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Sodium in PDB 1dty: Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor.

Enzymatic activity of Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor.

All present enzymatic activity of Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor.:
2.6.1.62;

Protein crystallography data

The structure of Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor., PDB code: 1dty was solved by D.Alexeev, L.Sawyer, R.L.Baxter, M.V.Alexeeva, D.Campopiano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.14
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.280, 56.270, 121.930, 90.00, 96.96, 90.00
R / Rfree (%) 19.6 / 32.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor. (pdb code 1dty). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor., PDB code: 1dty:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1dty

Go back to Sodium Binding Sites List in 1dty
Sodium binding site 1 out of 4 in the Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na471

b:31.7
occ:1.00
 O A:VAL96 2.2 11.6 1.0
OG1 A:THR99 2.2 11.9 1.0
O A:LEU103 2.3 12.6 1.0
O A:PRO100 3.0 22.6 1.0
O A:THR99 3.0 25.1 1.0
C A:VAL96 3.1 14.9 1.0
CA A:VAL96 3.4 12.5 1.0
C A:LEU103 3.4 14.4 1.0
C A:THR99 3.4 18.5 1.0
CB A:THR99 3.4 9.1 1.0
CG1 A:VAL96 3.7 23.1 1.0
CB A:LEU103 3.8 11.5 1.0
CA A:THR99 3.8 13.6 1.0
C A:PRO100 3.8 30.3 1.0
N A:THR99 3.9 20.5 1.0
O A:LEU95 4.0 19.2 1.0
CA A:LEU103 4.0 17.1 1.0
CB A:VAL96 4.2 16.3 1.0
N A:PRO100 4.2 18.7 1.0
N A:LEU103 4.3 22.7 1.0
O A:GLN101 4.3 41.8 1.0
N A:ALA97 4.3 14.5 1.0
N A:VAL96 4.5 8.5 1.0
N A:GLU104 4.5 12.6 1.0
N A:GLN101 4.5 27.4 1.0
CG2 A:THR99 4.6 1.0 1.0
C A:GLN101 4.6 18.8 1.0
CA A:PRO100 4.6 21.1 1.0
CA A:GLN101 4.6 23.4 1.0
C A:LEU95 4.7 13.9 1.0
CA A:GLU104 4.7 19.6 1.0
C A:ALA97 4.8 23.0 1.0
CD2 A:LEU287 4.8 26.3 1.0
CA A:ALA97 4.9 17.0 1.0
N A:MET98 4.9 18.2 1.0
CG2 A:VAL96 5.0 8.9 1.0

Sodium binding site 2 out of 4 in 1dty

Go back to Sodium Binding Sites List in 1dty
Sodium binding site 2 out of 4 in the Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na472

b:35.7
occ:1.00
 O A:SER297 2.4 19.3 1.0
OG1 B:THR21 3.3 20.1 1.0
C A:SER297 3.4 26.6 1.0
OD1 A:ASP298 3.7 38.2 1.0
OG B:SER22 3.8 22.1 1.0
OG B:SER19 3.8 16.5 1.0
CB B:SER19 4.0 23.3 1.0
CB A:SER297 4.2 21.5 1.0
O A:GLY302 4.2 21.1 1.0
N A:ASP298 4.3 32.3 1.0
CA A:ASP298 4.3 32.0 1.0
CA A:SER297 4.3 25.4 1.0
CA A:GLY302 4.3 18.7 1.0
C A:GLY302 4.4 21.6 1.0
CB B:SER22 4.6 8.6 1.0
CB B:THR21 4.7 15.8 1.0
CG A:ASP298 4.7 28.6 1.0
N B:SER22 4.8 12.1 1.0

Sodium binding site 3 out of 4 in 1dty

Go back to Sodium Binding Sites List in 1dty
Sodium binding site 3 out of 4 in the Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na476

b:35.8
occ:1.00
 O B:SER297 2.4 18.8 1.0
OG A:SER19 2.9 12.2 1.0
OG1 A:THR21 3.1 15.3 1.0
C B:SER297 3.4 26.6 1.0
CB A:SER19 3.5 20.6 1.0
OD1 B:ASP298 3.6 36.0 1.0
O B:GLY302 3.6 24.2 1.0
CA B:ASP298 4.1 32.2 1.0
CB B:SER297 4.1 22.2 1.0
OG A:SER22 4.1 25.6 1.0
N B:ASP298 4.2 31.0 1.0
C B:GLY302 4.2 22.0 1.0
CA B:SER297 4.3 25.5 1.0
CA B:GLY302 4.3 16.7 1.0
CB A:THR21 4.5 27.0 1.0
CB A:SER22 4.7 23.7 1.0
CG B:ASP298 4.7 27.8 1.0
N A:SER22 4.7 16.6 1.0
CA A:SER19 4.8 19.1 1.0
CB B:ASP298 5.0 23.6 1.0
CG2 A:THR21 5.0 25.1 1.0

Sodium binding site 4 out of 4 in 1dty

Go back to Sodium Binding Sites List in 1dty
Sodium binding site 4 out of 4 in the Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na475

b:29.5
occ:1.00
 O B:VAL96 2.2 10.6 1.0
O B:THR99 2.6 26.0 1.0
O B:LEU103 2.7 12.8 1.0
O B:PRO100 2.7 24.1 1.0
OG1 B:THR99 2.8 13.4 1.0
C B:VAL96 3.2 15.3 1.0
C B:THR99 3.3 17.4 1.0
C B:PRO100 3.4 31.9 1.0
C B:LEU103 3.7 15.2 1.0
CA B:VAL96 3.8 12.9 1.0
CB B:THR99 3.8 11.7 1.0
O B:GLN101 3.8 42.1 1.0
CA B:THR99 3.8 13.3 1.0
CG1 B:VAL96 3.9 23.2 1.0
N B:THR99 3.9 21.2 1.0
N B:GLN101 4.0 28.8 1.0
CA B:GLN101 4.1 22.3 1.0
N B:PRO100 4.1 19.3 1.0
C B:GLN101 4.1 17.9 1.0
N B:LEU103 4.2 22.6 1.0
CA B:LEU103 4.3 17.9 1.0
CA B:PRO100 4.3 21.5 1.0
CB B:LEU103 4.3 7.3 1.0
N B:ALA97 4.4 13.0 1.0
CB B:VAL96 4.4 16.6 1.0
O B:ALA97 4.5 18.1 1.0
C B:ALA97 4.5 22.4 1.0
O B:LEU95 4.6 17.5 1.0
CA B:ALA97 4.7 17.3 1.0
N B:GLU104 4.8 12.3 1.0

Reference:

D.Alexeev, L.Sawyer, R.L.Baxter, M.V.Alexeeva, D.Campopiano. Crystal Structure of Adenosylmethionine-8-Amino-7-Oxonanoate Aminotransferase with Pyridoxal Phosphate Cofactor To Be Published.
Page generated: Sun Oct 6 18:18:43 2024

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