Sodium in PDB 7rxx: Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site

Enzymatic activity of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site

All present enzymatic activity of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site:
2.5.1.6;

Protein crystallography data

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site, PDB code: 7rxx 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) 19.88 / 1.25
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 68.224, 94.121, 117.159, 90, 90, 90
R / Rfree (%) 12.9 / 14.1

Other elements in 7rxx:

The structure of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site (pdb code 7rxx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site, PDB code: 7rxx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7rxx

Go back to Sodium Binding Sites List in 7rxx
Sodium binding site 1 out of 4 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site


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 and Two Sulfate in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:38.4
occ:1.00
H22 A:EDO404 2.2 29.3 0.6
OD2 A:ASP49 2.7 12.5 1.0
O A:HOH838 3.1 27.8 1.0
HA A:SER73 3.1 10.3 1.0
HG3 A:ARG74 3.1 17.4 1.0
C2 A:EDO404 3.2 24.4 0.6
HO2 A:EDO404 3.4 32.4 0.6
H A:ARG74 3.4 10.6 1.0
O2 A:EDO404 3.6 26.9 0.6
CG A:ASP49 3.7 10.9 1.0
HA A:ALA52 3.7 9.1 1.0
HE A:ARG74 3.7 23.4 0.5
H21 A:EDO404 3.8 29.3 0.6
H11 A:EDO404 3.8 14.8 0.6
NE A:ARG74 3.9 19.5 0.4
OD1 A:ASP49 3.9 10.1 1.0
N A:ARG74 4.0 8.9 1.0
CA A:SER73 4.0 8.6 1.0
CG A:ARG74 4.0 14.5 1.0
O A:ASP51 4.1 8.6 1.0
HG22 A:THR72 4.1 12.2 1.0
O A:THR72 4.1 7.8 1.0
C1 A:EDO404 4.1 12.4 0.6
CZ A:ARG74 4.1 20.1 0.6
HH21 A:ARG74 4.2 25.4 0.5
HB2 A:ASP51 4.3 13.8 1.0
NH2 A:ARG74 4.3 21.2 0.7
C A:SER73 4.3 9.6 1.0
CD A:ARG74 4.3 20.7 1.0
HD3 A:ARG74 4.4 24.8 1.0
C A:ASP51 4.4 8.2 1.0
N A:SER73 4.5 7.2 1.0
HZ3 A:LYS53 4.5 13.1 0.5
CA A:ALA52 4.6 7.6 1.0
C A:THR72 4.6 7.1 1.0
HB2 A:ARG74 4.6 14.5 1.0
N A:ALA52 4.6 7.5 1.0
HB3 A:ASP51 4.7 13.8 1.0
HG2 A:ARG74 4.7 17.4 1.0
H A:LYS53 4.8 7.3 0.5
H A:LYS53 4.8 7.3 0.5
CB A:ARG74 4.8 12.1 1.0
HH22 A:ARG74 4.8 25.4 0.5
HG2 A:LYS53 4.8 9.3 0.5
NH1 A:ARG74 4.8 22.5 0.3
CB A:ASP51 4.9 11.5 1.0
O1 A:EDO404 4.9 24.5 0.6
H12 A:EDO404 4.9 14.8 0.6
CA A:ARG74 5.0 9.4 1.0
H A:SER73 5.0 8.6 1.0

Sodium binding site 2 out of 4 in 7rxx

Go back to Sodium Binding Sites List in 7rxx
Sodium binding site 2 out of 4 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site


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 and Two Sulfate in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:29.4
occ:1.00
O A:HOH545 2.3 11.2 0.4
O A:GLY273 2.8 7.3 1.0
HA A:TRP274 2.9 6.8 1.0
O A:HOH666 3.0 8.9 0.4
O A:GLY275 3.3 8.6 0.5
H A:GLY275 3.4 7.7 0.5
HZ A:PHE20 3.4 9.7 1.0
H A:GLY275 3.6 7.7 0.5
N A:GLY275 3.6 6.4 0.5
CA A:TRP274 3.6 5.6 1.0
O A:GLY275 3.7 7.9 0.5
N A:GLY275 3.7 6.4 0.5
H112 A:P3G403 3.7 25.8 0.3
C A:TRP274 3.8 5.3 1.0
C A:GLY273 3.8 5.9 1.0
O A:HOH666 3.8 9.0 0.6
HE2 A:PHE20 3.9 11.4 1.0
O A:HOH513 4.0 20.3 1.0
CZ A:PHE20 4.2 8.1 1.0
H111 A:P3G403 4.2 25.8 0.3
N A:TRP274 4.2 6.0 1.0
C A:GLY275 4.2 8.6 0.5
C11 A:P3G403 4.4 21.5 0.3
C A:GLY275 4.4 7.9 0.5
CE2 A:PHE20 4.4 9.5 1.0
CA A:GLY275 4.4 8.3 0.5
O A:TRP274 4.6 6.5 1.0
HA2 A:GLY275 4.6 9.9 0.5
H121 A:P3G403 4.6 23.5 0.3
CA A:GLY275 4.6 8.0 0.5
HE3 A:TRP274 4.7 8.3 1.0
CB A:TRP274 4.9 5.7 1.0
HB3 A:TRP274 4.9 6.9 1.0
HA2 A:GLY275 5.0 9.6 0.5

