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Magnesium in PDB 7l1a: Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor, Di-Imido Triphosphate (Pnpnp)

Enzymatic activity of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor, Di-Imido Triphosphate (Pnpnp)

All present enzymatic activity of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor, Di-Imido Triphosphate (Pnpnp):
2.5.1.6;

Protein crystallography data

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor, Di-Imido Triphosphate (Pnpnp), PDB code: 7l1a was solved by C.N.Niland, E.Fedorov, V.L.Schramm, A.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.92 / 1.25
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 68.113, 94.148, 117.237, 90, 90, 90
R / Rfree (%) 12.3 / 14.1

Other elements in 7l1a:

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

Sodium (Na) 7 atoms
Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor, Di-Imido Triphosphate (Pnpnp) (pdb code 7l1a). 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, Di-Imido Triphosphate (Pnpnp), PDB code: 7l1a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7l1a

Go back to Magnesium Binding Sites List in 7l1a
Magnesium binding site 1 out of 2 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor, Di-Imido Triphosphate (Pnpnp)


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, Di-Imido Triphosphate (Pnpnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:4.8
occ:1.00
 H1B1 A:XE1404 1.7 11.3 1.0
O1A A:XE1404 2.0 8.6 1.0
OD2 A:ASP31 2.1 6.6 1.0
O2G A:XE1404 2.1 8.8 1.0
O A:HOH527 2.1 10.6 1.0
O A:HOH528 2.2 9.9 1.0
O1B A:XE1404 2.2 9.4 1.0
HB1 A:XE1404 2.2 11.2 1.0
HZ3 A:LYS265 2.8 9.7 1.0
CG A:ASP31 3.0 5.8 1.0
PB A:XE1404 3.1 9.3 1.0
OD1 A:ASP31 3.3 5.7 1.0
PA A:XE1404 3.3 6.9 1.0
PG A:XE1404 3.3 7.2 1.0
HE1 A:HIS29 3.3 6.9 1.0
HZ1 A:LYS265 3.4 9.7 1.0
NZ A:LYS265 3.5 8.0 1.0
N3A A:XE1404 3.5 8.4 1.0
HH21 A:ARG264 3.7 15.7 1.0
N3B A:XE1404 3.7 8.5 1.0
K A:K403 3.7 11.3 1.0
HB3 A:ARG264 3.8 5.6 1.0
HZ2 A:LYS265 3.9 9.7 1.0
NH2 A:ARG264 4.1 13.1 1.0
O1G A:XE1404 4.1 7.8 1.0
O2A A:XE1404 4.1 7.4 1.0
OD2 A:ASP258 4.2 13.1 0.6
CE1 A:HIS29 4.2 5.7 1.0
HE A:ARG264 4.3 13.8 1.0
O4A A:XE1404 4.3 7.0 1.0
CB A:ASP31 4.3 5.0 1.0
H3A1 A:XE1404 4.3 10.1 1.0
HB2 A:ARG264 4.4 5.6 1.0
HB2 A:ASP31 4.4 5.9 1.0
O3G A:XE1404 4.4 9.9 1.0
O A:ALA259 4.4 9.2 1.0
HH22 A:ARG264 4.5 15.7 1.0
CB A:ARG264 4.5 4.7 1.0
HE2 A:LYS265 4.5 9.9 1.0
O2B A:XE1404 4.5 9.5 1.0
H3B1 A:XE1404 4.5 10.2 1.0
HE2 A:HIS29 4.6 7.4 1.0
NE A:ARG264 4.6 11.5 1.0
CZ A:ARG264 4.6 11.5 1.0
HA2 A:GLY260 4.6 7.8 1.0
CE A:LYS265 4.7 8.2 1.0
HG3 A:ARG264 4.8 8.2 1.0
NE2 A:HIS29 4.8 6.1 1.0
HB3 A:ASP31 4.8 5.9 1.0
O A:ARG264 4.8 4.5 1.0
H A:ASP31 4.9 4.8 1.0
CG A:ASP258 5.0 12.5 0.7

Magnesium binding site 2 out of 2 in 7l1a

Go back to Magnesium Binding Sites List in 7l1a
Magnesium binding site 2 out of 2 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor, Di-Imido Triphosphate (Pnpnp)


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, Di-Imido Triphosphate (Pnpnp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:5.2
occ:0.55
 O2A A:XE1404 2.0 7.4 1.0
O A:HOH531 2.1 10.6 1.0
O A:HOH656 2.1 12.4 1.0
O A:HOH755 2.1 11.7 1.0
O1G A:XE1404 2.1 7.8 1.0
O A:HOH588 2.3 9.8 1.0
HZ2 A:LYS265 3.2 9.7 1.0
HZ1 A:LYS181 3.3 9.6 1.0
PG A:XE1404 3.3 7.2 1.0
PA A:XE1404 3.3 6.9 1.0
N3B A:XE1404 3.5 8.5 1.0
HZ3 A:LYS265 3.6 9.7 1.0
H3B1 A:XE1404 3.6 10.2 1.0
NZ A:LYS265 3.8 8.0 1.0
HE3 A:LYS265 3.8 9.9 1.0
N3A A:XE1404 3.8 8.4 1.0
HZ3 A:LYS181 4.0 9.6 1.0
OE2 A:GLU23 4.0 8.9 1.0
NZ A:LYS181 4.1 8.0 1.0
O1A A:XE1404 4.1 8.6 1.0
O2G A:XE1404 4.2 8.8 1.0
H3A1 A:XE1404 4.3 10.1 1.0
O4A A:XE1404 4.3 7.0 1.0
O A:HOH609 4.3 7.4 1.0
HB1 A:XE1404 4.3 11.2 1.0
CE A:LYS265 4.3 8.2 1.0
O3G A:XE1404 4.4 9.9 1.0
PB A:XE1404 4.4 9.3 1.0
HZ1 A:LYS265 4.5 9.7 1.0
HZ2 A:LYS181 4.6 9.6 1.0
OE1 A:GLU23 4.6 9.8 1.0
CD A:GLU23 4.7 8.9 1.0
HE3 A:LYS181 4.8 9.3 1.0

Reference:

C.N.Niland, A.Ghosh, S.M.Cahill, V.L.Schramm. Mechanism and Inhibition of Human Methionine Adenosyltransferase 2A. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33656855
DOI: 10.1021/ACS.BIOCHEM.0C00998
Page generated: Wed Oct 2 23:03:10 2024

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