Magnesium in PDB 2q7g: Pyrrolysine Trna Synthetase Bound to A Pyrrolysine Analogue (Cyc) and Atp

The structure of Pyrrolysine Trna Synthetase Bound to A Pyrrolysine Analogue (Cyc) and Atp, PDB code: 2q7g was solved by J.M.Kavran, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.90
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	104.773, 104.773, 71.594, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 18.9

The binding sites of Magnesium atom in the Pyrrolysine Trna Synthetase Bound to A Pyrrolysine Analogue (Cyc) and Atp (pdb code 2q7g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pyrrolysine Trna Synthetase Bound to A Pyrrolysine Analogue (Cyc) and Atp, PDB code: 2q7g:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyrrolysine Trna Synthetase Bound to A Pyrrolysine Analogue (Cyc) and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyrrolysine Trna Synthetase Bound to A Pyrrolysine Analogue (Cyc) and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:44.0 occ:1.00 O2B A:ATP900 2.0 35.6 0.8 O2G A:ATP900 2.0 35.7 0.8 O A:HOH1088 2.2 42.2 1.0 O A:HOH998 2.2 42.6 1.0 O A:HOH1087 2.2 45.6 1.0 O A:HOH996 2.2 36.6 1.0 PB A:ATP900 3.2 40.3 0.8 PG A:ATP900 3.3 40.1 0.8 O3B A:ATP900 3.5 38.0 0.8 NH1 A:ARG330 3.7 42.6 1.0 O1G A:ATP900 3.9 39.2 0.8 O A:HOH1086 3.9 52.9 1.0 NE2 A:HIS338 4.1 44.8 1.0 O A:HOH1126 4.1 68.2 1.0 OE2 A:GLU332 4.1 46.2 1.0 O3A A:ATP900 4.3 45.7 1.0 O1B A:ATP900 4.3 45.1 0.8 O A:HOH1162 4.4 74.5 1.0 OE1 A:GLN287 4.5 51.2 1.0 CD2 A:HIS338 4.5 48.2 1.0 O3G A:ATP900 4.5 36.8 0.8 OE1 A:GLU332 4.5 43.4 1.0 O A:HOH1128 4.5 74.2 1.0 N7 A:ATP900 4.6 32.0 1.0 NE2 A:GLN287 4.7 49.1 1.0 CD A:GLU332 4.8 47.0 1.0 CZ A:ARG330 5.0 45.0 1.0

Magnesium binding site 2 out of 2 in the Pyrrolysine Trna Synthetase Bound to A Pyrrolysine Analogue (Cyc) and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyrrolysine Trna Synthetase Bound to A Pyrrolysine Analogue (Cyc) and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:39.4 occ:0.75 O1B A:ATP900 2.0 45.1 0.8 O A:HOH1158 2.2 57.6 1.0 O A:HOH1125 2.2 52.2 1.0 OG A:SER399 2.2 51.1 1.0 O2A A:ATP900 2.3 45.7 1.0 OE2 A:GLU396 2.4 44.0 1.0 CD A:GLU396 3.1 47.5 1.0 PB A:ATP900 3.2 40.3 0.8 OE1 A:GLU396 3.2 52.1 1.0 CB A:SER399 3.3 49.1 1.0 PA A:ATP900 3.3 41.1 1.0 O3A A:ATP900 3.3 45.7 1.0 O A:HOH1160 3.4 53.7 1.0 O A:HOH1128 3.8 74.2 1.0 O3B A:ATP900 3.9 38.0 0.8 O1A A:ATP900 4.3 35.6 1.0 OXT A:CCL901 4.4 71.6 1.0 CA A:SER399 4.4 41.9 1.0 O2B A:ATP900 4.5 35.6 0.8 OD1 A:ASP389 4.5 54.3 1.0 CG A:GLU396 4.5 47.5 1.0 O3' A:ATP900 4.6 35.2 1.0 O5' A:ATP900 4.6 38.0 1.0 N A:SER399 4.6 42.4 1.0 C5' A:ATP900 4.7 38.7 1.0 C3' A:ATP900 4.8 34.9 1.0 O A:HOH1159 4.8 64.2 1.0 O1G A:ATP900 4.8 39.2 0.8

J.M.Kavran, S.Gundllapalli, P.O'donoghue, M.Englert, D.Soll, T.A.Steitz. Structure of Pyrrolysyl-Trna Synthetase, An Archaeal Enzyme For Genetic Code Innovation. Proc.Natl.Acad.Sci.Usa V. 104 11268 2007.
ISSN: ISSN 0027-8424
PubMed: 17592110
DOI: 10.1073/PNAS.0704769104