Sodium binding site 3 out of 4 in 7rxx

Go back to Sodium Binding Sites List in 7rxx
Sodium binding site 3 out of 4 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na412

b:17.1
occ:1.00
O A:HOH712 2.7 15.4 1.0
O A:HOH572 2.8 13.9 1.0
O A:PRO386 2.8 7.7 1.0
HB A:VAL389 2.8 10.1 1.0
HE1 A:TRP300 3.3 8.3 1.0
HA A:PRO386 3.5 8.7 1.0
HB3 A:PRO386 3.5 10.9 1.0
O A:VAL389 3.5 8.8 1.0
HZ2 A:TRP300 3.7 11.1 1.0
C A:PRO386 3.7 7.0 1.0
NE1 A:TRP300 3.7 6.9 1.0
CB A:VAL389 3.8 8.4 1.0
CA A:PRO386 3.9 7.2 1.0
HD23 A:LEU364 4.0 10.3 1.0
HG12 A:VAL389 4.0 12.0 1.0
CZ2 A:TRP300 4.0 9.3 1.0
CE2 A:TRP300 4.0 7.0 1.0
CB A:PRO386 4.2 9.1 1.0
H A:VAL389 4.2 8.2 1.0
O A:HOH855 4.3 27.7 1.0
CG1 A:VAL389 4.3 9.9 1.0
HG11 A:VAL389 4.3 12.0 1.0
C A:VAL389 4.4 8.9 1.0
O A:ASP363 4.5 10.0 1.0
HD22 A:LEU364 4.5 10.3 1.0
HB2 A:PRO386 4.5 10.9 1.0
HG21 A:VAL389 4.6 11.0 1.0
CD2 A:LEU364 4.6 8.5 1.0
CA A:VAL389 4.6 8.1 1.0
CD1 A:TRP300 4.6 6.5 1.0
CG2 A:VAL389 4.6 9.2 1.0
HD21 A:LEU364 4.7 10.3 1.0
HG23 A:VAL389 4.7 11.0 1.0
O A:HOH808 4.7 28.3 1.0
N A:VAL389 4.8 6.8 1.0
O A:HOH718 4.8 30.6 1.0
N A:TRP387 4.9 6.0 1.0
O A:HOH793 4.9 31.8 1.0
HA A:TRP387 4.9 7.8 1.0
HD1 A:TRP300 4.9 7.8 1.0

Sodium binding site 4 out of 4 in 7rxx

Go back to Sodium Binding Sites List in 7rxx
Sodium binding site 4 out of 4 in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Two Sulfate in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na413

b:17.9
occ:1.00
O A:HOH595 2.3 9.2 0.3
O A:HOH595 2.8 7.1 0.7
O A:ASP291 2.8 7.2 0.9
HB2 A:ALA295 2.9 8.2 1.0
HE1 A:PHE282 3.0 8.2 1.0
O A:HOH760 3.0 7.3 1.0
HG3 A:MET138 3.1 7.7 1.0
HE1 A:HIS277 3.3 8.6 1.0
O A:GLY280 3.4 7.7 0.7
HA A:ASP291 3.5 8.0 0.9
H A:GLY280 3.5 8.4 0.7
H A:GLY280 3.5 8.5 0.3
HG2 A:MET138 3.6 7.7 1.0
HA A:MET138 3.6 6.4 1.0
CB A:ALA295 3.7 6.8 1.0
HA3 A:GLY280 3.7 8.7 0.3
CG A:MET138 3.7 6.4 1.0
O A:GLY280 3.7 7.7 0.3
CE1 A:PHE282 3.8 6.8 1.0
HB3 A:MET138 3.8 7.2 1.0
C A:ASP291 3.8 5.8 0.9
CE1 A:HIS277 3.8 7.1 1.0
HA3 A:GLY280 3.9 8.5 0.7
HB3 A:ALA295 3.9 8.2 1.0
HB1 A:ALA295 4.0 8.2 1.0
HB3 A:ASP291 4.0 10.0 0.9
CA A:ASP291 4.0 6.7 1.0
CB A:MET138 4.1 6.0 1.0
N A:GLY280 4.1 7.1 0.3
N A:GLY280 4.1 7.0 0.7
C A:GLY280 4.2 7.2 0.7
CA A:GLY280 4.2 7.2 0.3
H A:GLY278 4.3 6.8 1.0
CA A:GLY280 4.3 7.1 0.7
C A:GLY280 4.3 6.8 0.3
CA A:MET138 4.3 5.4 1.0
HD1 A:PHE282 4.4 7.6 1.0
O A:LEU137 4.4 5.4 1.0
CB A:ASP291 4.5 8.3 0.9
NE2 A:HIS277 4.5 7.5 1.0
ND1 A:HIS277 4.5 7.7 1.0
OD1 A:ASP291 4.5 7.4 0.7
H A:PHE139 4.5 6.4 1.0
HZ A:PHE282 4.5 7.7 1.0
CD1 A:PHE282 4.5 6.3 1.0
HE2 A:HIS277 4.6 9.0 1.0
CZ A:PHE282 4.6 6.4 1.0
O A:HOH590 4.6 9.0 1.0
HA3 A:GLY278 4.7 7.7 1.0
H A:GLY279 4.7 7.5 1.0
H A:ALA295 4.8 6.0 1.0
CG A:ASP291 4.8 5.5 0.6
CA A:ALA295 4.9 5.4 1.0
HA A:ALA295 5.0 6.5 1.0
N A:GLY278 5.0 5.7 1.0
HA A:ARG292 5.0 7.1 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 10:32:24 2021

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