.7 46.8 1.0
SG A:CYS36 4.7 45.8 1.0
SG A:CYS29 4.8 48.1 1.0
CD A:LYS131 4.9 41.9 1.0
C A:MET31 4.9 40.9 1.0

Iron binding site 2 out of 4 in 8fol

Go back to Iron Binding Sites List in 8fol
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 Sam, Alternate Crystal Form


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 Sam, Alternate Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:57.5
occ:1.00
 FE2 A:SF4301 0.0 57.5 1.0
S3 A:SF4301 2.3 44.4 1.0
S4 A:SF4301 2.3 39.6 1.0
S1 A:SF4301 2.3 45.2 1.0
O A:SAM302 2.3 58.8 1.0
N A:SAM302 2.6 54.0 1.0
FE4 A:SF4301 2.7 46.3 1.0
FE3 A:SF4301 2.7 47.5 1.0
FE1 A:SF4301 2.7 47.2 1.0
C A:SAM302 3.2 63.1 1.0
CA A:SAM302 3.4 55.9 1.0
SD A:SAM302 3.7 78.6 1.0
CE A:SAM302 3.7 64.3 1.0
CG A:SAM302 3.9 64.4 1.0
S2 A:SF4301 3.9 41.2 1.0
NZ A:LYS131 4.1 44.4 1.0
CB A:SAM302 4.2 63.1 1.0
OXT A:SAM302 4.3 67.7 1.0
SG A:CYS29 4.7 48.1 1.0
C2' A:SAM302 4.8 67.7 1.0
SG A:CYS36 4.8 45.8 1.0
SG A:CYS33 4.8 45.0 1.0
O A:GLY78 4.8 51.4 1.0
CE A:LYS131 4.9 46.3 1.0

Iron binding site 3 out of 4 in 8fol

Go back to Iron Binding Sites List in 8fol
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 Sam, Alternate Crystal Form


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 Sam, Alternate Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:47.5
occ:1.00
 FE3 A:SF4301 0.0 47.5 1.0
SG A:CYS36 2.3 45.8 1.0
S4 A:SF4301 2.3 39.6 1.0
S2 A:SF4301 2.3 41.2 1.0
S1 A:SF4301 2.3 45.2 1.0
FE1 A:SF4301 2.7 47.2 1.0
FE2 A:SF4301 2.7 57.5 1.0
FE4 A:SF4301 2.7 46.3 1.0
CB A:CYS36 3.2 46.8 1.0
NE1 A:TRP42 3.6 46.3 1.0
S3 A:SF4301 3.9 44.4 1.0
CA A:CYS36 4.0 51.0 1.0
CE A:SAM302 4.5 64.3 1.0
CD1 A:TRP42 4.5 52.1 1.0
CE2 A:TRP42 4.6 49.1 1.0
SG A:CYS33 4.7 45.0 1.0
CB A:CYS33 4.8 41.1 1.0
SG A:CYS29 4.9 48.1 1.0
O A:ASN38 4.9 46.5 1.0
CZ2 A:TRP42 4.9 49.7 1.0
O A:SAM302 5.0 58.8 1.0
C A:CYS36 5.0 53.8 1.0
N A:SAM302 5.0 54.0 1.0

Iron binding site 4 out of 4 in 8fol

Go back to Iron Binding Sites List in 8fol
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 Sam, Alternate Crystal Form


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 Sam, Alternate Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:46.3
occ:1.00
 FE4 A:SF4301 0.0 46.3 1.0
S1 A:SF4301 2.3 45.2 1.0
S3 A:SF4301 2.3 44.4 1.0
S2 A:SF4301 2.3 41.2 1.0
SG A:CYS29 2.3 48.1 1.0
FE1 A:SF4301 2.7 47.2 1.0
FE2 A:SF4301 2.7 57.5 1.0
FE3 A:SF4301 2.7 47.5 1.0
CB A:CYS29 3.4 43.7 1.0
S4 A:SF4301 3.9 39.6 1.0
N A:SAM302 3.9 54.0 1.0
O A:MET31 4.2 39.2 1.0
CB A:MET31 4.2 35.4 1.0
ND2 A:ASN106 4.4 44.1 1.0
NE1 A:TRP42 4.4 46.3 1.0
C A:MET31 4.6 40.9 1.0
CD1 A:TRP42 4.7 52.1 1.0
N A:MET31 4.7 42.4 1.0
O A:SAM302 4.7 58.8 1.0
CA A:MET31 4.7 40.0 1.0
SG A:CYS33 4.8 45.0 1.0
SG A:CYS36 4.8 45.8 1.0
CA A:CYS29 4.8 49.9 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 04:28:21 2024

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