Magnesium in PDB 8dqi: Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth

The structure of Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth, PDB code: 8dqi was solved by I.Gottfried-Lee, P.A.Karplus, R.A.Mehl, R.B.Cooley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.43 / 1.54
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	110.795, 110.795, 113.774, 90, 90, 90
R / Rfree (%)	16.7 / 18.6

The binding sites of Magnesium atom in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth (pdb code 8dqi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth, PDB code: 8dqi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg304 b:27.3 occ:0.71 O2B D:ATP301 2.1 32.9 0.8 O D:HOH533 2.1 38.0 1.0 O D:HOH563 2.1 35.7 1.0 O D:HOH418 2.1 31.2 1.0 O D:HOH567 2.2 38.5 1.0 O2G D:ATP301 2.2 29.5 0.8 HE2 D:HIS158 3.2 47.5 1.0 HH11 D:ARG150 3.2 36.8 1.0 PG D:ATP301 3.3 31.1 0.8 PB D:ATP301 3.4 30.1 0.8 O3B D:ATP301 3.4 29.9 0.8 HH12 D:ARG150 3.8 36.8 1.0 NH1 D:ARG150 3.8 30.7 1.0 O1G D:ATP301 3.9 32.8 0.8 NE2 D:HIS158 3.9 39.6 1.0 HE22 D:GLN107 3.9 48.5 1.0 O D:HOH619 4.1 52.9 1.0 O D:HOH651 4.2 58.0 1.0 OE2 D:GLU152 4.2 34.0 1.0 HD2 D:HIS158 4.3 37.2 1.0 O3A D:ATP301 4.4 28.3 0.8 CD2 D:HIS158 4.4 31.0 1.0 O1B D:ATP301 4.5 31.4 0.8 OE1 D:GLN107 4.5 44.4 1.0 OE1 D:GLU152 4.6 45.5 1.0 O3G D:ATP301 4.6 31.6 0.8 N7 D:ATP301 4.6 26.2 0.8 HD3 D:ARG150 4.7 33.0 1.0 NE2 D:GLN107 4.7 40.4 1.0 HD2 D:ARG150 4.8 33.0 1.0 CD D:GLU152 4.8 32.6 1.0 H8 D:ATP301 5.0 25.4 0.8 CE1 D:HIS158 5.0 49.6 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg305 b:27.2 occ:0.70 O D:HOH528 2.0 32.8 0.8 O1B D:ATP301 2.1 31.4 0.8 OG D:SER221 2.1 36.6 1.0 O2A D:ATP301 2.1 30.1 0.8 O D:HOH439 2.2 28.7 0.8 OE2 D:GLU218 2.2 31.0 1.0 HB2 D:SER221 3.1 33.8 1.0 CD D:GLU218 3.2 37.1 1.0 CB D:SER221 3.2 28.1 1.0 PB D:ATP301 3.3 30.1 0.8 MG D:MG306 3.3 32.1 0.7 O3A D:ATP301 3.3 28.3 0.8 PA D:ATP301 3.3 28.2 0.8 OE1 D:GLU218 3.5 35.8 1.0 HB3 D:SER221 3.6 33.8 1.0 H3' D:ATP301 3.9 29.5 0.8 O D:HOH480 4.0 32.7 1.0 O3B D:ATP301 4.0 29.9 0.8 OD2 D:ASP211 4.1 33.8 1.0 H5'2 D:ATP301 4.1 28.2 0.8 O1A D:ATP301 4.2 26.4 0.8 O3' D:ATP301 4.2 26.1 0.8 HG1 D:THR209 4.3 39.7 1.0 OD1 D:ASP211 4.3 28.8 1.0 HA D:T7Q302 4.4 56.1 0.8 CA D:SER221 4.4 22.3 1.0 O5' D:ATP301 4.5 24.7 0.8 CG D:GLU218 4.5 30.2 1.0 O D:HOH626 4.5 43.6 0.9 C3' D:ATP301 4.5 24.6 0.8 O2B D:ATP301 4.5 32.9 0.8 CG D:ASP211 4.6 31.2 1.0 HA D:SER221 4.6 26.8 1.0 HG3 D:GLU218 4.6 36.2 1.0 N D:SER221 4.7 22.9 1.0 C5' D:ATP301 4.7 23.5 0.8 HG2 D:GLU218 4.7 36.2 1.0 H D:SER221 4.8 27.5 1.0 HG21 D:THR209 4.8 38.4 1.0 N D:T7Q302 4.9 59.1 0.8 HN2 D:T7Q302 4.9 71.0 0.8 O1G D:ATP301 5.0 32.8 0.8

