Magnesium in PDB 3nem: Aspartyl-Trna Synthetase Complexed with Aspartyl Adenylate

All present enzymatic activity of Aspartyl-Trna Synthetase Complexed with Aspartyl Adenylate:
6.1.1.12;

The structure of Aspartyl-Trna Synthetase Complexed with Aspartyl Adenylate, PDB code: 3nem was solved by E.Schmitt, D.Moras, L.Moulinier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.58 / 1.89
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	123.220, 124.870, 86.930, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.3

The binding sites of Magnesium atom in the Aspartyl-Trna Synthetase Complexed with Aspartyl Adenylate (pdb code 3nem). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Aspartyl-Trna Synthetase Complexed with Aspartyl Adenylate, PDB code: 3nem:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Aspartyl-Trna Synthetase Complexed with Aspartyl Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aspartyl-Trna Synthetase Complexed with Aspartyl Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1040 b:27.9 occ:1.00 O2B B:ATP1039 2.3 24.7 1.0 O2G B:ATP1039 2.3 26.2 1.0 O B:HOH2248 2.3 21.7 1.0 O B:HOH2250 2.3 26.7 1.0 O B:HOH2251 2.4 20.6 1.0 O B:HOH2249 2.4 26.8 1.0 PG B:ATP1039 3.4 25.0 1.0 PB B:ATP1039 3.5 27.1 1.0 O3B B:ATP1039 3.7 25.8 1.0 O1G B:ATP1039 3.9 30.9 1.0 NE2 B:HIS223 4.2 16.4 1.0 NH1 B:ARG214 4.2 18.4 1.0 OE2 B:GLU216 4.3 17.5 1.0 OE1 B:GLU216 4.4 22.6 1.0 O1B B:ATP1039 4.4 27.8 1.0 O3A B:ATP1039 4.5 27.4 1.0 CD2 B:HIS223 4.6 18.3 1.0 O3G B:ATP1039 4.7 26.5 1.0 N7 B:ATP1039 4.7 17.2 1.0 CD B:GLU216 4.8 22.7 1.0

Magnesium binding site 2 out of 3 in the Aspartyl-Trna Synthetase Complexed with Aspartyl Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aspartyl-Trna Synthetase Complexed with Aspartyl Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1041 b:30.1 occ:1.00 OE2 B:GLU361 2.3 23.9 1.0 O1G B:ATP1039 2.3 30.9 1.0 O1B B:ATP1039 2.4 27.8 1.0 O B:HOH2253 2.4 25.9 1.0 O B:HOH2252 2.4 34.5 1.0 O B:HOH2340 2.6 33.2 1.0 MG B:MG1042 3.1 30.6 1.0 CD B:GLU361 3.2 20.5 1.0 O3B B:ATP1039 3.4 25.8 1.0 PG B:ATP1039 3.4 25.0 1.0 PB B:ATP1039 3.4 27.1 1.0 OE1 B:GLU361 3.6 15.4 1.0 OD2 B:ASP354 4.1 25.5 1.0 O2B B:ATP1039 4.2 24.7 1.0 O3G B:ATP1039 4.3 26.5 1.0 O B:HOH2249 4.4 26.8 1.0 O B:HOH2311 4.4 33.7 1.0 CG B:GLU361 4.6 15.9 1.0 O2G B:ATP1039 4.6 26.2 1.0 O3A B:ATP1039 4.7 27.4 1.0 O B:HOH2034 4.7 21.4 1.0 CB B:GLU361 4.8 12.7 1.0 O1A B:ATP1039 4.9 22.5 1.0

Magnesium binding site 3 out of 3 in the Aspartyl-Trna Synthetase Complexed with Aspartyl Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Aspartyl-Trna Synthetase Complexed with Aspartyl Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1042 b:30.6 occ:1.00 O1B B:ATP1039 2.2 27.8 1.0 O1A B:ATP1039 2.3 22.5 1.0 OE1 B:GLU361 2.3 15.4 1.0 O B:HOH2253 2.3 25.9 1.0 O B:HOH2311 2.5 33.7 1.0 CB B:SER364 3.0 14.9 1.0 CD B:GLU361 3.1 20.5 1.0 MG B:MG1041 3.1 30.1 1.0 OG B:SER364 3.2 25.0 1.0 OE2 B:GLU361 3.3 23.9 1.0 PB B:ATP1039 3.4 27.1 1.0 PA B:ATP1039 3.5 21.8 1.0 O3A B:ATP1039 3.6 27.4 1.0 OD2 B:ASP354 3.9 25.5 1.0 O3B B:ATP1039 4.1 25.8 1.0 OD1 B:ASP354 4.1 18.5 1.0 O2A B:ATP1039 4.3 18.1 1.0 CG B:ASP354 4.4 16.9 1.0 O3' B:ATP1039 4.4 13.3 1.0 CA B:SER364 4.4 13.6 1.0 CG B:GLU361 4.4 15.9 1.0 O B:HOH2252 4.4 34.5 1.0 O2B B:ATP1039 4.5 24.7 1.0 N B:SER364 4.6 9.5 1.0 O5' B:ATP1039 4.6 15.0 1.0 NZ B:LYS336 4.7 19.6 1.0 C5' B:ATP1039 4.7 15.8 1.0 C3' B:ATP1039 4.8 12.4 1.0 O1G B:ATP1039 4.9 30.9 1.0

E.Schmitt, L.Moulinier, S.Fujiwara, T.Imanaka, J.C.Thierry, D.Moras. Crystal Structure of Aspartyl-Trna Synthetase From Pyrococcus Kodakaraensis Kod: Archaeon Specificity and Catalytic Mechanism of Adenylate Formation Embo J. V. 17 5227 1998.
ISSN: ISSN 0261-4189
PubMed: 9724658
DOI: 10.1093/EMBOJ/17.17.5227