Fluorine in PDB 7rxv: Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3

Enzymatic activity of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3

All present enzymatic activity of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3:
2.5.1.6;

Protein crystallography data

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3, PDB code: 7rxv was solved by E.Fedorov, C.N.Niland, V.L.Schramm, A.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.86 / 1.07
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 67.981, 94.122, 117.315, 90, 90, 90
R / Rfree (%) 13 / 13.9

Other elements in 7rxv:

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3 also contains other interesting chemical elements:

Potassium (K) 1 atom
Sodium (Na) 2 atoms
Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3 (pdb code 7rxv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3, PDB code: 7rxv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7rxv

Go back to Fluorine Binding Sites List in 7rxv
Fluorine binding site 1 out of 3 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:15.6
occ:0.77
 F1 A:MGF504 0.0 15.6 0.8
MG A:MGF504 1.8 31.8 1.0
MG A:MG506 1.8 8.8 1.0
OD2 A:ASP31 2.5 7.9 1.0
HB3 A:ARG264 2.5 8.9 1.0
O A:HOH785 2.7 12.9 1.0
O A:HOH637 2.7 10.1 1.0
HH21 A:ARG264 2.8 14.3 1.0
HZ3 A:LYS265 2.8 13.5 1.0
HZ1 A:LYS265 2.9 13.5 1.0
O1A A:MLA503 2.9 9.2 1.0
O3B A:MLA503 3.0 11.4 1.0
HE A:ARG264 3.0 13.3 1.0
F3 A:MGF504 3.1 25.9 0.4
F2 A:MGF504 3.1 21.7 0.7
NZ A:LYS265 3.2 11.3 1.0
HZ2 A:LYS265 3.3 13.5 1.0
NH2 A:ARG264 3.4 11.9 1.0
NE A:ARG264 3.4 11.1 1.0
CB A:ARG264 3.5 7.4 1.0
O A:ARG264 3.5 8.3 1.0
CG A:ASP31 3.6 7.1 1.0
C3 A:MLA503 3.7 10.7 1.0
CZ A:ARG264 3.7 10.2 1.0
HB2 A:ARG264 3.7 8.9 1.0
C1 A:MLA503 3.8 9.7 1.0
O A:HOH631 3.9 9.8 1.0
HH22 A:ARG264 4.0 14.3 1.0
OD1 A:ASP31 4.0 7.9 1.0
C2 A:MLA503 4.0 14.7 1.0
HC22 A:MLA503 4.0 17.6 1.0
HG3 A:ARG264 4.1 10.4 1.0
CG A:ARG264 4.2 8.6 1.0
C A:ARG264 4.3 7.3 1.0
CD A:ARG264 4.3 10.1 1.0
HE1 A:HIS29 4.5 10.3 1.0
CA A:ARG264 4.5 7.5 1.0
CE A:LYS265 4.6 10.9 1.0
O3A A:MLA503 4.6 14.8 1.0
HD2 A:ARG264 4.6 12.1 1.0
HG2 A:LYS265 4.7 10.1 1.0
HA A:ARG264 4.7 9.1 1.0
HE2 A:LYS265 4.7 13.1 1.0
O A:HOH807 4.8 17.1 1.0
CB A:ASP31 4.8 7.8 1.0
NH1 A:ARG264 4.9 12.2 1.0
HB2 A:ASP31 4.9 9.4 1.0
HB3 A:ASP31 4.9 9.4 1.0
O1B A:MLA503 5.0 10.3 1.0
O A:HOH701 5.0 22.6 1.0
HC21 A:MLA503 5.0 17.6 1.0

Fluorine binding site 2 out of 3 in 7rxv

Go back to Fluorine Binding Sites List in 7rxv
Fluorine binding site 2 out of 3 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:21.7
occ:0.68
 F2 A:MGF504 0.0 21.7 0.7
MG A:MGF504 1.8 31.8 1.0
HH21 A:ARG264 2.1 14.3 1.0
O A:HOH785 2.7 12.9 1.0
NH2 A:ARG264 2.9 11.9 1.0
HE A:ARG264 3.0 13.3 1.0
F3 A:MGF504 3.1 25.9 0.4
F1 A:MGF504 3.1 15.6 0.8
HH22 A:ARG264 3.4 14.3 1.0
NE A:ARG264 3.6 11.1 1.0
CZ A:ARG264 3.7 10.2 1.0
O3B A:MLA503 3.9 11.4 1.0
C3 A:MLA503 4.0 10.7 1.0
O3A A:MLA503 4.2 14.8 1.0
HC22 A:MLA503 4.2 17.6 1.0
MG A:MG506 4.3 8.8 1.0
O A:HOH748 4.6 17.2 0.5
C2 A:MLA503 4.6 14.7 1.0
HB3 A:ARG264 4.6 8.9 1.0
O A:HOH637 4.8 10.1 1.0
NH1 A:ARG264 4.9 12.2 1.0
CD A:ARG264 5.0 10.1 1.0

Fluorine binding site 3 out of 3 in 7rxv

Go back to Fluorine Binding Sites List in 7rxv
Fluorine binding site 3 out of 3 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:25.9
occ:0.42
 F3 A:MGF504 0.0 25.9 0.4
MG A:MGF504 1.8 31.8 1.0
HC22 A:MLA503 2.5 17.6 1.0
O A:HOH701 2.6 22.6 1.0
HZ2 A:LYS265 2.8 13.5 1.0
HZ1 A:LYS265 2.8 13.5 1.0
F2 A:MGF504 3.1 21.7 0.7
F1 A:MGF504 3.1 15.6 0.8
C2 A:MLA503 3.2 14.7 1.0
NZ A:LYS265 3.2 11.3 1.0
C1 A:MLA503 3.4 9.7 1.0
O1A A:MLA503 3.4 9.2 1.0
O A:HOH785 3.4 12.9 1.0
O A:HOH807 3.6 17.1 1.0
HZ3 A:LYS265 3.7 13.5 1.0
C3 A:MLA503 3.7 10.7 1.0
MG A:MG506 4.0 8.8 1.0
HC21 A:MLA503 4.0 17.6 1.0
O3B A:MLA503 4.1 11.4 1.0
O1B A:MLA503 4.1 10.3 1.0
HE3 A:LYS265 4.2 13.1 1.0
CE A:LYS265 4.4 10.9 1.0
O A:HOH661 4.4 12.6 1.0
O3A A:MLA503 4.4 14.8 1.0
HH21 A:ARG264 4.5 14.3 1.0
O A:ARG264 4.5 8.3 1.0
HZ3 A:LYS181 4.6 13.4 1.0
O A:HOH748 4.8 17.2 0.5
OD2 A:ASP31 4.8 7.9 1.0
HE A:ARG264 4.9 13.3 1.0
HZ1 A:LYS181 4.9 13.4 1.0
HE2 A:LYS265 5.0 13.1 1.0
HD3 A:LYS265 5.0 11.5 1.0

Reference:

A.Ghosh, C.N.Niland, S.M.Cahill, N.M.Karadkhelkar, V.L.Schramm. Mechanism of Triphosphate Hydrolysis By Human MAT2A at 1.07 Angstrom Resolution. J.Am.Chem.Soc. 2021.
ISSN: ESSN 1520-5126
PubMed: 34668717
DOI: 10.1021/JACS.1C09328
Page generated: Fri Nov 5 13:17:23 2021

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