Fluorine in PDB 8gky: Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF359 Inhibitor

All present enzymatic activity of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF359 Inhibitor:
2.1.2.1;

The structure of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF359 Inhibitor, PDB code: 8gky 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)	48.52 / 2.77
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	157.971, 157.971, 206.46, 90, 90, 120
R / Rfree (%)	19.9 / 24.3

The binding sites of Fluorine atom in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF359 Inhibitor (pdb code 8gky). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF359 Inhibitor, PDB code: 8gky:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF359 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 AGF359 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:77.7 occ:1.00 F33 A:ZVR601 0.0 77.7 1.0 C13 A:ZVR601 1.4 61.9 1.0 C12 A:ZVR601 2.4 60.5 1.0 N19 A:ZVR601 2.4 69.5 1.0 C15 A:ZVR601 2.4 45.7 1.0 C17 A:ZVR601 2.8 62.3 1.0 CE2 B:PHE105 3.0 88.3 1.0 CZ B:PHE105 3.3 92.6 1.0 C20 A:ZVR601 3.6 77.5 1.0 C32 A:ZVR601 3.6 45.0 1.0 C14 A:ZVR601 3.6 58.8 1.0 CB B:PRO321 3.7 31.4 1.0 CG B:PRO321 3.7 31.6 1.0 CE2 B:PHE320 3.8 35.6 1.0 CD2 B:PHE105 3.8 91.2 1.0 O28 A:ZVR601 3.8 89.0 1.0 C26 A:ZVR601 3.9 92.5 1.0 O18 A:ZVR601 4.0 48.5 1.0 C16 A:ZVR601 4.1 62.1 1.0 CZ B:PHE320 4.2 33.4 1.0 CE1 B:PHE105 4.2 100.4 1.0 CD B:PRO321 4.3 23.9 1.0 CD2 B:PHE320 4.6 28.9 1.0 CG B:PHE105 4.7 95.5 1.0 O27 A:ZVR601 4.8 97.2 1.0 CD1 B:PHE105 4.9 106.9 1.0 C21 A:ZVR601 4.9 68.1 1.0 CA B:PRO321 4.9 23.0 1.0 N B:PRO321 4.9 28.8 1.0 C31 A:ZVR601 4.9 26.1 1.0

Fluorine binding site 2 out of 2 in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF359 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) Y105F in Complex with Plp, Glycine and AGF359 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:104.9 occ:1.00 F33 B:ZVR601 0.0 104.9 1.0 C13 B:ZVR601 1.4 89.2 1.0 C12 B:ZVR601 2.4 79.6 1.0 C15 B:ZVR601 2.4 74.0 1.0 O18 B:ZVR601 2.6 89.1 1.0 C17 B:ZVR601 2.9 89.1 1.0 CE1 B:TYR176 3.3 51.0 1.0 C14 B:ZVR601 3.6 62.3 1.0 C32 B:ZVR601 3.7 59.5 1.0 CD2 B:LEU166 3.8 57.3 1.0 CD1 B:LEU166 3.8 43.5 1.0 CD1 B:TYR176 3.9 42.2 1.0 C16 B:ZVR601 4.1 58.2 1.0 CZ B:TYR176 4.2 46.4 1.0 N19 B:ZVR601 4.3 93.4 1.0 CD2 B:LEU172 4.4 51.0 1.0 CG B:LEU166 4.4 48.1 1.0 OH B:TYR176 4.4 48.9 1.0 CG2 B:ILE183 4.7 37.1 1.0 C31 B:ZVR601 5.0 50.0 1.0 CG B:TYR176 5.0 41.0 1.0

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