Sodium 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:

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

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 7 binding sites of Sodium where determined in the Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor, Di-Imido Triphosphate (Pnpnp), PDB code: 7l1a:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 7l1a

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Sodium binding site 1 out of 7 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 Sodium with other atoms in the Na 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:Na407

b:46.2
occ:1.00
 O A:ILE198 3.3 10.9 1.0
HD2 A:LYS234 3.7 25.1 1.0
HE1 A:TYR235 3.8 19.2 1.0
HB2 A:LYS234 3.9 17.0 1.0
HA A:ILE198 3.9 11.3 0.4
HA A:ILE198 4.0 11.5 0.6
HD1 A:TYR235 4.0 17.5 1.0
HG23 A:ILE198 4.3 13.4 0.4
C A:ILE198 4.3 9.2 1.0
O A:LYS234 4.3 12.5 1.0
CE1 A:TYR235 4.4 16.0 1.0
HG23 A:ILE198 4.4 14.7 0.6
CD1 A:TYR235 4.5 14.6 1.0
CA A:ILE198 4.6 9.4 0.4
CA A:ILE198 4.6 9.5 0.6
CD A:LYS234 4.7 20.9 1.0
HG3 A:LYS234 4.7 20.8 1.0
CB A:LYS234 4.8 14.2 1.0
O A:PRO197 4.8 12.5 1.0
HA A:TYR235 4.9 10.3 1.0
CG A:LYS234 5.0 17.3 1.0
C A:LYS234 5.0 10.5 1.0

Sodium binding site 2 out of 7 in 7l1a

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Sodium binding site 2 out of 7 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 Sodium with other atoms in the Na 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:Na408

b:52.3
occ:1.00
 HD2 A:HIS89 2.4 37.9 1.0
CD2 A:HIS89 3.1 31.6 1.0
HE A:ARG169 3.2 16.6 1.0
O A:HIS89 3.4 9.1 1.0
NE A:ARG169 3.6 13.8 1.0
HA A:HIS89 3.7 13.2 1.0
HD3 A:ARG169 3.7 15.4 1.0
HE2 A:HIS89 3.7 40.7 1.0
NE2 A:HIS89 3.8 33.9 1.0
O A:HOH721 3.9 17.3 1.0
HH21 A:ARG169 3.9 16.4 1.0
CZ A:ARG169 4.1 13.6 1.0
CD A:ARG169 4.2 12.9 1.0
NH2 A:ARG169 4.2 13.7 1.0
CG A:HIS89 4.2 27.6 1.0
O A:HOH793 4.3 36.2 1.0
C A:HIS89 4.3 8.5 1.0
CA A:HIS89 4.4 11.0 1.0
HG2 A:ARG169 4.6 12.4 1.0
CB A:HIS89 4.8 18.4 1.0
HH22 A:ARG169 4.8 16.4 1.0
HD2 A:ARG169 4.9 15.4 1.0
CE1 A:HIS89 4.9 35.4 1.0

Sodium binding site 3 out of 7 in 7l1a

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Sodium binding site 3 out of 7 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 Sodium with other atoms in the Na binding site number 3 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:Na409

b:48.4
occ:1.00
 HZ3 A:LYS307 3.1 27.4 0.8
HA A:ASP144 3.1 9.7 1.0
HG A:CYS149 3.2 12.4 0.8
HA A:GLU147 3.2 15.1 1.0
HB2 A:ASP144 3.3 13.4 1.0
O A:THR146 3.4 9.7 1.0
O A:ASP144 3.8 9.8 1.0
CA A:ASP144 3.9 8.1 1.0
HE2 A:LYS307 3.9 25.2 0.8
NZ A:LYS307 3.9 22.9 1.0
SG A:CYS149 3.9 10.3 0.8
O A:HOH652 3.9 36.0 1.0
CB A:ASP144 4.0 11.1 1.0
HZ2 A:LYS307 4.0 27.4 0.8
HD3 A:LYS307 4.0 22.1 1.0
O A:GLU147 4.0 14.2 1.0
CA A:GLU147 4.1 12.6 1.0
C A:THR146 4.2 9.9 1.0
C A:ASP144 4.2 7.9 1.0
HB3 A:ASP144 4.2 13.4 1.0
HG11 A:VAL306 4.3 10.9 1.0
CE A:LYS307 4.3 21.0 0.9
C A:GLU147 4.4 13.3 1.0
N A:GLU147 4.6 11.5 1.0
HZ1 A:LYS307 4.6 27.4 0.8
HA A:CYS149 4.6 9.0 0.2
HA A:CYS149 4.6 7.9 0.8
H A:CYS149 4.6 9.3 1.0
CD A:LYS307 4.7 18.4 1.0
SG A:CYS149 4.7 11.7 0.2
HG12 A:VAL306 4.8 10.9 1.0
HG2 A:GLU147 4.9 16.7 0.8
CG1 A:VAL306 4.9 9.1 1.0

