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Fluorine in PDB 8gkz: Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF362 Inhibitor

Enzymatic activity of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF362 Inhibitor

All present enzymatic activity of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF362 Inhibitor:
2.1.2.1;

Protein crystallography data

The structure of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF362 Inhibitor, PDB code: 8gkz was solved by J.M.Katinas, C.E.Dann Iii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.74 / 2.75
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 158.25, 158.25, 207.99, 90, 90, 120
R / Rfree (%) 21.5 / 26.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF362 Inhibitor (pdb code 8gkz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF362 Inhibitor, PDB code: 8gkz:

Fluorine binding site 1 out of 1 in 8gkz

Go back to Fluorine Binding Sites List in 8gkz
Fluorine binding site 1 out of 1 in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF362 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF362 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:87.4
occ:0.91
 F33 B:Y72601 0.0 87.4 0.9
C12 B:Y72601 1.4 85.5 0.9
C13 B:Y72601 2.4 83.6 0.9
C16 B:Y72601 2.5 82.4 0.9
C31 B:Y72601 2.9 83.6 0.9
C17 B:Y72601 3.0 83.2 0.9
CZ B:PHE105 3.1 86.1 1.0
C32 B:Y72601 3.1 86.8 0.9
N19 B:Y72601 3.2 93.3 0.9
CE2 B:PHE105 3.3 90.4 1.0
CG B:PRO321 3.3 32.8 1.0
CB B:PRO321 3.4 29.1 1.0
CE2 B:PHE320 3.7 35.8 1.0
C15 B:Y72601 3.7 72.8 0.9
S14 B:Y72601 3.8 80.7 0.9
O18 B:Y72601 3.9 70.6 0.9
CZ B:PHE320 4.0 30.4 1.0
CE1 B:PHE105 4.0 74.3 1.0
CD1 A:LEU172 4.1 44.6 1.0
C30 B:Y72601 4.3 84.5 0.9
CD2 B:PHE105 4.3 80.5 1.0
C20 B:Y72601 4.4 94.1 0.9
CD2 A:LEU172 4.5 31.8 1.0
CD2 B:PHE320 4.5 35.0 1.0
CD B:PRO321 4.6 17.2 1.0
CA B:PRO321 4.7 18.9 1.0
C21 B:Y72601 4.7 96.4 0.9
CG A:LEU172 4.8 35.2 1.0
CD1 B:PHE105 4.9 72.6 1.0
N B:PRO321 5.0 27.0 1.0
CG B:PHE105 5.0 68.3 1.0

Reference:

J.M.Katinas, M.J.Nayeen, M.Schneider, K.Shah, A.N.Fifer, L.M.Klapper, A.Sharma, K.Thalluri, M.S.Van Nieuwenhze, Z.Hou, A.Gangjee, L.H.Matherly, C.E.Dann 3Rd. Structural Characterization of 5-Substituted Pyrrolo[3,2- D ]Pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 38324671
DOI: 10.1021/ACS.BIOCHEM.3C00613
Page generated: Wed Jul 16 05:06:39 2025

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