Sodium in PDB 8tc8: Human Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate

All present enzymatic activity of Human Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate:
6.1.1.22;

The structure of Human Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate, PDB code: 8tc8 was solved by C.Dogovski, R.D.Metcalfe, S.C.Xie, C.J.Morton, L.Tilley, M.D.W.Griffin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.29 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.851, 126.285, 160.598, 90, 90, 90
R / Rfree (%)	18.1 / 21.7

The binding sites of Sodium atom in the Human Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate (pdb code 8tc8). 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 Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate, PDB code: 8tc8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Human Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na608 b:31.3 occ:1.00 OAY A:NSS601 2.2 25.1 1.0 O A:HOH893 2.3 26.7 1.0 O A:HOH889 2.4 31.6 1.0 OE2 A:GLU471 2.4 30.7 1.0 O A:HOH985 2.5 30.7 1.0 O1 A:GOL604 2.8 42.2 1.0 C1 A:GOL604 2.9 32.0 1.0 CD A:GLU471 3.2 36.7 1.0 OE1 A:GLU471 3.5 40.2 1.0 SBE A:NSS601 3.6 24.1 1.0 O A:HOH1084 3.9 46.3 1.0 O A:HOH972 4.0 42.4 1.0 OAX A:NSS601 4.0 25.1 1.0 H3' A:NSS601 4.0 26.9 1.0 O A:HOH1050 4.0 35.9 1.0 O A:HOH860 4.2 23.2 1.0 OD1 A:ASP463 4.3 31.0 1.0 O A:HOH806 4.3 22.6 1.0 HAT A:NSS601 4.4 26.9 1.0 OD2 A:ASP463 4.4 31.4 1.0 C2 A:GOL604 4.5 48.6 1.0 H5'1 A:NSS601 4.5 31.0 1.0 CG A:GLU471 4.5 28.9 1.0 NAT A:NSS601 4.5 22.4 1.0 CG A:ASP463 4.6 32.4 1.0 O A:HOH1037 4.6 45.0 1.0 CA A:GLY474 4.6 21.2 1.0 O A:HOH792 4.6 34.2 1.0 O5' A:NSS601 4.7 28.1 1.0 NZ A:LYS445 4.7 30.9 1.0 O3' A:NSS601 4.7 23.5 1.0 C3' A:NSS601 4.8 22.4 1.0 O A:HOH817 4.8 33.7 1.0

Sodium binding site 2 out of 4 in the Human Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na608 b:30.4 occ:1.00 O B:HOH942 2.1 34.1 1.0 OAY B:NSS601 2.3 23.3 1.0 O3 B:GOL605 2.4 40.6 1.0 O B:HOH855 2.4 33.6 1.0 OE2 B:GLU471 2.4 29.3 1.0 O B:HOH1029 2.4 29.3 1.0 CD B:GLU471 3.2 38.4 1.0 C3 B:GOL605 3.3 45.4 1.0 OE1 B:GLU471 3.5 45.7 1.0 SBE B:NSS601 3.7 23.6 1.0 O B:HOH1067 4.0 44.4 1.0 H2 B:NSS601 4.0 24.8 1.0 O B:HOH1074 4.0 35.4 1.0 OAX B:NSS601 4.0 26.2 1.0 O B:HOH1024 4.1 44.6 1.0 H3' B:NSS601 4.1 24.9 1.0 OD1 B:ASP463 4.2 32.1 1.0 OD2 B:ASP463 4.3 34.2 1.0 O B:HOH863 4.4 20.1 1.0 O B:HOH799 4.4 26.4 1.0 O B:HOH721 4.4 40.8 1.0 CG B:GLU471 4.5 32.5 1.0 C2 B:GOL605 4.5 58.2 1.0 CG B:ASP463 4.5 30.8 1.0 HAT B:NSS601 4.5 25.4 1.0 NZ B:LYS445 4.7 30.6 1.0 CA B:GLY474 4.7 23.0 1.0 NAT B:NSS601 4.7 21.2 1.0 H5'1 B:NSS601 4.7 28.0 1.0 O3' B:NSS601 4.7 20.6 1.0 O B:HOH801 4.8 32.6 1.0 O5' B:NSS601 4.8 29.9 1.0 O B:HOH1079 4.8 47.1 1.0 C3' B:NSS601 4.9 20.8 1.0 O2 B:GOL605 4.9 40.0 1.0

