Magnesium in PDB 7rxw: Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp)

Enzymatic activity of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp)

All present enzymatic activity of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp):
2.5.1.6;

Protein crystallography data

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp), PDB code: 7rxw 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) 19.89 / 1.07
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 68.322, 94.069, 117.344, 90, 90, 90
R / Rfree (%) 12.8 / 13.8

Other elements in 7rxw:

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp) also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp) (pdb code 7rxw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp), PDB code: 7rxw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7rxw

Go back to Magnesium Binding Sites List in 7rxw
Magnesium binding site 1 out of 2 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:11.6
occ:0.53
O A:HOH557 1.9 17.6 1.0
O3 A:2PN403 2.0 10.5 0.5
O6 A:2PN403 2.0 18.1 0.6
OD2 A:ASP31 2.1 9.7 1.0
O A:HOH526 2.1 16.9 1.0
O A:HOH520 2.1 19.4 1.0
HZ3 A:LYS265 2.9 14.7 1.0
CG A:ASP31 3.0 8.0 1.0
P2 A:2PN403 3.1 13.7 0.4
OD1 A:ASP31 3.2 8.6 1.0
P1 A:2PN403 3.3 13.3 0.7
HE1 A:HIS29 3.4 10.8 1.0
N1 A:2PN403 3.4 17.0 0.6
HZ2 A:LYS265 3.6 14.7 1.0
HH21 A:ARG264 3.6 16.2 1.0
NZ A:LYS265 3.6 12.2 1.0
O4 A:2PN403 3.6 18.3 0.4
HB3 A:ARG264 3.7 8.2 1.0
K A:K407 4.0 16.2 0.4
HZ1 A:LYS265 4.0 14.7 1.0
NH2 A:ARG264 4.0 13.5 1.0
O1 A:2PN403 4.0 14.7 0.5
O A:HOH552 4.1 28.7 1.0
HN1 A:2PN403 4.1 20.4 0.6
OD2 A:ASP258 4.1 10.2 0.6
CE1 A:HIS29 4.2 9.0 1.0
HH22 A:ARG264 4.3 16.2 1.0
O2 A:2PN403 4.3 15.3 0.9
O A:HOH506 4.3 22.9 1.0
CB A:ASP31 4.3 7.9 1.0
HB2 A:ARG264 4.4 8.2 1.0
HB2 A:ASP31 4.4 9.5 1.0
O5 A:2PN403 4.4 17.8 0.5
O A:ALA259 4.4 11.2 1.0
CB A:ARG264 4.5 6.9 1.0
HE A:ARG264 4.5 13.2 1.0
HE2 A:HIS29 4.6 10.4 1.0
CZ A:ARG264 4.6 10.4 1.0
HA2 A:GLY260 4.6 10.0 1.0
HE2 A:LYS265 4.7 14.1 1.0
NE A:ARG264 4.7 11.0 1.0
HG3 A:ARG264 4.7 10.0 1.0
O A:ARG264 4.8 7.6 1.0
HB3 A:ASP31 4.8 9.5 1.0
CE A:LYS265 4.8 11.8 1.0
O A:HOH656 4.8 14.2 1.0
MG A:MG406 4.8 13.3 0.4
NE2 A:HIS29 4.8 8.7 1.0
H A:ASP31 4.9 8.5 1.0
HD12 A:LEU261 5.0 14.5 0.4

Magnesium binding site 2 out of 2 in 7rxw

Go back to Magnesium Binding Sites List in 7rxw
Magnesium binding site 2 out of 2 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor Imido-Diphosphate (Pnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:13.3
occ:0.40
O A:HOH552 2.0 28.7 1.0
O4 A:2PN403 2.0 18.3 0.4
O1 A:2PN403 2.2 14.7 0.5
O A:HOH506 3.0 22.9 1.0
P2 A:2PN403 3.2 13.7 0.4
P1 A:2PN403 3.3 13.3 0.7
N1 A:2PN403 3.4 17.0 0.6
O A:HOH557 3.8 17.6 1.0
HZ1 A:LYS265 3.8 14.7 1.0
O A:HOH546 3.8 22.9 1.0
O A:HOH570 3.9 11.3 1.0
HN1 A:2PN403 4.0 20.4 0.6
O3 A:2PN403 4.0 10.5 0.5
O5 A:2PN403 4.2 17.8 0.5
HZ3 A:LYS265 4.2 14.7 1.0
O6 A:2PN403 4.3 18.1 0.6
HZ1 A:LYS181 4.4 12.0 1.0
O2 A:2PN403 4.4 15.3 0.9
NZ A:LYS265 4.5 12.2 1.0
O A:HOH732 4.5 18.4 1.0
O A:HOH656 4.7 14.2 1.0
HZ2 A:LYS181 4.7 12.0 1.0
MG A:MG405 4.8 11.6 0.5
HH21 A:ARG264 4.8 16.2 1.0
NZ A:LYS181 5.0 10.0 1.0
HZ2 A:LYS265 5.0 14.7 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: Thu Nov 25 10:09:46 2021

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