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Magnesium in PDB 7rwh: Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Inhibitor Agi-41998

Enzymatic activity of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Inhibitor Agi-41998

All present enzymatic activity of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Inhibitor Agi-41998:
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Inhibitor Agi-41998, PDB code: 7rwh was solved by L.Jin, A.K.Padyana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.95 / 1.17
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 68.56, 94.11, 116.69, 90, 90, 90
R / Rfree (%) 11.4 / 13.4

Other elements in 7rwh:

The structure of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Inhibitor Agi-41998 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Fluorine (F) 3 atoms
Bromine (Br) 1 atom

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 Inhibitor Agi-41998 (pdb code 7rwh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Inhibitor Agi-41998, PDB code: 7rwh:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7rwh

Go back to Magnesium Binding Sites List in 7rwh
Magnesium binding site 1 out of 3 in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Inhibitor Agi-41998


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 Inhibitor Agi-41998 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:21.2
occ:1.00
 HB1 A:SAM401 2.8 19.4 1.0
N A:SAM401 3.3 15.4 1.0
CB A:SAM401 3.5 16.2 1.0
HG1 A:SAM401 3.5 21.5 1.0
CA A:SAM401 3.8 14.0 1.0
HG2 A:SAM401 3.9 21.5 1.0
CG A:SAM401 3.9 18.0 1.0
HN1 A:SAM401 4.0 18.4 1.0
HB2 A:SAM401 4.4 19.4 1.0
O A:HOH572 4.4 28.8 1.0
HA A:SAM401 4.5 16.7 1.0
OD1 A:ASP258 4.6 15.5 1.0
C A:SAM401 4.6 11.7 1.0

Magnesium binding site 2 out of 3 in 7rwh

Go back to Magnesium Binding Sites List in 7rwh
Magnesium binding site 2 out of 3 in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Inhibitor Agi-41998


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 Inhibitor Agi-41998 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg411

b:14.1
occ:1.00
 H A:GLY275 2.2 8.7 1.0
HH11 A:ARG313 2.2 10.0 1.0
HH A:TYR141 2.8 10.6 0.0
HE3 A:TRP274 2.8 9.3 1.0
O A:HOH608 2.9 10.5 1.0
NH1 A:ARG313 3.0 8.4 1.0
N A:GLY275 3.0 7.3 1.0
OH A:TYR335 3.2 8.8 1.0
HE1 A:TYR141 3.2 9.2 1.0
HA2 A:GLY275 3.2 9.5 1.0
H261 A:7UI402 3.3 11.2 1.0
HE A:ARG313 3.3 10.8 1.0
HH12 A:ARG313 3.4 10.0 1.0
HE2 A:TYR335 3.5 11.1 1.0
HB3 A:TRP274 3.5 8.6 1.0
HH A:TYR335 3.5 10.5 0.0
C26 A:7UI402 3.5 9.4 1.0
CE1 A:TYR141 3.5 7.7 1.0
OH A:TYR141 3.6 8.8 1.0
CA A:GLY275 3.7 7.9 1.0
CZ A:TYR141 3.7 7.6 1.0
CZ A:TYR335 3.7 7.9 1.0
HA A:TRP274 3.8 8.1 1.0
CE3 A:TRP274 3.8 7.8 1.0
C25 A:7UI402 3.8 10.2 1.0
CE2 A:TYR335 3.8 9.3 1.0
CZ A:ARG313 3.8 8.4 1.0
NE A:ARG313 3.9 9.1 1.0
BR28 A:7UI402 3.9 12.1 1.0
C A:TRP274 4.1 7.2 1.0
CA A:TRP274 4.2 6.8 1.0
CB A:TRP274 4.3 7.2 1.0
C27 A:7UI402 4.3 9.2 1.0
O A:GLY275 4.4 7.9 1.0
CD1 A:TYR141 4.4 7.6 1.0
HA3 A:GLY275 4.4 9.5 1.0
HZ3 A:TRP274 4.4 10.9 1.0
C A:GLY275 4.5 7.2 1.0
CZ3 A:TRP274 4.6 9.1 1.0
H271 A:7UI402 4.6 10.9 1.0
CE2 A:TYR141 4.7 7.9 1.0
HD1 A:TYR141 4.7 9.1 1.0
CD2 A:TRP274 4.7 6.8 1.0
C24 A:7UI402 4.7 10.6 1.0
CE1 A:TYR335 4.8 8.7 1.0
CG A:TRP274 4.9 7.4 1.0
CD2 A:TYR335 4.9 9.2 1.0
O A:HOH864 5.0 20.2 1.0

Magnesium binding site 3 out of 3 in 7rwh

Go back to Magnesium Binding Sites List in 7rwh
Magnesium binding site 3 out of 3 in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Inhibitor Agi-41998


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Inhibitor Agi-41998 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg412

b:14.8
occ:0.46
 O A:HOH864 3.0 20.2 1.0
O A:HOH608 3.0 10.5 1.0
H241 A:7UI402 3.3 12.7 1.0
HE2 A:TYR335 3.5 11.1 1.0
C24 A:7UI402 3.7 10.6 1.0
O A:HOH650 4.0 17.8 0.5
H231 A:7UI402 4.2 12.0 1.0
C23 A:7UI402 4.2 10.1 1.0
HE2 A:PHE333 4.3 15.4 1.0
CE2 A:TYR335 4.3 9.3 1.0
C25 A:7UI402 4.5 10.2 1.0
BR28 A:7UI402 4.8 12.1 1.0
OH A:TYR335 4.9 8.8 1.0

Reference:

M.Li, Z.Konteatis, N.Nagaraja, Y.Chen, S.Zhou, G.Ma, S.Gross, K.Marjon, M.L.Hyer, E.Mandley, M.Lein, A.K.Padyana, L.Jin, S.Tong, R.Peters, J.Murtie, J.Travins, M.Medeiros, P.Liu, V.Frank, E.T.Judd, S.A.Biller, K.M.Marks, Z.Sui, S.K.Reznik. Leveraging Structure-Based Drug Design to Identify Next-Generation MAT2A Inhibitors, Including Brain-Penetrant and Peripherally Efficacious Leads. J.Med.Chem. V. 65 4600 2022.
ISSN: ISSN 0022-2623
PubMed: 35293760
DOI: 10.1021/ACS.JMEDCHEM.1C01595
Page generated: Thu Oct 3 08:08:05 2024

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