Sodium in PDB 7rxv: 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;

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

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

Fluorine	(F)	3 atoms
Potassium	(K)	1 atom
Magnesium	(Mg)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3, PDB code: 7rxv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na508 b:14.8 occ:1.00 H A:ALA321 2.1 10.4 1.0 HA A:TYR320 2.7 9.8 1.0 HB A:VAL324 2.7 11.7 1.0 HD13 A:LEU328 2.7 10.5 0.5 HD2 A:TYR320 2.7 9.9 1.0 HB3 A:TYR320 2.8 9.8 1.0 O A:VAL324 2.8 9.4 1.0 O A:HIS326 2.9 10.2 1.0 N A:ALA321 2.9 8.6 1.0 HG12 A:VAL324 3.0 12.6 1.0 CA A:TYR320 3.3 8.2 1.0 HD11 A:LEU328 3.3 10.5 0.5 CD1 A:LEU328 3.3 8.8 0.5 O A:ALA321 3.4 9.1 1.0 CB A:TYR320 3.4 8.2 1.0 HD12 A:LEU328 3.5 10.5 0.5 CD2 A:TYR320 3.5 8.2 1.0 CB A:VAL324 3.5 9.8 1.0 C A:VAL324 3.5 8.9 1.0 HD23 A:LEU328 3.5 12.9 0.5 HA A:PRO327 3.6 11.8 1.0 C A:TYR320 3.6 8.7 1.0 HG A:LEU328 3.6 13.2 0.5 HD21 A:LEU328 3.6 12.9 0.5 CG1 A:VAL324 3.6 10.5 1.0 HB2 A:ALA132 3.7 10.9 1.0 HB3 A:ALA321 3.8 11.3 1.0 C A:HIS326 3.8 9.7 1.0 HG11 A:VAL324 3.8 12.6 1.0 CG A:TYR320 3.8 8.2 1.0 HB3 A:ALA132 3.9 10.9 1.0 CD2 A:LEU328 3.9 10.8 0.5 CA A:ALA321 3.9 8.9 1.0 CA A:VAL324 4.0 8.9 1.0 C A:ALA321 4.1 8.2 1.0 H A:VAL324 4.1 11.2 1.0 H A:LEU328 4.1 11.1 0.5 H A:LEU328 4.1 11.1 0.5 CA A:PRO327 4.2 9.9 1.0 CG A:LEU328 4.3 11.0 0.5 HB2 A:TYR320 4.3 9.8 1.0 C A:SER325 4.3 9.7 1.0 CB A:ALA132 4.3 9.1 1.0 CB A:ALA321 4.3 9.4 1.0 O A:SER325 4.3 10.7 1.0 N A:SER325 4.4 9.6 1.0 N A:PRO327 4.4 9.9 1.0 N A:LEU328 4.4 9.3 1.0 N A:HIS326 4.5 10.1 1.0 H A:ALA132 4.5 11.6 1.0 HG13 A:VAL324 4.5 12.6 1.0 N A:VAL324 4.6 9.4 1.0 C A:PRO327 4.6 8.8 1.0 CE2 A:TYR320 4.6 8.8 1.0 N A:TYR320 4.6 8.1 1.0 HB2 A:ALA321 4.6 11.3 1.0 O A:SER319 4.7 8.6 1.0 CG2 A:VAL324 4.7 11.0 1.0 HE2 A:TYR320 4.7 10.5 1.0 CG A:LEU328 4.7 10.1 0.5 HA A:ALA321 4.8 10.7 1.0 CA A:SER325 4.8 10.1 0.4 H A:HIS326 4.8 12.2 1.0 HA A:SER325 4.8 12.1 0.4 CA A:HIS326 4.8 10.9 1.0 CA A:SER325 4.8 10.0 0.6 HD22 A:LEU328 4.8 11.3 0.5 O A:TYR320 4.8 8.8 1.0 HG21 A:VAL324 4.8 13.2 1.0 HD11 A:LEU328 4.8 11.6 0.5 HB1 A:ALA132 4.8 10.9 1.0 HD22 A:LEU328 4.8 12.9 0.5 HA A:SER325 4.9 12.0 0.6 HA A:VAL324 4.9 10.7 1.0 HG23 A:VAL324 4.9 13.2 1.0 O A:HOH857 4.9 13.6 1.0 H A:SER325 5.0 11.5 0.6 H A:SER325 5.0 11.5 0.4

Sodium binding site 2 out of 2 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine, Malonate (Mla) and MGF3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na509 b:23.8 occ:1.00 HH22 A:ARG199 2.5 15.7 0.6 HH12 A:ARG199 2.5 18.3 0.6 O A:HIS201 2.8 10.1 1.0 O A:ASP239 2.9 15.2 1.0 HA A:HIS201 2.9 12.2 1.0 HA A:THR240 3.1 14.3 1.0 HG13 A:ILE241 3.3 16.7 1.0 NH2 A:ARG199 3.3 13.1 0.6 NH1 A:ARG199 3.3 15.3 0.6 CD2 A:HIS201 3.4 13.6 1.0 CG A:HIS201 3.5 11.5 1.0 C A:ASP239 3.6 14.2 1.0 C A:HIS201 3.6 9.6 1.0 CA A:HIS201 3.6 10.2 1.0 HB3 A:ASP239 3.6 24.2 1.0 HD2 A:HIS201 3.7 16.4 1.0 H A:ILE241 3.7 13.1 1.0 HD12 A:ILE241 3.7 19.8 0.9 NE2 A:HIS201 3.7 17.7 1.0 CZ A:ARG199 3.8 14.8 0.6 ND1 A:HIS201 3.8 14.4 1.0 HD11 A:ILE241 3.9 19.8 0.8 CA A:THR240 3.9 11.9 1.0 CE1 A:HIS201 3.9 15.7 1.0 HH21 A:ARG199 4.0 15.7 0.6 CB A:HIS201 4.0 10.9 1.0 HH11 A:ARG199 4.0 18.3 0.6 CD1 A:ILE241 4.1 16.5 1.0 CG1 A:ILE241 4.1 13.9 1.0 N A:THR240 4.1 13.4 1.0 HE2 A:HIS201 4.1 21.2 1.0 N A:ILE241 4.1 10.9 1.0 HB2 A:ASP239 4.2 24.2 1.0 CB A:ASP239 4.3 20.2 1.0 HB2 A:HIS201 4.3 13.1 1.0 O A:HOH801 4.4 28.8 1.0 C A:THR240 4.4 11.7 1.0 HE1 A:HIS201 4.5 18.9 1.0 HB A:ILE241 4.5 13.7 1.0 CA A:ASP239 4.6 18.7 1.0 HG12 A:ILE241 4.8 16.7 1.0 CB A:ILE241 4.8 11.4 1.0 H A:THR240 4.8 16.1 1.0 HB3 A:HIS201 4.9 13.1 1.0 N A:THR202 4.9 9.0 1.0 OG1 A:THR202 4.9 11.4 1.0 O A:VAL200 4.9 11.9 1.0 N A:HIS201 4.9 10.0 1.0 HG1 A:THR240 4.9 15.2 1.0 HA A:ASP239 5.0 22.4 1.0

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