Potassium 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:

Iron (Fe) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total only one binding site of Potassium was 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:

Potassium binding site 1 out of 1 in 8fo0

Go back to Potassium Binding Sites List in 8fo0
Potassium binding site 1 out of 1 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 Potassium with other atoms in the K 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:K303

b:26.3
occ:0.62
 OD1 A:ASP104 2.4 38.3 1.0
OD1 A:ASP129 2.5 37.0 1.0
HH21 A:ARG166 2.6 56.3 0.7
OXT A:SAM302 2.6 41.0 0.4
OXT A:SAM302 2.8 41.1 0.6
H A:ASP129 2.9 25.2 1.0
O A:THR105 3.0 20.7 1.0
HB2 A:ASP129 3.1 36.6 1.0
O A:MET127 3.1 25.4 1.0
H A:THR105 3.1 30.4 1.0
HE A:ARG166 3.2 42.6 0.7
HB2 A:SAM302 3.2 49.5 0.4
HO3' A:SAM302 3.3 45.6 0.6
HO3' A:SAM302 3.3 45.7 0.4
N A:ASP129 3.3 21.0 1.0
CG A:ASP129 3.3 41.9 1.0
NH2 A:ARG166 3.4 46.9 0.7
HB2 A:SAM302 3.5 49.5 0.6
N A:THR105 3.5 25.3 1.0
CB A:ASP129 3.5 30.5 1.0
CG A:ASP104 3.6 37.7 1.0
C A:THR105 3.6 26.8 1.0
H3' A:SAM302 3.6 52.6 0.4
C A:SAM302 3.7 40.6 0.4
H3' A:SAM302 3.8 52.6 0.6
C A:SAM302 3.8 40.9 0.6
HA A:LEU128 3.8 25.5 1.0
NE A:ARG166 3.9 35.5 0.7
C A:MET127 3.9 21.6 1.0
CA A:ASP129 3.9 25.4 1.0
HH22 A:ARG166 3.9 56.3 0.7
HA A:ASP104 4.0 22.6 1.0
C A:LEU128 4.0 20.7 1.0
C A:ASP104 4.1 37.2 1.0
CZ A:ARG166 4.1 38.0 0.7
HB2 A:ARG166 4.1 35.0 0.3
O3' A:SAM302 4.1 38.0 0.6
HA A:ASP129 4.1 30.5 1.0
CA A:THR105 4.1 23.2 1.0
O3' A:SAM302 4.2 38.0 0.4
CB A:SAM302 4.2 41.2 0.4
HG3 A:ARG166 4.2 38.5 0.3
CB A:SAM302 4.2 41.3 0.6
HB2 A:ARG166 4.2 35.5 0.7
CA A:LEU128 4.3 21.3 1.0
HA A:SAM302 4.3 49.7 0.6
OD2 A:ASP104 4.3 40.1 1.0
HA A:SAM302 4.3 49.5 0.4
CA A:SAM302 4.3 41.2 0.4
HB3 A:MET127 4.4 25.1 1.0
CA A:SAM302 4.4 41.4 0.6
C3' A:SAM302 4.4 43.8 0.4
N A:LEU128 4.4 20.0 1.0
CA A:ASP104 4.4 18.8 1.0
HB2 A:MET127 4.4 25.1 1.0
HA A:ASN106 4.4 27.1 1.0
HB3 A:ASP129 4.5 36.6 1.0
C3' A:SAM302 4.5 43.8 0.6
OD2 A:ASP129 4.5 37.0 1.0
HA A:THR105 4.5 27.8 1.0
HB1 A:SAM302 4.5 49.5 0.6
N A:ASN106 4.5 21.6 1.0
O A:SAM302 4.6 31.2 0.6
HB1 A:SAM302 4.6 49.5 0.4
CB A:ASP104 4.6 21.1 1.0
O A:SAM302 4.7 31.1 0.4
CB A:MET127 4.8 20.9 1.0
O A:ASP104 4.8 36.5 1.0
O A:LEU128 4.8 22.4 1.0
CB A:ARG166 4.9 29.1 0.3
HG3 A:ARG166 4.9 37.1 0.7
CA A:MET127 5.0 19.2 1.0
CG A:ARG166 5.0 32.1 0.3

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: Mon Aug 12 23:43:04 2024

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