Sodium binding site 4 out of 7 in 7l1a

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Sodium binding site 4 out of 7 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 Sodium with other atoms in the Na binding site number 4 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:Na410

b:49.5
occ:1.00
 H A:GLU211 2.2 16.8 1.0
HB2 A:GLU211 2.8 33.1 1.0
HH21 A:ARG177 2.9 28.4 0.5
N A:GLU211 3.0 14.0 1.0
HA A:ASP210 3.1 10.6 1.0
HB2 A:ASP210 3.1 13.7 1.0
HB3 A:GLU211 3.3 33.1 1.0
NH2 A:ARG177 3.4 23.7 0.5
HH22 A:ARG177 3.4 28.4 0.5
CB A:GLU211 3.4 27.6 1.0
CA A:ASP210 3.7 8.8 1.0
CB A:ASP210 3.8 11.4 1.0
CA A:GLU211 3.8 19.5 1.0
C A:ASP210 3.8 11.0 1.0
HG13 A:VAL251 4.0 11.3 1.0
HH21 A:ARG177 4.1 22.1 0.5
O A:SER96 4.3 16.8 1.0
OE2 A:GLU212 4.3 30.1 0.6
HB3 A:ASP210 4.3 13.7 1.0
HA A:GLU211 4.3 23.4 1.0
O A:HOH617 4.4 22.8 1.0
CZ A:ARG177 4.4 23.2 0.5
HB2 A:SER96 4.4 19.6 1.0
HG12 A:VAL251 4.5 11.3 1.0
HE A:ARG177 4.6 25.2 0.5
OE1 A:GLU212 4.6 30.0 0.6
CG1 A:VAL251 4.7 9.4 1.0
H A:GLU212 4.7 20.2 1.0
NH2 A:ARG177 4.8 18.4 0.5
CG A:GLU211 4.8 36.3 1.0
HG2 A:GLU211 4.8 43.6 1.0
CD A:GLU212 4.9 29.0 0.5
NE A:ARG177 4.9 21.0 0.5
CG A:ASP210 4.9 13.7 1.0
HE A:ARG177 4.9 19.4 0.5

Sodium binding site 5 out of 7 in 7l1a

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Sodium binding site 5 out of 7 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 Sodium with other atoms in the Na binding site number 5 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:Na411

b:10.8
occ:0.68
 NA A:NA411 0.0 10.8 0.7
NA A:NA411 1.4 17.6 0.3
H A:GLY273 2.1 5.8 1.0
O A:HOH589 2.7 12.9 1.0
O A:TRP274 2.7 5.4 1.0
N A:GLY273 2.8 4.8 1.0
HG23 A:ILE267 2.9 7.1 1.0
HA2 A:GLY273 2.9 6.8 1.0
HD11 A:ILE267 3.0 8.5 1.0
HB2 A:TYR271 3.0 7.3 1.0
CA A:GLY273 3.1 5.7 1.0
C A:GLY273 3.2 5.2 1.0
N A:TRP274 3.4 4.5 1.0
H A:TRP274 3.5 5.5 1.0
H A:TYR271 3.5 5.5 1.0
C A:TRP274 3.7 4.5 1.0
O A:GLY273 3.7 6.4 1.0
C A:TYR271 3.8 5.5 1.0
N A:GLY272 3.8 5.4 1.0
CG2 A:ILE267 3.8 5.9 1.0
H A:GLY272 3.8 6.4 1.0
CD1 A:ILE267 3.9 7.1 1.0
CB A:TYR271 3.9 6.1 1.0
C A:GLY272 4.0 5.2 1.0
HG22 A:ILE267 4.0 7.1 1.0
HD13 A:ILE267 4.0 8.5 1.0
HA3 A:GLY273 4.0 6.8 1.0
HG1 A:THR270 4.1 7.0 1.0
CA A:TYR271 4.1 5.2 1.0
O A:TYR271 4.2 6.0 1.0
HD2 A:TYR271 4.2 6.6 1.0
CA A:TRP274 4.2 4.4 1.0
N A:TYR271 4.2 4.6 1.0
HB2 A:HIS277 4.3 7.9 1.0
HG21 A:ILE267 4.3 7.1 1.0
HA A:ILE267 4.3 4.2 1.0
HB3 A:TYR271 4.4 7.3 1.0
HD12 A:ILE267 4.4 8.5 1.0
CA A:GLY272 4.4 5.4 1.0
OG1 A:THR270 4.4 5.9 1.0
O A:ALA276 4.6 7.3 1.0
HA A:ALA276 4.6 7.6 1.0
N A:ALA276 4.7 6.3 1.0
C A:GLY275 4.7 6.7 0.5
CB A:ILE267 4.7 4.3 1.0
HB2 A:TRP274 4.8 5.7 1.0
C A:ALA276 4.8 6.8 1.0
CG1 A:ILE267 4.8 5.3 1.0
H A:ALA276 4.8 7.5 1.0
HA2 A:GLY272 4.8 6.4 1.0
HA A:TRP274 4.8 5.3 1.0
O A:GLY275 4.8 7.1 0.5
N A:GLY275 4.9 5.9 0.5
HD2 A:HIS277 4.9 9.3 1.0
N A:GLY275 4.9 5.9 0.5
CD2 A:TYR271 4.9 5.5 1.0
CG A:TYR271 4.9 5.5 1.0
CA A:ALA276 4.9 6.3 1.0
HA3 A:GLY275 5.0 8.4 0.5
O A:GLY272 5.0 5.9 1.0
HG13 A:ILE267 5.0 6.4 1.0
CA A:ILE267 5.0 3.5 1.0
O A:ILE267 5.0 4.4 1.0