Magnesium binding site 3 out of 5 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg306 b:32.1 occ:0.72 O D:HOH626 2.2 43.6 0.9 O1B D:ATP301 2.4 31.4 0.8 OE1 D:GLU218 2.4 35.8 1.0 O1G D:ATP301 2.5 32.8 0.8 O D:HOH439 2.5 28.7 0.8 O D:HOH625 2.5 46.5 1.0 MG D:MG305 3.3 27.2 0.7 CD D:GLU218 3.4 37.1 1.0 O3B D:ATP301 3.4 29.9 0.8 PB D:ATP301 3.4 30.1 0.8 PG D:ATP301 3.5 31.1 0.8 OE2 D:GLU218 3.6 31.0 1.0 O D:HOH556 3.7 44.6 1.0 O D:HOH501 4.2 40.3 1.0 O D:HOH528 4.3 32.8 0.8 O2B D:ATP301 4.3 32.9 0.8 O3G D:ATP301 4.3 31.6 0.8 OD2 D:ASP211 4.4 33.8 1.0 O3A D:ATP301 4.6 28.3 0.8 O D:HOH480 4.6 32.7 1.0 O2G D:ATP301 4.6 29.5 0.8 O D:HOH567 4.7 38.5 1.0 CG D:GLU218 4.8 30.2 1.0 OG D:SER221 4.9 36.6 1.0 HB3 D:GLU218 4.9 32.2 1.0 HB2 D:GLU218 5.0 32.2 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:56.4 occ:0.81 O2A A:ATP302 2.1 68.5 0.7 O1B A:ATP302 2.3 72.6 0.7 OE2 A:GLU218 2.6 61.1 1.0 O3A A:ATP302 2.9 60.7 0.7 PA A:ATP302 2.9 56.8 0.7 PB A:ATP302 3.0 56.1 0.7 HB2 A:SER221 3.1 50.0 1.0 O5' A:ATP302 3.3 67.1 0.7 CD A:GLU218 3.4 74.8 1.0 OE1 A:GLU218 3.4 69.3 1.0 O3B A:ATP302 3.7 58.6 0.7 HB3 A:SER221 3.8 50.0 1.0 CB A:SER221 3.8 41.7 1.0 HG A:SER221 3.8 82.0 1.0 H3' A:ATP302 3.8 43.4 0.7 OG A:SER221 4.3 68.3 1.0 O3' A:ATP302 4.3 44.2 0.7 O1A A:ATP302 4.3 54.3 0.7 O2B A:ATP302 4.4 50.4 0.7 C3' A:ATP302 4.5 36.2 0.7 OD2 A:ASP211 4.7 78.3 1.0 C5' A:ATP302 4.7 43.1 0.7 O2G A:ATP302 4.8 57.2 0.7 CG A:GLU218 4.8 59.2 1.0 PG A:ATP302 4.9 62.1 0.7

Magnesium binding site 5 out of 5 in the Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Pyrrolysyl-Trna Synthetase From Methanomethylophilus Alvus Engineered For Acridone Amino Acid (RS1) Bound to Atp and Acridone After 2- Weeks of Crystal Growth within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:57.2 occ:1.00 O2B A:ATP302 2.1 50.4 0.7 O A:HOH453 2.3 45.2 1.0 O3G A:ATP302 2.4 53.4 0.7 HH11 A:ARG150 3.1 59.8 1.0 PB A:ATP302 3.3 56.1 0.7 O3B A:ATP302 3.4 58.6 0.7 PG A:ATP302 3.5 62.1 0.7 HH12 A:ARG150 3.6 59.8 1.0 NH1 A:ARG150 3.7 49.8 1.0 O2G A:ATP302 4.0 57.2 0.7 O1B A:ATP302 4.1 72.6 0.7 HE22 A:GLN107 4.3 77.0 1.0 O3A A:ATP302 4.4 60.7 0.7 OE1 A:GLN107 4.5 59.4 1.0 N7 A:ATP302 4.5 34.9 0.7 OE2 A:GLU152 4.6 52.8 1.0 HD2 A:ARG150 4.6 47.6 1.0 HD3 A:ARG150 4.7 47.6 1.0 O1G A:ATP302 4.8 53.0 0.7 H8 A:ATP302 4.9 41.3 0.7 CZ A:ARG150 5.0 51.2 1.0 NE2 A:GLN107 5.0 64.2 1.0

I.Gottfried-Lee, J.J.Perona, P.A.Karplus, R.A.Mehl, R.B.Cooley. Structures of Methanomethylophilus Alvus Pyrrolysine Trna-Synthetases Support the Need For De Novo Selections When Altering the Substrate Specificity. Acs Chem.Biol. V. 17 3470 2022.
ISSN: ESSN 1554-8937
PubMed: 36395426
DOI: 10.1021/ACSCHEMBIO.2C00640