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Magnesium in PDB 8p4h: Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A

Enzymatic activity of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A

All present enzymatic activity of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A:
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A, PDB code: 8p4h was solved by M.Thomsen, G.Thieulin-Pardo, L.Neumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.30 / 1.71
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.898, 106.742, 114.996, 90, 93.18, 90
R / Rfree (%) 15.3 / 18.4

Other elements in 8p4h:

The structure of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Fluorine (F) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A (pdb code 8p4h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A, PDB code: 8p4h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8p4h

Go back to Magnesium Binding Sites List in 8p4h
Magnesium binding site 1 out of 2 in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:39.1
occ:1.00
 O A:HOH519 2.0 36.0 1.0
O B:HOH603 2.1 34.0 1.0
O B:ALA259 2.1 29.3 1.0
O B:HOH642 2.1 35.3 1.0
OD1 B:ASP258 2.1 35.8 0.8
O B:HOH792 2.2 46.3 1.0
CG B:ASP258 2.8 28.4 0.8
OD2 B:ASP258 2.9 39.5 0.8
C B:ALA259 3.3 24.9 1.0
N B:ALA259 3.9 26.2 1.0
OE2 A:GLU57 3.9 23.3 0.6
OD1 B:ASP31 4.0 27.9 1.0
CA B:ALA259 4.1 25.7 1.0
C B:ASP258 4.1 27.6 1.0
CB B:ASP258 4.2 26.7 1.0
O A:HOH502 4.2 37.1 1.0
O B:HOH645 4.2 35.9 1.0
O A:HOH776 4.2 42.7 1.0
N B:GLY260 4.3 25.7 1.0
OD2 B:ASP31 4.4 27.3 1.0
CA B:GLY260 4.5 24.9 1.0
O B:ASP258 4.5 28.9 1.0
CB B:ALA259 4.5 30.2 1.0
CG B:ASP31 4.5 27.9 1.0
CA B:ASP258 4.6 24.9 1.0
CD A:GLU57 4.9 28.9 1.0
NH2 B:ARG264 5.0 28.5 1.0

Magnesium binding site 2 out of 2 in 8p4h

Go back to Magnesium Binding Sites List in 8p4h
Magnesium binding site 2 out of 2 in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:40.7
occ:1.00
 O D:HOH510 2.1 32.6 1.0
O C:HOH509 2.1 35.4 1.0
O D:ALA259 2.1 31.9 1.0
OD1 D:ASP258 2.1 35.4 0.8
O D:HOH712 2.3 43.0 1.0
O D:HOH514 2.4 35.9 1.0
CG D:ASP258 2.8 39.8 0.8
OD2 D:ASP258 3.0 49.3 0.8
C D:ALA259 3.3 29.1 1.0
OE2 C:GLU57 3.8 27.9 0.6
N D:ALA259 3.9 27.8 1.0
OD1 D:ASP31 4.1 26.3 1.0
O D:HOH509 4.1 45.0 1.0
CA D:ALA259 4.1 29.4 1.0
CB D:ASP258 4.1 31.3 1.0
C D:ASP258 4.1 30.9 1.0
O C:HOH757 4.3 57.5 1.0
N D:GLY260 4.3 26.2 1.0
O C:HOH503 4.3 37.2 1.0
OD2 D:ASP31 4.4 27.6 1.0
CA D:GLY260 4.5 27.4 1.0
CA D:ASP258 4.5 32.2 1.0
CB D:ALA259 4.6 27.6 1.0
CG D:ASP31 4.6 27.0 1.0
O D:ASP258 4.6 31.0 1.0
O D:HOH680 4.6 53.8 1.0
CD C:GLU57 4.8 30.6 1.0
NH2 D:ARG264 5.0 27.3 1.0
N D:SAM401 5.0 45.1 0.5

Reference:

T.Kalliokoski, H.Kettunen, E.Kumpulainen, E.Kettunen, G.Thieulin-Pardo, L.Neumann, M.Thomsen, R.Paul, A.Malyutina, M.Georgiadou. Discovery of Novel Methionine Adenosyltransferase 2A (MAT2A) Allosteric Inhibitors By Structure-Based Virtual Screening. Bioorg.Med.Chem.Lett. V. 94 29450 2023.
ISSN: ESSN 1464-3405
PubMed: 37591318
DOI: 10.1016/J.BMCL.2023.129450
Page generated: Fri Oct 4 15:47:33 2024

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