Sodium binding site 6 out of 7 in 7l1a

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Sodium binding site 6 out of 7 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 Sodium with other atoms in the Na binding site number 6 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:Na411

b:17.6
occ:0.32
 NA A:NA411 0.0 17.6 0.3
NA A:NA411 1.4 10.8 0.7
H A:TYR271 2.2 5.5 1.0
O A:HOH589 2.3 12.9 1.0
H A:GLY273 2.3 5.8 1.0
HG23 A:ILE267 2.5 7.1 1.0
HB2 A:TYR271 2.6 7.3 1.0
H A:GLY272 2.8 6.4 1.0
N A:TYR271 2.9 4.6 1.0
HG1 A:THR270 3.0 7.0 1.0
N A:GLY272 3.0 5.4 1.0
HD11 A:ILE267 3.1 8.5 1.0
C A:TYR271 3.1 5.5 1.0
N A:GLY273 3.1 4.8 1.0
OG1 A:THR270 3.2 5.9 1.0
CA A:TYR271 3.2 5.2 1.0
CB A:TYR271 3.3 6.1 1.0
HA A:ILE267 3.4 4.2 1.0
CG2 A:ILE267 3.5 5.9 1.0
O A:TRP274 3.5 5.4 1.0
HD2 A:TYR271 3.6 6.6 1.0
HD13 A:ILE267 3.7 8.5 1.0
CD1 A:ILE267 3.8 7.1 1.0
O A:ILE267 3.8 4.4 1.0
O A:TYR271 3.9 6.0 1.0
HG21 A:ILE267 3.9 7.1 1.0
HA2 A:GLY273 3.9 6.8 1.0
CA A:GLY272 3.9 5.4 1.0
CA A:GLY273 4.0 5.7 1.0
HG22 A:ILE267 4.0 7.1 1.0
C A:GLY272 4.0 5.2 1.0
HB3 A:TYR271 4.0 7.3 1.0
H A:TRP274 4.0 5.5 1.0
CA A:ILE267 4.1 3.5 1.0
HB A:THR270 4.1 6.0 1.0
C A:THR270 4.1 4.8 1.0
HA A:TYR271 4.2 6.2 1.0
HD2 A:HIS277 4.2 9.3 1.0
CB A:THR270 4.2 5.0 1.0
N A:TRP274 4.2 4.5 1.0
CG A:TYR271 4.2 5.5 1.0
CD2 A:TYR271 4.3 5.5 1.0
CB A:ILE267 4.3 4.3 1.0
HA2 A:GLY272 4.3 6.4 1.0
C A:GLY273 4.3 5.2 1.0
C A:ILE267 4.4 3.5 1.0
HB2 A:HIS277 4.4 7.9 1.0
HD12 A:ILE267 4.5 8.5 1.0
CG1 A:ILE267 4.6 5.3 1.0
C A:TRP274 4.6 4.5 1.0
CA A:THR270 4.7 4.6 1.0
H A:THR270 4.7 5.0 1.0
HA3 A:GLY272 4.8 6.4 1.0
HA3 A:GLY273 4.8 6.8 1.0
O A:ALA276 4.9 7.3 1.0

Sodium binding site 7 out of 7 in 7l1a

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Sodium binding site 7 out of 7 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 Sodium with other atoms in the Na binding site number 7 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:Na412

b:37.7
occ:1.00
 OG A:SER384 2.8 14.5 1.0
HG A:SER384 3.0 17.5 1.0
O A:HOH650 3.2 37.5 1.0
H A:SER384 3.4 16.7 1.0
H A:ASP383 3.5 19.6 1.0
HA A:ASP383 3.5 22.7 1.0
N A:SER384 3.6 13.9 1.0
O A:HOH757 3.6 37.5 1.0
O A:HOH713 3.7 17.9 1.0
N A:ASP383 3.9 16.3 1.0
CB A:SER384 3.9 13.3 1.0
CA A:ASP383 3.9 18.9 1.0
C A:ASP383 4.0 17.0 1.0
HB2 A:SER384 4.1 16.0 1.0
CA A:SER384 4.3 12.3 1.0
HA A:SER384 4.5 14.7 1.0
O A:ASP383 4.7 17.0 1.0
HB3 A:SER384 4.7 16.0 1.0
C A:ARG382 4.8 14.7 1.0
HA A:ARG382 5.0 17.0 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: Sat Apr 3 17:56:23 2021

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