Sodium binding site 3 out of 4 in the Human Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na604 b:38.3 occ:1.00 O C:HOH789 2.2 34.5 1.0 OAY C:NSS601 2.3 28.7 1.0 OE2 C:GLU471 2.4 35.6 1.0 O C:HOH951 2.4 37.3 1.0 O C:HOH811 2.5 38.5 1.0 O3 C:GOL603 2.9 44.0 1.0 CD C:GLU471 3.2 38.4 1.0 OE1 C:GLU471 3.5 46.0 1.0 SBE C:NSS601 3.7 27.9 1.0 C3 C:GOL603 3.8 42.6 1.0 O C:HOH894 4.0 44.5 1.0 H3' C:NSS601 4.0 34.7 1.0 O C:HOH993 4.1 38.7 1.0 OAX C:NSS601 4.1 25.6 1.0 OD1 C:ASP463 4.1 40.7 1.0 O C:HOH836 4.2 27.3 1.0 O C:HOH758 4.2 29.9 1.0 OD2 C:ASP463 4.3 40.9 1.0 HAT C:NSS601 4.4 32.2 1.0 CG C:ASP463 4.5 39.7 1.0 CG C:GLU471 4.5 35.2 1.0 H5'1 C:NSS601 4.5 38.0 1.0 NAT C:NSS601 4.5 26.9 1.0 CA C:GLY474 4.6 29.7 1.0 H2 C:NSS601 4.6 32.5 1.0 O C:HOH743 4.6 34.8 1.0 O3' C:NSS601 4.7 27.0 1.0 O C:HOH969 4.7 46.3 1.0 O C:HOH803 4.7 45.6 1.0 O5' C:NSS601 4.8 31.8 1.0 NZ C:LYS445 4.8 39.6 1.0 C3' C:NSS601 4.8 28.9 1.0

Sodium binding site 4 out of 4 in the Human Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Asparaginyl-Trna Synthetase Bound to Adenosine 5'-Sulfamate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na604 b:30.9 occ:1.00 O D:HOH778 2.2 32.2 1.0 O D:HOH744 2.4 34.8 1.0 OAY D:NSS601 2.4 25.6 1.0 OE2 D:GLU471 2.4 33.4 1.0 O D:HOH917 2.4 32.4 1.0 O1 D:GOL603 2.8 35.9 1.0 CD D:GLU471 3.1 39.9 1.0 OE1 D:GLU471 3.3 46.4 1.0 C1 D:GOL603 3.6 46.7 1.0 SBE D:NSS601 3.8 27.4 1.0 O D:HOH787 3.8 47.2 1.0 O D:HOH929 3.9 43.8 1.0 OD1 D:ASP463 4.0 34.4 1.0 O D:HOH1039 4.0 33.4 1.0 H3' D:NSS601 4.1 29.3 1.0 OAX D:NSS601 4.2 25.3 1.0 OD2 D:ASP463 4.2 39.7 1.0 O D:HOH818 4.3 23.0 1.0 CG D:ASP463 4.4 39.4 1.0 O D:HOH723 4.4 29.7 1.0 CG D:GLU471 4.4 36.5 1.0 H2 D:NSS601 4.4 31.4 1.0 HAT D:NSS601 4.5 30.6 1.0 O D:HOH750 4.5 41.1 1.0 NZ D:LYS445 4.6 36.6 1.0 CA D:GLY474 4.7 25.6 1.0 H5'1 D:NSS601 4.7 32.2 1.0 NAT D:NSS601 4.7 25.5 1.0 O3' D:NSS601 4.8 26.2 1.0 C2 D:GOL603 4.8 46.1 1.0 O D:HOH870 4.8 37.7 1.0 C3' D:NSS601 4.8 24.4 1.0 O5' D:NSS601 4.9 29.0 1.0 O D:HOH1018 4.9 47.3 1.0

S.C.Xie, L.Tilley. Human Asparaginyl-Trna Synthetase, Apo Form Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-45224-Z